def wrapped_in_wf(self):
from copy import copy
from janis_core.workflow.workflow import WorkflowBuilder
wf = WorkflowBuilder(self.id() + "Wf")
inpmap = {}
for i in self.inputs():
if isinstance(i.input_type, Filename):
intp = String(optional=True)
else:
intp = copy(i.input_type)
if i.default:
intp.optional = True
inpmap[i.id()] = wf.input(i.id(), intp)
stp = wf.step(self.tool().lower(), self(**inpmap))
for o in self.outputs():
wf.output(o.id(), source=stp[o.id()])
return wf
from datetime import datetime
from typing import List, Optional, Dict, Any
from janis_core import *
from janis_core.types.common_data_types import Int, Boolean, File, String
Adjlist_V0_1_0 = CommandToolBuilder(tool="AdjList", base_command=["AdjList"], inputs=[ToolInput(tag="in_length_kmer_is", input_type=Int(optional=True), prefix="--kmer", doc=InputDocumentation(doc="the length of a k-mer (when -K is not set)\nor the span of a k-mer pair (when -K is set)")), ToolInput(tag="in_single_km_er", input_type=Int(optional=True), prefix="--single-kmer", doc=InputDocumentation(doc="the length of a single k-mer in a k-mer pair")), ToolInput(tag="in_min_overlap", input_type=Int(optional=True), prefix="--min-overlap", doc=InputDocumentation(doc="require a minimum overlap of M bases [50]")), ToolInput(tag="in_adj", input_type=Boolean(optional=True), prefix="--adj", doc=InputDocumentation(doc="output the graph in ADJ format [default]")), ToolInput(tag="in_as_qg", input_type=Boolean(optional=True), prefix="--asqg", doc=InputDocumentation(doc="output the graph in ASQG format")), ToolInput(tag="in_dot", input_type=Boolean(optional=True), prefix="--dot", doc=InputDocumentation(doc="output the graph in GraphViz format")), ToolInput(tag="in_gfa", input_type=Boolean(optional=True), prefix="--gfa", doc=InputDocumentation(doc="output the graph in GFA1 format")), ToolInput(tag="in_gfa_one", input_type=Boolean(optional=True), prefix="--gfa1", doc=InputDocumentation(doc="output the graph in GFA1 format")), ToolInput(tag="in_gfa_two", input_type=Boolean(optional=True), prefix="--gfa2", doc=InputDocumentation(doc="output the graph in GFA2 format")), ToolInput(tag="in_gv", input_type=Boolean(optional=True), prefix="--gv", doc=InputDocumentation(doc="output the graph in GraphViz format")), ToolInput(tag="in_sam", input_type=Boolean(optional=True), prefix="--sam", doc=InputDocumentation(doc="output the graph in SAM format")), ToolInput(tag="in_ss", input_type=Boolean(optional=True), prefix="--SS", doc=InputDocumentation(doc="expect contigs to be oriented correctly")), ToolInput(tag="in_no_ss", input_type=Boolean(optional=True), prefix="--no-SS", doc=InputDocumentation(doc="no assumption about contig orientation")), ToolInput(tag="in_verbose", input_type=Boolean(optional=True), prefix="--verbose", doc=InputDocumentation(doc="display verbose output")), ToolInput(tag="in_db", input_type=File(optional=True), prefix="--db", doc=InputDocumentation(doc="specify path of database repository in FILE")), ToolInput(tag="in_library", input_type=String(optional=True), prefix="--library", doc=InputDocumentation(doc="specify library NAME for database")), ToolInput(tag="in_strain", input_type=String(optional=True), prefix="--strain", doc=InputDocumentation(doc="specify strain NAME for database")), ToolInput(tag="in_species", input_type=String(optional=True), prefix="--species", doc=InputDocumentation(doc="specify species NAME for database")), ToolInput(tag="in_var_18", input_type=String(), position=0, doc=InputDocumentation(doc=""))], outputs=[], container="quay.io/biocontainers/abyss:2.2.5--ha4ec83a_0", version="v0.1.0")
if __name__ == "__main__":
# or "cwl"
Adjlist_V0_1_0().translate("wdl")
ToolInput(
tag="in_di_align_d",
input_type=Int(optional=True),
prefix="--dialign-d",
doc=InputDocumentation(doc="dialign debug level, default: 0")),
ToolInput(tag="in_di_align_m",
input_type=File(optional=True),
prefix="--dialign-m",
doc=InputDocumentation(
doc="score matrix, default: dna_matrix.scr")),
ToolInput(
tag="in_di_align_p",
input_type=File(optional=True),
prefix="--dialign-p",
doc=InputDocumentation(
doc=
"diagonal length probability distribution\ndefault: dna_diag_prob_100_exp_550000"
)),
ToolInput(tag="in_fast_a",
input_type=String(),
position=0,
doc=InputDocumentation(doc="sequences in FASTA format"))
],
outputs=[],
container="quay.io/biocontainers/abyss:2.3.1--hd403d74_0",
version="v0.1.0")
if __name__ == "__main__":
# or "cwl"
Abyss_Align_V0_1_0().translate("wdl")
from datetime import datetime
from typing import List, Optional, Dict, Any
from janis_core import *
from janis_core.types.common_data_types import Boolean, String, File, Int, Float
Abyss_P_V0_1_0 = CommandToolBuilder(tool="ABYSS_P", base_command=["ABYSS-P"], inputs=[ToolInput(tag="in_chastity", input_type=Boolean(optional=True), prefix="--chastity", doc=InputDocumentation(doc="discard unchaste reads [default]")), ToolInput(tag="in_no_chastity", input_type=Boolean(optional=True), prefix="--no-chastity", doc=InputDocumentation(doc="do not discard unchaste reads")), ToolInput(tag="in_trim_masked", input_type=Boolean(optional=True), prefix="--trim-masked", doc=InputDocumentation(doc="trim masked bases from the ends of reads\n[default]")), ToolInput(tag="in_no_trim_masked", input_type=Boolean(optional=True), prefix="--no-trim-masked", doc=InputDocumentation(doc="do not trim masked bases from the ends of")), ToolInput(tag="in_mask_quality", input_type=String(optional=True), prefix="--mask-quality", doc=InputDocumentation(doc="mask all low quality bases as `N'")), ToolInput(tag="in_standard_quality", input_type=Boolean(optional=True), prefix="--standard-quality", doc=InputDocumentation(doc="zero quality is `!' (33)\ndefault for FASTQ and SAM files")), ToolInput(tag="in_illumina_quality", input_type=Boolean(optional=True), prefix="--illumina-quality", doc=InputDocumentation(doc="zero quality is `@' (64)\ndefault for qseq and export files")), ToolInput(tag="in_ss", input_type=Boolean(optional=True), prefix="--SS", doc=InputDocumentation(doc="assemble in strand-specific mode")), ToolInput(tag="in_no_ss", input_type=Boolean(optional=True), prefix="--no-SS", doc=InputDocumentation(doc="do not assemble in strand-specific mode")), ToolInput(tag="in_out", input_type=File(optional=True), prefix="--out", doc=InputDocumentation(doc="write the contigs to FILE")), ToolInput(tag="in_km_er", input_type=Int(optional=True), prefix="--kmer", doc=InputDocumentation(doc="the length of a k-mer (when -K is not set) [<=128]\nor the span of a k-mer pair (when -K is set)")), ToolInput(tag="in_single_km_er", input_type=Int(optional=True), prefix="--single-kmer", doc=InputDocumentation(doc="the length of a single k-mer in a k-mer pair")), ToolInput(tag="in_trim_length", input_type=Int(optional=True), prefix="--trim-length", doc=InputDocumentation(doc="maximum length of blunt contigs to trim [k]")), ToolInput(tag="in_coverage", input_type=Float(optional=True), prefix="--coverage", doc=InputDocumentation(doc="remove contigs with mean k-mer coverage\nless than this threshold")), ToolInput(tag="in_kc", input_type=Int(optional=True), prefix="--kc", doc=InputDocumentation(doc="remove all k-mers with multiplicity < N [0]")), ToolInput(tag="in_bubbles", input_type=Int(optional=True), prefix="--bubbles", doc=InputDocumentation(doc="pop bubbles shorter than N bp [3*k]")), ToolInput(tag="in_no_bubbles", input_type=Boolean(optional=True), prefix="--no-bubbles", doc=InputDocumentation(doc="do not pop bubbles")), ToolInput(tag="in_erode", input_type=String(optional=True), prefix="--erode", doc=InputDocumentation(doc="erode bases at the ends of blunt contigs with coverage\nless than this threshold [round(sqrt(median))]")), ToolInput(tag="in_erode_strand", input_type=Int(optional=True), prefix="--erode-strand", doc=InputDocumentation(doc="erode bases at the ends of blunt contigs\nwith coverage less than this threshold on\neither strand [1 if sqrt(median) > 2 else 0]")), ToolInput(tag="in_coverage_hist", input_type=File(optional=True), prefix="--coverage-hist", doc=InputDocumentation(doc="write the k-mer coverage histogram to FILE")), ToolInput(tag="in_mask_cov", input_type=Boolean(optional=True), prefix="--mask-cov", doc=InputDocumentation(doc="do not include kmers containing masked bases in\ncoverage calculations [experimental]")), ToolInput(tag="in_snp", input_type=File(optional=True), prefix="--snp", doc=InputDocumentation(doc="record popped bubbles in FILE")), ToolInput(tag="in_verbose", input_type=Boolean(optional=True), prefix="--verbose", doc=InputDocumentation(doc="display verbose output")), ToolInput(tag="in_db", input_type=File(optional=True), prefix="--db", doc=InputDocumentation(doc="specify path of database repository in FILE")), ToolInput(tag="in_library", input_type=String(optional=True), prefix="--library", doc=InputDocumentation(doc="specify library NAME for database")), ToolInput(tag="in_strain", input_type=String(optional=True), prefix="--strain", doc=InputDocumentation(doc="specify strain NAME for database")), ToolInput(tag="in_species", input_type=String(optional=True), prefix="--species", doc=InputDocumentation(doc="specify species NAME for database")), ToolInput(tag="in_graph", input_type=File(optional=True), prefix="--graph", doc=InputDocumentation(doc="generate a graph in dot format")), ToolInput(tag="in_reads", input_type=String(), position=0, doc=InputDocumentation(doc="-q, --trim-quality=N trim bases from the ends of reads whose"))], outputs=[], container=None, version="v0.1.0")
if __name__ == "__main__":
# or "cwl"
Abyss_P_V0_1_0().translate("wdl", allow_empty_container=True)
from datetime import datetime
from typing import List, Optional, Dict, Any
from janis_core import *
from janis_core.types.common_data_types import String
Expfit_Sh_V0_1_0 = CommandToolBuilder(tool="expfit.sh", base_command=["expfit.sh"], inputs=[ToolInput(tag="in_par_file", input_type=String(), position=0, doc=InputDocumentation(doc=""))], outputs=[], container="quay.io/biocontainers/admixtools:7.0.1--h1d3628b_0", version="v0.1.0")
if __name__ == "__main__":
# or "cwl"
Expfit_Sh_V0_1_0().translate("wdl")
from datetime import datetime
from typing import List, Optional, Dict, Any
from janis_core import *
from janis_core.types.common_data_types import Int, String, Boolean, File
Distanceest_V0_1_0 = CommandToolBuilder(tool="DistanceEst", base_command=["DistanceEst"], inputs=[ToolInput(tag="in_mind", input_type=Int(optional=True), prefix="--mind", doc=InputDocumentation(doc="minimum distance between contigs [-(k-1)]")), ToolInput(tag="in_maxd", input_type=String(optional=True), prefix="--maxd", doc=InputDocumentation(doc="maximum distance between contigs")), ToolInput(tag="in_fr", input_type=Boolean(optional=True), prefix="--fr", doc=InputDocumentation(doc="force the orientation to forward-reverse")), ToolInput(tag="in_rf", input_type=Boolean(optional=True), prefix="--rf", doc=InputDocumentation(doc="force the orientation to reverse-forward")), ToolInput(tag="in_km_er", input_type=Int(optional=True), prefix="--kmer", doc=InputDocumentation(doc="set --mind to -(k-1) bp")), ToolInput(tag="in_min_align", input_type=Int(optional=True), prefix="--min-align", doc=InputDocumentation(doc="the minimal alignment size [1]")), ToolInput(tag="in_n_pairs", input_type=Int(optional=True), prefix="--npairs", doc=InputDocumentation(doc="minimum number of pairs")), ToolInput(tag="in_seed_length", input_type=Int(optional=True), prefix="--seed-length", doc=InputDocumentation(doc="minimum length of the seed contigs")), ToolInput(tag="in_min_mapq", input_type=Int(optional=True), prefix="--min-mapq", doc=InputDocumentation(doc="ignore alignments with mapping quality\nless than this threshold [10]")), ToolInput(tag="in_out", input_type=File(optional=True), prefix="--out", doc=InputDocumentation(doc="write result to FILE")), ToolInput(tag="in_mle", input_type=Boolean(optional=True), prefix="--mle", doc=InputDocumentation(doc="use the MLE [default]\n(maximum likelihood estimator)")), ToolInput(tag="in_median", input_type=Boolean(optional=True), prefix="--median", doc=InputDocumentation(doc="use the difference of the population median\nand the sample median")), ToolInput(tag="in_mean", input_type=Boolean(optional=True), prefix="--mean", doc=InputDocumentation(doc="use the difference of the population mean\nand the sample mean")), ToolInput(tag="in_dist", input_type=Boolean(optional=True), prefix="--dist", doc=InputDocumentation(doc="output the graph in dist format [default]")), ToolInput(tag="in_dot", input_type=Boolean(optional=True), prefix="--dot", doc=InputDocumentation(doc="output the graph in GraphViz format")), ToolInput(tag="in_gv", input_type=Boolean(optional=True), prefix="--gv", doc=InputDocumentation(doc="output the graph in GraphViz format")), ToolInput(tag="in_gfa", input_type=Boolean(optional=True), prefix="--gfa", doc=InputDocumentation(doc="output the graph in GFA2 format")), ToolInput(tag="in_gfa_two", input_type=Boolean(optional=True), prefix="--gfa2", doc=InputDocumentation(doc="output the graph in GFA2 format")), ToolInput(tag="in_threads", input_type=Int(optional=True), prefix="--threads", doc=InputDocumentation(doc="use N parallel threads [1]")), ToolInput(tag="in_verbose", input_type=Boolean(optional=True), prefix="--verbose", doc=InputDocumentation(doc="display verbose output")), ToolInput(tag="in_db", input_type=File(optional=True), prefix="--db", doc=InputDocumentation(doc="specify path of database repository in FILE")), ToolInput(tag="in_library", input_type=String(optional=True), prefix="--library", doc=InputDocumentation(doc="specify library NAME for sqlite")), ToolInput(tag="in_strain", input_type=String(optional=True), prefix="--strain", doc=InputDocumentation(doc="specify strain NAME for sqlite")), ToolInput(tag="in_species", input_type=String(optional=True), prefix="--species", doc=InputDocumentation(doc="specify species NAME for sqlite")), ToolInput(tag="in_hist", input_type=String(), position=0, doc=InputDocumentation(doc="distribution of fragments size")), ToolInput(tag="in_pair", input_type=String(), position=1, doc=InputDocumentation(doc="alignments between contigs"))], outputs=[], container=None, version="v0.1.0")
if __name__ == "__main__":
# or "cwl"
Distanceest_V0_1_0().translate("wdl", allow_empty_container=True)
from datetime import datetime
from typing import List, Optional, Dict, Any
from janis_core import *
from janis_core.types.common_data_types import Int, Boolean, File, String
Abyss_Scaffold_V0_1_0 = CommandToolBuilder(tool="abyss_scaffold", base_command=["abyss-scaffold"], inputs=[ToolInput(tag="in_n_pairs", input_type=Int(optional=True), prefix="--npairs", doc=InputDocumentation(doc="minimum number of pairs [0]\nor -n A-B:S Find the value of n in [A,B] with step size S\nthat maximizes the scaffold N50.\nDefault value for the step size is 1, if unspecified.")), ToolInput(tag="in_seed_length", input_type=Int(optional=True), prefix="--seed-length", doc=InputDocumentation(doc="minimum contig length [1000]\nor -s A-B Find the value of s in [A,B]\nthat maximizes the scaffold N50.\n--grid optimize using a grid search [default]\n--line optimize using a line search")), ToolInput(tag="in_km_er", input_type=Int(optional=True), prefix="--kmer", doc=InputDocumentation(doc="length of a k-mer")), ToolInput(tag="in_genome_size", input_type=Int(optional=True), prefix="--genome-size", doc=InputDocumentation(doc="expected genome size. Used to calculate NG50\nand associated stats [disabled]")), ToolInput(tag="in_min_gap", input_type=Int(optional=True), prefix="--min-gap", doc=InputDocumentation(doc="minimum scaffold gap length to output [50]")), ToolInput(tag="in_max_gap", input_type=Int(optional=True), prefix="--max-gap", doc=InputDocumentation(doc="maximum scaffold gap length to output [inf]")), ToolInput(tag="in_complex", input_type=Boolean(optional=True), prefix="--complex", doc=InputDocumentation(doc="remove complex transitive edges")), ToolInput(tag="in_no_complex", input_type=Boolean(optional=True), prefix="--no-complex", doc=InputDocumentation(doc="don't remove complex transitive edges [default]")), ToolInput(tag="in_ss", input_type=Boolean(optional=True), prefix="--SS", doc=InputDocumentation(doc="expect contigs to be oriented correctly")), ToolInput(tag="in_no_ss", input_type=Boolean(optional=True), prefix="--no-SS", doc=InputDocumentation(doc="no assumption about contig orientation [default]")), ToolInput(tag="in_out", input_type=File(optional=True), prefix="--out", doc=InputDocumentation(doc="write the paths to FILE")), ToolInput(tag="in_graph", input_type=File(optional=True), prefix="--graph", doc=InputDocumentation(doc="write the graph to FILE")), ToolInput(tag="in_verbose", input_type=Boolean(optional=True), prefix="--verbose", doc=InputDocumentation(doc="display verbose output")), ToolInput(tag="in_db", input_type=File(optional=True), prefix="--db", doc=InputDocumentation(doc="specify path of database repository in FILE")), ToolInput(tag="in_library", input_type=String(optional=True), prefix="--library", doc=InputDocumentation(doc="specify library NAME for sqlite")), ToolInput(tag="in_strain", input_type=String(optional=True), prefix="--strain", doc=InputDocumentation(doc="specify strain NAME for sqlite")), ToolInput(tag="in_species", input_type=String(optional=True), prefix="--species", doc=InputDocumentation(doc="specify species NAME for sqlite")), ToolInput(tag="in_fast_a", input_type=String(), position=0, doc=InputDocumentation(doc="contigs in FASTA format")), ToolInput(tag="in_overlap", input_type=String(), position=1, doc=InputDocumentation(doc="the contig overlap graph")), ToolInput(tag="in_dist", input_type=String(), position=2, doc=InputDocumentation(doc="estimates of the distance between contigs"))], outputs=[], container="quay.io/biocontainers/abyss:2.3.1--hd403d74_0", version="v0.1.0")
if __name__ == "__main__":
# or "cwl"
Abyss_Scaffold_V0_1_0().translate("wdl")
from typing import List, Optional, Dict, Any
from janis_core import *
from janis_core.types.common_data_types import Int, String, Array, File, Boolean
Design_Py_Complete_Targets_Auto_From_Args_V0_1_0 = CommandToolBuilder(
tool="design.py_complete_targets_auto_from_args",
base_command=["design.py", "complete-targets", "auto-from-args"],
inputs=[
ToolInput(tag="in_guide_length",
input_type=Int(optional=True),
prefix="--guide-length",
doc=InputDocumentation(doc="Length of guide to construct")),
ToolInput(
tag="in_obj",
input_type=String(optional=True),
prefix="--obj",
doc=InputDocumentation(
doc=
"Objective function to solve. 'maximize-activity'\nmaximizes the expected activity of the guide set of\nthe target genomes subject to soft and hard\nconstraints on the size of the guide set. 'minimize-\nguides' minimizes the number of guides in the guide\nset subject to coverage constraints across the target\ngenomes."
)),
ToolInput(
tag="in_guide_mismatches",
input_type=Int(optional=True),
prefix="--guide-mismatches",
doc=InputDocumentation(
doc=
"Allow for this number of mismatches when determining\nwhether a guide covers a sequence"
)),
ToolInput(
tag="in_guide_cover_frac",
from datetime import datetime
from typing import List, Optional, Dict, Any
from janis_core import *
from janis_core.types.common_data_types import Int, Boolean, String
Dassembler_V0_1_0 = CommandToolBuilder(tool="DAssembler", base_command=["DAssembler"], inputs=[ToolInput(tag="in_max_overlap", input_type=Int(optional=True), prefix="--max_overlap", doc=InputDocumentation(doc="maximum tier overlap for consensus calling [10]")), ToolInput(tag="in_max_mismatch", input_type=Int(optional=True), prefix="--max_mismatch", doc=InputDocumentation(doc="maximum mismatches allowed for consensus calling [2]")), ToolInput(tag="in_min_coverage", input_type=Int(optional=True), prefix="--min_coverage", doc=InputDocumentation(doc="minimum coverage to call a consensus base [2]")), ToolInput(tag="in_read_length", input_type=Int(optional=True), prefix="--read_length", doc=InputDocumentation(doc="read length")), ToolInput(tag="in_verbose", input_type=Boolean(optional=True), prefix="--verbose", doc=InputDocumentation(doc="display verbose output")), ToolInput(tag="in_reads", input_type=String(), position=0, doc=InputDocumentation(doc="fasta-formatted reads file: the first read is used as the seed."))], outputs=[], container="quay.io/biocontainers/abyss:2.3.0--ha4ec83a_0", version="v0.1.0")
if __name__ == "__main__":
# or "cwl"
Dassembler_V0_1_0().translate("wdl")
from datetime import datetime
from typing import List, Optional, Dict, Any
from janis_core import *
from janis_core.types.common_data_types import Int, String, Boolean
Logcounter_V0_1_0 = CommandToolBuilder(tool="logcounter", base_command=["logcounter"], inputs=[ToolInput(tag="in_threads", input_type=Int(optional=True), prefix="--threads", doc=InputDocumentation(doc="use N parallel threads [1]")), ToolInput(tag="in_km_er", input_type=Int(optional=True), prefix="--kmer", doc=InputDocumentation(doc="the size of a k-mer")), ToolInput(tag="in_seed", input_type=String(optional=True), prefix="--seed", doc=InputDocumentation(doc="the seed value used")), ToolInput(tag="in_bloom_size", input_type=Int(optional=True), prefix="--bloom-size", doc=InputDocumentation(doc="size of bloom filter [500M]")), ToolInput(tag="in_chastity", input_type=Boolean(optional=True), prefix="--chastity", doc=InputDocumentation(doc="discard unchaste reads [default]")), ToolInput(tag="in_no_chastity", input_type=Boolean(optional=True), prefix="--no-chastity", doc=InputDocumentation(doc="do not discard unchaste reads")), ToolInput(tag="in_trim_masked", input_type=Boolean(optional=True), prefix="--trim-masked", doc=InputDocumentation(doc="trim masked bases from the ends of reads")), ToolInput(tag="in_no_trim_masked", input_type=Boolean(optional=True), prefix="--no-trim-masked", doc=InputDocumentation(doc="do not trim masked bases from the ends\nof reads [default]")), ToolInput(tag="in_trim_quality", input_type=String(optional=True), prefix="--trim-quality", doc=InputDocumentation(doc="trim bases from the ends of reads whose\nquality is less than the threshold")), ToolInput(tag="in_standard_quality", input_type=Boolean(optional=True), prefix="--standard-quality", doc=InputDocumentation(doc="zero quality is `!' (33)\ndefault for FASTQ and SAM files")), ToolInput(tag="in_illumina_quality", input_type=Boolean(optional=True), prefix="--illumina-quality", doc=InputDocumentation(doc="zero quality is `@' (64)\ndefault for qseq and export files")), ToolInput(tag="in_verbose", input_type=Boolean(optional=True), prefix="--verbose", doc=InputDocumentation(doc="display verbose output"))], outputs=[], container="quay.io/biocontainers/abyss:2.3.0--ha4ec83a_0", version="v0.1.0")
if __name__ == "__main__":
# or "cwl"
Logcounter_V0_1_0().translate("wdl")
from datetime import datetime
from typing import List, Optional, Dict, Any
from janis_core import *
from janis_core.types.common_data_types import Int, Boolean, Float, String
Abpoa_V0_1_0 = CommandToolBuilder(tool="abpoa", base_command=["abpoa"], inputs=[ToolInput(tag="in_aln_mode", input_type=Int(optional=True), prefix="--aln-mode", doc=InputDocumentation(doc="alignment mode [0]\n0: global, 1: local, 2: extension")), ToolInput(tag="in_match", input_type=Boolean(optional=True), prefix="--match", doc=InputDocumentation(doc="INT match score [2]")), ToolInput(tag="in_mismatch", input_type=Int(optional=True), prefix="--mismatch", doc=InputDocumentation(doc="mismatch penalty [4]")), ToolInput(tag="in_gap_open", input_type=Int(optional=True), prefix="--gap-open", doc=InputDocumentation(doc="(,INT) gap opening penalty (O1,O2) [4,24]")), ToolInput(tag="in_gap_ext", input_type=Boolean(optional=True), prefix="--gap-ext", doc=InputDocumentation(doc="INT(,INT) gap extension penalty (E1,E2) [2,1]\nabPOA provides three gap penalty modes, cost of a g-long gap:\n- convex (default): min{O1+g*E1, O2+g*E2}\n- affine (set O2 as 0): O1+g*E1\n- linear (set O1 as 0): g*E1")), ToolInput(tag="in_amb_strand", input_type=Boolean(optional=True), prefix="--amb-strand", doc=InputDocumentation(doc="ambiguous strand mode [False]\nfor each input sequence, try the reverse complement if the current\nalignment score is too low, and pick the strand with a higher score")), ToolInput(tag="in_extra_b", input_type=Boolean(optional=True), prefix="--extra-b", doc=InputDocumentation(doc="INT first adaptive banding parameter [10]\nset b as < 0 to disable adaptive banded DP")), ToolInput(tag="in_extra_f", input_type=Boolean(optional=True), prefix="--extra-f", doc=InputDocumentation(doc="FLOAT second adaptive banding parameter [0.01]\nthe number of extra bases added on both sites of the band is\nb+f*L, where L is the length of the aligned sequence")), ToolInput(tag="in_in_list", input_type=Boolean(optional=True), prefix="--in-list", doc=InputDocumentation(doc="input file is a list of sequence file names [False]\neach line is one sequence file containing a set of sequences\nwhich will be aligned by abPOA to generate a consensus sequence")), ToolInput(tag="in_output", input_type=Boolean(optional=True), prefix="--output", doc=InputDocumentation(doc="FILE ouput to FILE [stdout]")), ToolInput(tag="in_result", input_type=Boolean(optional=True), prefix="--result", doc=InputDocumentation(doc="INT output result mode [0]\n- 0: consensus (FASTA format)\n- 1: MSA (PIR format)\n- 2: both 0 & 1\n- 3: graph (GFA format)\n- 4: graph with consensus path (GFA format)")), ToolInput(tag="in_msa_header", input_type=Boolean(optional=True), prefix="--msa-header", doc=InputDocumentation(doc="add read ID as header of each sequence in MSA output [False]")), ToolInput(tag="in_out_pog", input_type=Boolean(optional=True), prefix="--out-pog", doc=InputDocumentation(doc="FILE dump final alignment graph to FILE (.pdf/.png) [Null]")), ToolInput(tag="in_cons_alg", input_type=Int(optional=True), prefix="--cons-alg", doc=InputDocumentation(doc="algorithm to use for consensus calling [0]\n- 0: heaviest bundling\n- 1: heaviest in column")), ToolInput(tag="in_diploid", input_type=Boolean(optional=True), prefix="--diploid", doc=InputDocumentation(doc="input data is diploid [False]")), ToolInput(tag="in_min_freq", input_type=Float(optional=True), prefix="--min-freq", doc=InputDocumentation(doc="min frequency of each consensus for diploid input [0.30]")), ToolInput(tag="in_in_dot_f_a_slash_fq", input_type=String(), position=0, doc=InputDocumentation(doc=""))], outputs=[], container="quay.io/biocontainers/abpoa:1.0.6--hed695b0_0", version="v0.1.0")
if __name__ == "__main__":
# or "cwl"
Abpoa_V0_1_0().translate("wdl")
from datetime import datetime
from typing import List, Optional, Dict, Any
from janis_core import *
from janis_core.types.common_data_types import Boolean, Int, String, File
Ac_V0_1_0 = CommandToolBuilder(tool="AC", base_command=["AC"], inputs=[ToolInput(tag="in_show_ac_levels", input_type=Boolean(optional=True), prefix="-s", doc=InputDocumentation(doc="show AC compression levels,")), ToolInput(tag="in_verbose_mode_more", input_type=Boolean(optional=True), prefix="-v", doc=InputDocumentation(doc="verbose mode (more information),")), ToolInput(tag="in_display_version_number", input_type=Boolean(optional=True), prefix="-V", doc=InputDocumentation(doc="display version number,")), ToolInput(tag="in_force_overwrite_output", input_type=Boolean(optional=True), prefix="-f", doc=InputDocumentation(doc="force overwrite of output,")), ToolInput(tag="in_level_compression_lazy", input_type=Int(optional=True), prefix="-l", doc=InputDocumentation(doc="level of compression [1;7] (lazy -tm setup),")), ToolInput(tag="in_threshold_frequency_discard", input_type=String(optional=True), prefix="-t", doc=InputDocumentation(doc="threshold frequency to discard from alphabet,")), ToolInput(tag="in_it_creates_file", input_type=Boolean(optional=True), prefix="-e", doc=InputDocumentation(doc="it creates a file with the extension '.iae'\nwith the respective information content.")), ToolInput(tag="in_reference_file_loaded", input_type=File(optional=True), prefix="-r", doc=InputDocumentation(doc="reference file ('-rm' are loaded here),"))], outputs=[], container=None, version="v0.1.0")
if __name__ == "__main__":
# or "cwl"
Ac_V0_1_0().translate("wdl", allow_empty_container=True)
from datetime import datetime
from typing import List, Optional, Dict, Any
from janis_core import *
from janis_core.types.common_data_types import Int, File, Boolean, String
Mergepaths_V0_1_0 = CommandToolBuilder(tool="MergePaths", base_command=["MergePaths"], inputs=[ToolInput(tag="in_km_er", input_type=Int(optional=True), prefix="--kmer", doc=InputDocumentation(doc="k-mer size")), ToolInput(tag="in_seed_length", input_type=Int(optional=True), prefix="--seed-length", doc=InputDocumentation(doc="minimum length of a seed contig [0]")), ToolInput(tag="in_genome_size", input_type=Int(optional=True), prefix="--genome-size", doc=InputDocumentation(doc="expected genome size. Used to calculate NG50\nand associated stats [disabled]")), ToolInput(tag="in_out", input_type=File(optional=True), prefix="--out", doc=InputDocumentation(doc="write result to FILE")), ToolInput(tag="in_no_greedy", input_type=Boolean(optional=True), prefix="--no-greedy", doc=InputDocumentation(doc="use the non-greedy algorithm [default]")), ToolInput(tag="in_greedy", input_type=Boolean(optional=True), prefix="--greedy", doc=InputDocumentation(doc="use the greedy algorithm")), ToolInput(tag="in_graph", input_type=File(optional=True), prefix="--graph", doc=InputDocumentation(doc="write the path overlap graph to FILE")), ToolInput(tag="in_threads", input_type=Int(optional=True), prefix="--threads", doc=InputDocumentation(doc="use N parallel threads [1]")), ToolInput(tag="in_verbose", input_type=Boolean(optional=True), prefix="--verbose", doc=InputDocumentation(doc="display verbose output")), ToolInput(tag="in_db", input_type=File(optional=True), prefix="--db", doc=InputDocumentation(doc="specify path of database repository in FILE")), ToolInput(tag="in_library", input_type=String(optional=True), prefix="--library", doc=InputDocumentation(doc="specify library NAME for database")), ToolInput(tag="in_strain", input_type=String(optional=True), prefix="--strain", doc=InputDocumentation(doc="specify strain NAME for database")), ToolInput(tag="in_species", input_type=String(optional=True), prefix="--species", doc=InputDocumentation(doc="specify species NAME for database")), ToolInput(tag="in_len", input_type=String(), position=0, doc=InputDocumentation(doc="lengths of the contigs")), ToolInput(tag="in_path", input_type=File(), position=1, doc=InputDocumentation(doc="sequences of contig IDs"))], outputs=[], container=None, version="v0.1.0")
if __name__ == "__main__":
# or "cwl"
Mergepaths_V0_1_0().translate("wdl", allow_empty_container=True)
from datetime import datetime
from typing import List, Optional, Dict, Any
from janis_core import *
from janis_core.types.common_data_types import Boolean, String, Int
Abyss_Index_V0_1_0 = CommandToolBuilder(tool="abyss_index", base_command=["abyss-index"], inputs=[ToolInput(tag="in_both", input_type=Boolean(optional=True), prefix="--both", doc=InputDocumentation(doc="build both FAI and FM indexes [default]")), ToolInput(tag="in_fai", input_type=Boolean(optional=True), prefix="--fai", doc=InputDocumentation(doc="build a FAI index")), ToolInput(tag="in_fm", input_type=Boolean(optional=True), prefix="--fm", doc=InputDocumentation(doc="build a FM index")), ToolInput(tag="in_fa_two_bwt", input_type=Boolean(optional=True), prefix="--fa2bwt", doc=InputDocumentation(doc="build the BWT directly without the SA")), ToolInput(tag="in_bwt_two_fm", input_type=Boolean(optional=True), prefix="--bwt2fm", doc=InputDocumentation(doc="build the FM index from the BWT")), ToolInput(tag="in_alphabet", input_type=String(optional=True), prefix="--alphabet", doc=InputDocumentation(doc="use the alphabet STRING [-ACGT]")), ToolInput(tag="in_alpha", input_type=Boolean(optional=True), prefix="--alpha", doc=InputDocumentation(doc="equivalent to -a' ABCDEFGHIJKLMNOPQRSTUVWXYZ'")), ToolInput(tag="in_dna", input_type=Boolean(optional=True), prefix="--dna", doc=InputDocumentation(doc="equivalent to -a'-ACGT'")), ToolInput(tag="in_protein", input_type=Boolean(optional=True), prefix="--protein", doc=InputDocumentation(doc="equivalent to -a'#*ACDEFGHIKLMNPQRSTVWY'")), ToolInput(tag="in_sample", input_type=Int(optional=True), prefix="--sample", doc=InputDocumentation(doc="sample the suffix array [16]")), ToolInput(tag="in_decompress", input_type=Boolean(optional=True), prefix="--decompress", doc=InputDocumentation(doc="decompress the index FILE")), ToolInput(tag="in_stdout", input_type=Boolean(optional=True), prefix="--stdout", doc=InputDocumentation(doc="write output to standard output")), ToolInput(tag="in_verbose", input_type=Boolean(optional=True), prefix="--verbose", doc=InputDocumentation(doc="display verbose output"))], outputs=[], container="quay.io/biocontainers/abyss:2.3.1--hd403d74_0", version="v0.1.0")
if __name__ == "__main__":
# or "cwl"
Abyss_Index_V0_1_0().translate("wdl")
from datetime import datetime
from typing import List, Optional, Dict, Any
from janis_core import *
from janis_core.types.common_data_types import String, Boolean
Abyss_Dida_V0_1_0 = CommandToolBuilder(tool="abyss_dida", base_command=["abyss-dida"], inputs=[ToolInput(tag="in_additional_command_line", input_type=String(optional=True), prefix="-d", doc=InputDocumentation(doc="additional command line opts for DIDA")), ToolInput(tag="in_number_of_threads", input_type=Boolean(optional=True), prefix="-j", doc=InputDocumentation(doc="number of threads [1]")), ToolInput(tag="in_path_of_executable", input_type=Boolean(optional=True), prefix="-m", doc=InputDocumentation(doc="path of 'mpirun' executable [mpirun]")), ToolInput(tag="in_number_ranks_dida", input_type=Boolean(optional=True), prefix="-n", doc=InputDocumentation(doc="number of ranks in DIDA MPI job [3]")), ToolInput(tag="in_value_set_environment", input_type=String(optional=True), prefix="-x", doc=InputDocumentation(doc="=value set environment variable for MPI job"))], outputs=[], container=None, version="v0.1.0")
if __name__ == "__main__":
# or "cwl"
Abyss_Dida_V0_1_0().translate("wdl", allow_empty_container=True)
from datetime import datetime
from typing import List, Optional, Dict, Any
from janis_core import *
from janis_core.types.common_data_types import Boolean, Directory, String, File
Abyss_Pe_V0_1_0 = CommandToolBuilder(tool="abyss_pe", base_command=["abyss-pe"], inputs=[ToolInput(tag="in_ignored_for_compatibility", input_type=Boolean(optional=True), prefix="-b", doc=InputDocumentation(doc="Ignored for compatibility.")), ToolInput(tag="in_always_make", input_type=Boolean(optional=True), prefix="--always-make", doc=InputDocumentation(doc="Unconditionally make all targets.")), ToolInput(tag="in_directory", input_type=Directory(optional=True), prefix="--directory", doc=InputDocumentation(doc="Change to DIRECTORY before doing anything.")), ToolInput(tag="in_print_lots_debugging", input_type=Boolean(optional=True), prefix="-d", doc=InputDocumentation(doc="Print lots of debugging information.")), ToolInput(tag="in_debug", input_type=Boolean(optional=True), prefix="--debug", doc=InputDocumentation(doc="[=FLAGS] Print various types of debugging information.")), ToolInput(tag="in_environment_overrides", input_type=Boolean(optional=True), prefix="--environment-overrides", doc=InputDocumentation(doc="Environment variables override makefiles.")), ToolInput(tag="in_eval", input_type=String(optional=True), prefix="--eval", doc=InputDocumentation(doc="Evaluate STRING as a makefile statement.")), ToolInput(tag="in_makefile", input_type=File(optional=True), prefix="--makefile", doc=InputDocumentation(doc="Read FILE as a makefile.")), ToolInput(tag="in_ignore_errors", input_type=Boolean(optional=True), prefix="--ignore-errors", doc=InputDocumentation(doc="Ignore errors from recipes.")), ToolInput(tag="in_include_dir", input_type=Directory(optional=True), prefix="--include-dir", doc=InputDocumentation(doc="Search DIRECTORY for included makefiles.")), ToolInput(tag="in_allow_n_jobs", input_type=Boolean(optional=True), prefix="-j", doc=InputDocumentation(doc="[N], --jobs[=N] Allow N jobs at once; infinite jobs with no arg.")), ToolInput(tag="in_keep_going", input_type=Boolean(optional=True), prefix="--keep-going", doc=InputDocumentation(doc="Keep going when some targets can't be made.")), ToolInput(tag="in_start_multiple_jobs", input_type=Boolean(optional=True), prefix="-l", doc=InputDocumentation(doc="[N], --load-average[=N], --max-load[=N]\nDon't start multiple jobs unless load is below N.")), ToolInput(tag="in_check_symlink_times", input_type=Boolean(optional=True), prefix="--check-symlink-times", doc=InputDocumentation(doc="Use the latest mtime between symlinks and target.")), ToolInput(tag="in_just_print", input_type=Boolean(optional=True), prefix="--just-print", doc=InputDocumentation(doc="Don't actually run any recipe; just print them.")), ToolInput(tag="in_assume_old", input_type=File(optional=True), prefix="--assume-old", doc=InputDocumentation(doc="Consider FILE to be very old and don't remake it.")), ToolInput(tag="in_synchronize_output_parallel", input_type=Boolean(optional=True), prefix="-O", doc=InputDocumentation(doc="[TYPE], --output-sync[=TYPE]\nSynchronize output of parallel jobs by TYPE.")), ToolInput(tag="in_print_data_base", input_type=Boolean(optional=True), prefix="--print-data-base", doc=InputDocumentation(doc="Print make's internal database.")), ToolInput(tag="in_question", input_type=Boolean(optional=True), prefix="--question", doc=InputDocumentation(doc="Run no recipe; exit status says if up to date.")), ToolInput(tag="in_no_built_in_rules", input_type=Boolean(optional=True), prefix="--no-builtin-rules", doc=InputDocumentation(doc="Disable the built-in implicit rules.")), ToolInput(tag="in_no_built_in_variables", input_type=Boolean(optional=True), prefix="--no-builtin-variables", doc=InputDocumentation(doc="Disable the built-in variable settings.")), ToolInput(tag="in_silent", input_type=Boolean(optional=True), prefix="--silent", doc=InputDocumentation(doc="Don't echo recipes.")), ToolInput(tag="in_no_silent", input_type=Boolean(optional=True), prefix="--no-silent", doc=InputDocumentation(doc="Echo recipes (disable --silent mode).")), ToolInput(tag="in_no_keep_going", input_type=Boolean(optional=True), prefix="--no-keep-going", doc=InputDocumentation(doc="Turns off -k.")), ToolInput(tag="in_touch", input_type=Boolean(optional=True), prefix="--touch", doc=InputDocumentation(doc="Touch targets instead of remaking them.")), ToolInput(tag="in_trace", input_type=Boolean(optional=True), prefix="--trace", doc=InputDocumentation(doc="Print tracing information.")), ToolInput(tag="in_print_directory", input_type=Boolean(optional=True), prefix="--print-directory", doc=InputDocumentation(doc="Print the current directory.")), ToolInput(tag="in_no_print_directory", input_type=Boolean(optional=True), prefix="--no-print-directory", doc=InputDocumentation(doc="Turn off -w, even if it was turned on implicitly.")), ToolInput(tag="in_assume_new", input_type=File(optional=True), prefix="--assume-new", doc=InputDocumentation(doc="Consider FILE to be infinitely new.")), ToolInput(tag="in_warn_undefined_variables", input_type=Boolean(optional=True), prefix="--warn-undefined-variables", doc=InputDocumentation(doc="Warn when an undefined variable is referenced.")), ToolInput(tag="in_make", input_type=String(), position=0, doc=InputDocumentation(doc="")), ToolInput(tag="in_target", input_type=String(optional=True), position=1, doc=InputDocumentation(doc=""))], outputs=[], container="quay.io/biocontainers/abyss:2.3.1--hd403d74_0", version="v0.1.0")
if __name__ == "__main__":
# or "cwl"
Abyss_Pe_V0_1_0().translate("wdl")
from datetime import datetime
from typing import List, Optional, Dict, Any
from janis_core import *
from janis_core.types.common_data_types import String, Boolean, File
Abyss_Todot_V0_1_0 = CommandToolBuilder(tool="abyss_todot", base_command=["abyss-todot"], inputs=[ToolInput(tag="in_km_er", input_type=String(optional=True), prefix="--kmer", doc=InputDocumentation(doc="report the mean k-mer coverage, otherwise\nthe sum k-mer coverage is reported")), ToolInput(tag="in_adj", input_type=Boolean(optional=True), prefix="--adj", doc=InputDocumentation(doc="output the graph in adj format")), ToolInput(tag="in_as_qg", input_type=Boolean(optional=True), prefix="--asqg", doc=InputDocumentation(doc="output the graph in asqg format")), ToolInput(tag="in_dist", input_type=Boolean(optional=True), prefix="--dist", doc=InputDocumentation(doc="output the graph in dist format")), ToolInput(tag="in_dot", input_type=Boolean(optional=True), prefix="--dot", doc=InputDocumentation(doc="output the graph in GraphViz format [default]")), ToolInput(tag="in_gv", input_type=Boolean(optional=True), prefix="--gv", doc=InputDocumentation(doc="output the graph in GraphViz format")), ToolInput(tag="in_dot_mean_cov", input_type=Boolean(optional=True), prefix="--dot-meancov", doc=InputDocumentation(doc="same as above but give the mean coverage")), ToolInput(tag="in_gfa", input_type=Boolean(optional=True), prefix="--gfa", doc=InputDocumentation(doc="output the graph in GFA1 format")), ToolInput(tag="in_gfa_one", input_type=Boolean(optional=True), prefix="--gfa1", doc=InputDocumentation(doc="output the graph in GFA1 format")), ToolInput(tag="in_gfa_two", input_type=Boolean(optional=True), prefix="--gfa2", doc=InputDocumentation(doc="output the graph in GFA2 format")), ToolInput(tag="in_sam", input_type=Boolean(optional=True), prefix="--sam", doc=InputDocumentation(doc="output the graph in SAM format")), ToolInput(tag="in_estimate", input_type=String(optional=True), prefix="--estimate", doc=InputDocumentation(doc="distance estimates")), ToolInput(tag="in_add_complements", input_type=String(optional=True), prefix="--add-complements", doc=InputDocumentation(doc="missing complementary edges")), ToolInput(tag="in_verbose", input_type=Boolean(optional=True), prefix="--verbose", doc=InputDocumentation(doc="display verbose output")), ToolInput(tag="in_file", input_type=File(optional=True), position=0, doc=InputDocumentation(doc=""))], outputs=[], container="quay.io/biocontainers/abyss:2.3.1--hd403d74_0", version="v0.1.0")
if __name__ == "__main__":
# or "cwl"
Abyss_Todot_V0_1_0().translate("wdl")
from datetime import datetime
from typing import List, Optional, Dict, Any
from janis_core import *
from janis_core.types.common_data_types import String
Convertf_File_V0_1_0 = CommandToolBuilder(tool="convertf_file", base_command=["convertf", "file"], inputs=[ToolInput(tag="in_bad", input_type=String(), position=0, doc=InputDocumentation(doc="")), ToolInput(tag="in_params_dot_dot_dot_dot", input_type=String(), position=1, doc=InputDocumentation(doc=""))], outputs=[], container="quay.io/biocontainers/admixtools:7.0.1--h1d3628b_0", version="v0.1.0")
if __name__ == "__main__":
# or "cwl"
Convertf_File_V0_1_0().translate("wdl")
from datetime import datetime
from typing import List, Optional, Dict, Any
from janis_core import *
from janis_core.types.common_data_types import Int, File, Boolean, Float, String
Pathconsensus_V0_1_0 = CommandToolBuilder(tool="PathConsensus", base_command=["PathConsensus"], inputs=[ToolInput(tag="in_km_er", input_type=Int(optional=True), prefix="--kmer", doc=InputDocumentation(doc="k-mer size")), ToolInput(tag="in_dist_error", input_type=Int(optional=True), prefix="--dist-error", doc=InputDocumentation(doc="acceptable error of a distance estimate\ndefault: 6 bp")), ToolInput(tag="in_out", input_type=File(optional=True), prefix="--out", doc=InputDocumentation(doc="output contig paths to FILE")), ToolInput(tag="in_consensus", input_type=File(optional=True), prefix="--consensus", doc=InputDocumentation(doc="output consensus sequences to FILE")), ToolInput(tag="in_graph", input_type=File(optional=True), prefix="--graph", doc=InputDocumentation(doc="output the contig adjacency graph to FILE")), ToolInput(tag="in_output_graph_adj", input_type=Boolean(optional=True), prefix="--adj", doc=InputDocumentation(doc="output the graph in ADJ format [default]")), ToolInput(tag="in_as_qg", input_type=Boolean(optional=True), prefix="--asqg", doc=InputDocumentation(doc="output the graph in ASQG format")), ToolInput(tag="in_dot", input_type=Boolean(optional=True), prefix="--dot", doc=InputDocumentation(doc="output the graph in GraphViz format")), ToolInput(tag="in_gfa", input_type=Boolean(optional=True), prefix="--gfa", doc=InputDocumentation(doc="output the graph in GFA1 format")), ToolInput(tag="in_gfa_one", input_type=Boolean(optional=True), prefix="--gfa1", doc=InputDocumentation(doc="output the graph in GFA1 format")), ToolInput(tag="in_gfa_two", input_type=Boolean(optional=True), prefix="--gfa2", doc=InputDocumentation(doc="output the graph in GFA2 format")), ToolInput(tag="in_gv", input_type=Boolean(optional=True), prefix="--gv", doc=InputDocumentation(doc="output the graph in GraphViz format")), ToolInput(tag="in_sam", input_type=Boolean(optional=True), prefix="--sam", doc=InputDocumentation(doc="output the graph in SAM format")), ToolInput(tag="in_branches", input_type=Int(optional=True), prefix="--branches", doc=InputDocumentation(doc="maximum number of sequences to align\ndefault: 4")), ToolInput(tag="in_identity", input_type=Float(optional=True), prefix="--identity", doc=InputDocumentation(doc="minimum identity, default: 0.9")), ToolInput(tag="in_verbose", input_type=Boolean(optional=True), prefix="--verbose", doc=InputDocumentation(doc="display verbose output")), ToolInput(tag="in_db", input_type=File(optional=True), prefix="--db", doc=InputDocumentation(doc="specify path of database repository in FILE")), ToolInput(tag="in_library", input_type=String(optional=True), prefix="--library", doc=InputDocumentation(doc="specify library NAME for database")), ToolInput(tag="in_strain", input_type=String(optional=True), prefix="--strain", doc=InputDocumentation(doc="specify strain NAME for database")), ToolInput(tag="in_species", input_type=String(optional=True), prefix="--species", doc=InputDocumentation(doc="specify species NAME for database")), ToolInput(tag="in_di_align_d", input_type=Int(optional=True), prefix="--dialign-d", doc=InputDocumentation(doc="dialign debug level, default: 0")), ToolInput(tag="in_di_align_m", input_type=File(optional=True), prefix="--dialign-m", doc=InputDocumentation(doc="score matrix, default: dna_matrix.scr")), ToolInput(tag="in_di_align_p", input_type=File(optional=True), prefix="--dialign-p", doc=InputDocumentation(doc="diagonal length probability distribution\ndefault: dna_diag_prob_100_exp_550000")), ToolInput(tag="in_fast_a", input_type=String(), position=0, doc=InputDocumentation(doc="contigs in FASTA format")), ToolInput(tag="in_contig_adjacency_graph", input_type=String(), position=1, doc=InputDocumentation(doc="contig adjacency graph")), ToolInput(tag="in_path", input_type=File(), position=2, doc=InputDocumentation(doc="paths of these contigs"))], outputs=[ToolOutput(tag="out_out", output_type=File(optional=True), selector=InputSelector(input_to_select="in_out", type_hint=File()), doc=OutputDocumentation(doc="output contig paths to FILE")), ToolOutput(tag="out_consensus", output_type=File(optional=True), selector=InputSelector(input_to_select="in_consensus", type_hint=File()), doc=OutputDocumentation(doc="output consensus sequences to FILE")), ToolOutput(tag="out_graph", output_type=File(optional=True), selector=InputSelector(input_to_select="in_graph", type_hint=File()), doc=OutputDocumentation(doc="output the contig adjacency graph to FILE"))], container="quay.io/biocontainers/abyss:2.2.5--ha4ec83a_0", version="v0.1.0")
if __name__ == "__main__":
# or "cwl"
Pathconsensus_V0_1_0().translate("wdl")
from datetime import datetime
from typing import List, Optional, Dict, Any
from janis_core import *
from janis_core.types.common_data_types import Int, Boolean, String, File
Abyss_Map_Ssq_V0_1_0 = CommandToolBuilder(tool="abyss_map_ssq", base_command=["abyss-map-ssq"], inputs=[ToolInput(tag="in_min_align", input_type=Int(optional=True), prefix="--min-align", doc=InputDocumentation(doc="find matches at least N bp [1]")), ToolInput(tag="in_threads", input_type=Int(optional=True), prefix="--threads", doc=InputDocumentation(doc="use N parallel threads [1]")), ToolInput(tag="in_append_comment", input_type=Boolean(optional=True), prefix="--append-comment", doc=InputDocumentation(doc="append the FASTA/FASTQ comment to the SAM tags")), ToolInput(tag="in_sample", input_type=Int(optional=True), prefix="--sample", doc=InputDocumentation(doc="sample the suffix array [1]")), ToolInput(tag="in_dup", input_type=Boolean(optional=True), prefix="--dup", doc=InputDocumentation(doc="identify and print duplicate sequence\nIDs between QUERY and TARGET")), ToolInput(tag="in_order", input_type=Boolean(optional=True), prefix="--order", doc=InputDocumentation(doc="print alignments in the same order as\nread from QUERY")), ToolInput(tag="in_no_order", input_type=Boolean(optional=True), prefix="--no-order", doc=InputDocumentation(doc="print alignments ASAP [default]")), ToolInput(tag="in_multi", input_type=Boolean(optional=True), prefix="--multi", doc=InputDocumentation(doc="Align unaligned segments of primary")), ToolInput(tag="in_ss", input_type=Boolean(optional=True), prefix="--SS", doc=InputDocumentation(doc="expect contigs to be oriented correctly")), ToolInput(tag="in_no_ss", input_type=Boolean(optional=True), prefix="--no-SS", doc=InputDocumentation(doc="no assumption about contig orientation")), ToolInput(tag="in_rc", input_type=Boolean(optional=True), prefix="--rc", doc=InputDocumentation(doc="map the sequence and its reverse complement [default]")), ToolInput(tag="in_no_rc", input_type=Boolean(optional=True), prefix="--no-rc", doc=InputDocumentation(doc="do not map the reverse complement sequence")), ToolInput(tag="in_alphabet", input_type=String(optional=True), prefix="--alphabet", doc=InputDocumentation(doc="use the alphabet STRING [-ACGT]")), ToolInput(tag="in_alpha", input_type=Boolean(optional=True), prefix="--alpha", doc=InputDocumentation(doc="equivalent to --no-rc -a' ABCDEFGHIJKLMNOPQRSTUVWXYZ'")), ToolInput(tag="in_dna", input_type=Boolean(optional=True), prefix="--dna", doc=InputDocumentation(doc="equivalent to --rc -a'-ACGT'")), ToolInput(tag="in_protein", input_type=Boolean(optional=True), prefix="--protein", doc=InputDocumentation(doc="equivalent to --no-rc -a'#*ACDEFGHIKLMNPQRSTVWY'")), ToolInput(tag="in_chastity", input_type=Boolean(optional=True), prefix="--chastity", doc=InputDocumentation(doc="discard unchaste reads")), ToolInput(tag="in_no_chastity", input_type=Boolean(optional=True), prefix="--no-chastity", doc=InputDocumentation(doc="do not discard unchaste reads [default]")), ToolInput(tag="in_verbose", input_type=Boolean(optional=True), prefix="--verbose", doc=InputDocumentation(doc="display verbose output")), ToolInput(tag="in_db", input_type=File(optional=True), prefix="--db", doc=InputDocumentation(doc="specify path of database repository in FILE")), ToolInput(tag="in_library", input_type=String(optional=True), prefix="--library", doc=InputDocumentation(doc="specify library NAME for database")), ToolInput(tag="in_strain", input_type=String(optional=True), prefix="--strain", doc=InputDocumentation(doc="specify strain NAME for database")), ToolInput(tag="in_species", input_type=String(optional=True), prefix="--species", doc=InputDocumentation(doc="specify species NAME for database")), ToolInput(tag="in_alignment", input_type=String(), position=0, doc=InputDocumentation(doc="--no-multi don't Align unaligned segments [default]"))], outputs=[], container="quay.io/biocontainers/abyss:2.2.5--ha4ec83a_0", version="v0.1.0")
if __name__ == "__main__":
# or "cwl"
Abyss_Map_Ssq_V0_1_0().translate("wdl")
from datetime import datetime
from typing import List, Optional, Dict, Any
from janis_core import *
from janis_core.types.common_data_types import Int, File, String, Boolean
Abyss_Rresolver_Short_V0_1_0 = CommandToolBuilder(tool="abyss_rresolver_short", base_command=["abyss-rresolver-short"], inputs=[ToolInput(tag="in_bloom_size", input_type=Int(optional=True), prefix="--bloom-size", doc=InputDocumentation(doc="read Bloom filter size. Unit suffixes 'K' (kilobytes), 'M' (megabytes), or 'G' (gigabytes) may be used. [required]")), ToolInput(tag="in_graph", input_type=File(optional=True), prefix="--graph", doc=InputDocumentation(doc="write the contig adjacency graph to FILE. [required]")), ToolInput(tag="in_contigs", input_type=File(optional=True), prefix="--contigs", doc=InputDocumentation(doc="write the contigs to FILE. [required]")), ToolInput(tag="in_threads", input_type=Int(optional=True), prefix="--threads", doc=InputDocumentation(doc="use N parallel threads [1]")), ToolInput(tag="in_km_er", input_type=Int(optional=True), prefix="--kmer", doc=InputDocumentation(doc="assembly k-mer size")), ToolInput(tag="in_hist", input_type=String(optional=True), prefix="--hist", doc=InputDocumentation(doc="write the algorithm histograms with the given prefix. Histograms are omitted if no prefix is given.")), ToolInput(tag="in_threshold", input_type=File(optional=True), prefix="--threshold", doc=InputDocumentation(doc="set path support threshold to N. [4]")), ToolInput(tag="in_extract", input_type=Int(optional=True), prefix="--extract", doc=InputDocumentation(doc="extract N r-mers per read. [4]")), ToolInput(tag="in_min_tests", input_type=Int(optional=True), prefix="--min-tests", doc=InputDocumentation(doc="set minimum number of sliding window moves to N. Cannot be higher than 127. [20]")), ToolInput(tag="in_max_tests", input_type=Int(optional=True), prefix="--max-tests", doc=InputDocumentation(doc="set maximum number of sliding window moves to N. Cannot be higher than 127. [36]")), ToolInput(tag="in_branching", input_type=Int(optional=True), prefix="--branching", doc=InputDocumentation(doc="set maximum number of branching paths to N. [75]")), ToolInput(tag="in_r_mer", input_type=Int(optional=True), prefix="--rmer", doc=InputDocumentation(doc="explicitly set r value (k value used by rresolver). The number of set r values should be equal to the number of read sizes.")), ToolInput(tag="in_approx_factor", input_type=Boolean(optional=True), prefix="--approx-factor", doc=InputDocumentation(doc="explicitly set coverage approximation factor.")), ToolInput(tag="in_quality_threshold", input_type=Int(optional=True), prefix="--quality--threshold", doc=InputDocumentation(doc="minimum quality all bases in rmers should have, on average. [35] (UNUSED)")), ToolInput(tag="in_error_correction", input_type=Boolean(optional=True), prefix="--error-correction", doc=InputDocumentation(doc="enable correction of a 1bp error in kmers. [false]")), ToolInput(tag="in_supported", input_type=File(optional=True), prefix="--supported", doc=InputDocumentation(doc="write supported paths to FILE.")), ToolInput(tag="in_unsupported", input_type=File(optional=True), prefix="--unsupported", doc=InputDocumentation(doc="write unsupported paths to FILE.\nUsed for path sequence quality check.")), ToolInput(tag="in_adj", input_type=Boolean(optional=True), prefix="--adj", doc=InputDocumentation(doc="output the graph in ADJ format [default]")), ToolInput(tag="in_as_qg", input_type=Boolean(optional=True), prefix="--asqg", doc=InputDocumentation(doc="output the graph in ASQG format")), ToolInput(tag="in_dot", input_type=Boolean(optional=True), prefix="--dot", doc=InputDocumentation(doc="output the graph in GraphViz format")), ToolInput(tag="in_gfa", input_type=Boolean(optional=True), prefix="--gfa", doc=InputDocumentation(doc="output the graph in GFA1 format")), ToolInput(tag="in_gfa_one", input_type=Boolean(optional=True), prefix="--gfa1", doc=InputDocumentation(doc="output the graph in GFA1 format")), ToolInput(tag="in_gfa_two", input_type=Boolean(optional=True), prefix="--gfa2", doc=InputDocumentation(doc="output the graph in GFA2 format")), ToolInput(tag="in_gv", input_type=Boolean(optional=True), prefix="--gv", doc=InputDocumentation(doc="output the graph in GraphViz format")), ToolInput(tag="in_sam", input_type=Boolean(optional=True), prefix="--sam", doc=InputDocumentation(doc="output the graph in SAM format")), ToolInput(tag="in_verbose", input_type=Boolean(optional=True), prefix="--verbose", doc=InputDocumentation(doc="display verbose output"))], outputs=[], container="quay.io/biocontainers/abyss:2.3.1--hd403d74_0", version="v0.1.0")
if __name__ == "__main__":
# or "cwl"
Abyss_Rresolver_Short_V0_1_0().translate("wdl")
from datetime import datetime
from typing import List, Optional, Dict, Any
from janis_core import *
from janis_core.types.common_data_types import Int, String
Advntr_Filtering_V0_1_0 = CommandToolBuilder(tool="adVNTR_Filtering", base_command=["adVNTR-Filtering"], inputs=[ToolInput(tag="in_min_matches", input_type=Int(optional=True), prefix="--min_matches", doc=InputDocumentation(doc="Minimum number of matches to accept a read")), ToolInput(tag="in_sequences_dot_fa", input_type=String(), position=0, doc=InputDocumentation(doc="")), ToolInput(tag="in_keywords_dot_txt", input_type=String(), position=1, doc=InputDocumentation(doc="")), ToolInput(tag="in_output_dot_txt", input_type=String(), position=2, doc=InputDocumentation(doc=""))], outputs=[], container="quay.io/biocontainers/advntr:1.4.1--py27h76bc9d7_0", version="v0.1.0")
if __name__ == "__main__":
# or "cwl"
Advntr_Filtering_V0_1_0().translate("wdl")
from datetime import datetime
from typing import List, Optional, Dict, Any
from janis_core import *
from janis_core.types.common_data_types import File, Int, Directory, Boolean, String
After_Py_V0_1_0 = CommandToolBuilder(tool="after.py", base_command=["after.py"], inputs=[ToolInput(tag="in_read_one_file", input_type=File(optional=True), prefix="--read1_file", doc=InputDocumentation(doc="file name of read1, required. If input_dir is\nspecified, then this arg is ignored.")), ToolInput(tag="in_read_two_file", input_type=File(optional=True), prefix="--read2_file", doc=InputDocumentation(doc="file name of read2, if paired. If input_dir is\nspecified, then this arg is ignored.")), ToolInput(tag="in_index_one_file", input_type=File(optional=True), prefix="--index1_file", doc=InputDocumentation(doc="file name of 7' index. If input_dir is specified, then\nthis arg is ignored.")), ToolInput(tag="in_index_two_file", input_type=File(optional=True), prefix="--index2_file", doc=InputDocumentation(doc="file name of 5' index. If input_dir is specified, then\nthis arg is ignored.")), ToolInput(tag="in_input_dir", input_type=Int(optional=True), prefix="--input_dir", doc=InputDocumentation(doc="the input dir to process automatically. If read1_file\nare input_dir are not specified, then current dir (.)\nis specified to input_dir")), ToolInput(tag="in_good_output_folder", input_type=Directory(optional=True), prefix="--good_output_folder", doc=InputDocumentation(doc="the folder to store good reads, by default it is named\n'good', in the current directory")), ToolInput(tag="in_bad_output_folder", input_type=Directory(optional=True), prefix="--bad_output_folder", doc=InputDocumentation(doc="the folder to store bad reads, by default it is named\n'bad', in the same folder as good_output_folder")), ToolInput(tag="in_report_output_folder", input_type=Directory(optional=True), prefix="--report_output_folder", doc=InputDocumentation(doc="the folder to store QC reports, by default it is named\n'QC', in the same folder as good_output_folder")), ToolInput(tag="in_read_one_flag", input_type=Int(optional=True), prefix="--read1_flag", doc=InputDocumentation(doc="specify the name flag of read1, default is R1, which\nmeans a file with name *R1* is read1 file")), ToolInput(tag="in_read_two_flag", input_type=Int(optional=True), prefix="--read2_flag", doc=InputDocumentation(doc="specify the name flag of read2, default is R2, which\nmeans a file with name *R2* is read2 file")), ToolInput(tag="in_index_one_flag", input_type=Int(optional=True), prefix="--index1_flag", doc=InputDocumentation(doc="specify the name flag of index1, default is I1, which\nmeans a file with name *I1* is index2 file")), ToolInput(tag="in_index_two_flag", input_type=Int(optional=True), prefix="--index2_flag", doc=InputDocumentation(doc="specify the name flag of index2, default is I2, which\nmeans a file with name *I2* is index2 file")), ToolInput(tag="in_trim_front", input_type=Int(optional=True), prefix="--trim_front", doc=InputDocumentation(doc="number of bases to be trimmed in the head of read. -1\nmeans auto detect")), ToolInput(tag="in_trim_tail", input_type=Int(optional=True), prefix="--trim_tail", doc=InputDocumentation(doc="number of bases to be trimmed in the tail of read. -1\nmeans auto detect")), ToolInput(tag="in_trim_pair_same", input_type=Int(optional=True), prefix="--trim_pair_same", doc=InputDocumentation(doc="use same trimming configuration for read1 and read2 to\nkeep their sequence length identical, default is true")), ToolInput(tag="in_qualified_quality_phred", input_type=Int(optional=True), prefix="--qualified_quality_phred", doc=InputDocumentation(doc="the quality value that a base is qualifyed. Default 15\nmeans phred base quality >=Q15 is qualified.")), ToolInput(tag="in_unqualified_base_limit", input_type=Int(optional=True), prefix="--unqualified_base_limit", doc=InputDocumentation(doc="if exists more than unqualified_base_limit bases that\nquality is lower than qualified quality, then this\nread/pair is bad. Default is 60")), ToolInput(tag="in_poly_size_limit", input_type=Int(optional=True), prefix="--poly_size_limit", doc=InputDocumentation(doc="if exists one polyX(polyG means GGGGGGGGG...), and its\nlength is >= poly_size_limit, then this read/pair is\nbad. Default is 35")), ToolInput(tag="in_allow_mismatch_in_poly", input_type=Int(optional=True), prefix="--allow_mismatch_in_poly", doc=InputDocumentation(doc="the count of allowed mismatches when detection polyX.\nDefault 2 means allow 2 mismatches for polyX detection")), ToolInput(tag="in_n_base_limit", input_type=Int(optional=True), prefix="--n_base_limit", doc=InputDocumentation(doc="if exists more than maxn bases have N, then this\nread/pair is bad. Default is 5")), ToolInput(tag="in_seq_len_req", input_type=Int(optional=True), prefix="--seq_len_req", doc=InputDocumentation(doc="if the trimmed read is shorter than seq_len_req, then\nthis read/pair is bad. Default is 35")), ToolInput(tag="in_de_bubble", input_type=Boolean(optional=True), prefix="--debubble", doc=InputDocumentation(doc="specify whether apply debubble algorithm to remove the\nreads in the bubbles. Default is False")), ToolInput(tag="in_de_bubble_dir", input_type=Directory(optional=True), prefix="--debubble_dir", doc=InputDocumentation(doc="specify the folder to store output of debubble\nalgorithm, default is debubble")), ToolInput(tag="in_draw", input_type=String(optional=True), prefix="--draw", doc=InputDocumentation(doc="specify whether draw the pictures or not, when use\ndebubble or QC. Default is on")), ToolInput(tag="in_barcode", input_type=File(optional=True), prefix="--barcode", doc=InputDocumentation(doc="specify whether deal with barcode sequencing files,\ndefault is on, which means all files with barcode_flag\nin filename will be treated as barcode sequencing\nfiles")), ToolInput(tag="in_barcode_length", input_type=Int(optional=True), prefix="--barcode_length", doc=InputDocumentation(doc="specify the designed length of barcode")), ToolInput(tag="in_barcode_flag", input_type=File(optional=True), prefix="--barcode_flag", doc=InputDocumentation(doc="specify the name flag of a barcoded file, default is\nbarcode, which means a file with name *barcode* is a\nbarcoded file")), ToolInput(tag="in_barcode_verify", input_type=String(optional=True), prefix="--barcode_verify", doc=InputDocumentation(doc="specify the verify sequence of a barcode which is\nadjunct to the barcode")), ToolInput(tag="in_store_overlap", input_type=String(optional=True), prefix="--store_overlap", doc=InputDocumentation(doc="specify whether store only overlapped bases of the\ngood reads")), ToolInput(tag="in_overlap_output_folder", input_type=Directory(optional=True), prefix="--overlap_output_folder", doc=InputDocumentation(doc="the folder to store only overlapped bases of the good\nreads")), ToolInput(tag="in_qc_only", input_type=Boolean(optional=True), prefix="--qc_only", doc=InputDocumentation(doc="if qconly is true, only QC result will be output, this\ncan be much fast")), ToolInput(tag="in_qc_sample", input_type=Int(optional=True), prefix="--qc_sample", doc=InputDocumentation(doc="sample up to qc_sample reads when do QC, 0 means\nsample all reads. Default is 200,000")), ToolInput(tag="in_qc_km_er", input_type=Int(optional=True), prefix="--qc_kmer", doc=InputDocumentation(doc="specify the kmer length for KMER statistics for QC,\ndefault is 8")), ToolInput(tag="in_no_correction", input_type=Boolean(optional=True), prefix="--no_correction", doc=InputDocumentation(doc="disable base correction for mismatched base pairs in\noverlapped areas")), ToolInput(tag="in_mask_mismatch", input_type=Boolean(optional=True), prefix="--mask_mismatch", doc=InputDocumentation(doc="set the qual num to 0 for mismatched base pairs in\noverlapped areas to mask them out")), ToolInput(tag="in_no_overlap", input_type=Boolean(optional=True), prefix="--no_overlap", doc=InputDocumentation(doc="disable overlap analysis (usually much faster with\nthis option)")), ToolInput(tag="in_gzip", input_type=Boolean(optional=True), prefix="--gzip", doc=InputDocumentation(doc="force gzip compression for output, even the input is\nnot gzip compressed")), ToolInput(tag="in_compression", input_type=Int(optional=True), prefix="--compression", doc=InputDocumentation(doc="set compression level (0~9) for gzip output, default\nis 2 (0 = best speed, 9 = best compression).\n")), ToolInput(tag="in_automatic", input_type=String(), position=0, doc=InputDocumentation(doc="")), ToolInput(tag="in_filtering", input_type=String(), position=1, doc=InputDocumentation(doc=""))], outputs=[ToolOutput(tag="out_good_output_folder", output_type=Directory(optional=True), selector=InputSelector(input_to_select="in_good_output_folder", type_hint=File()), doc=OutputDocumentation(doc="the folder to store good reads, by default it is named\n'good', in the current directory")), ToolOutput(tag="out_bad_output_folder", output_type=Directory(optional=True), selector=InputSelector(input_to_select="in_bad_output_folder", type_hint=File()), doc=OutputDocumentation(doc="the folder to store bad reads, by default it is named\n'bad', in the same folder as good_output_folder")), ToolOutput(tag="out_report_output_folder", output_type=Directory(optional=True), selector=InputSelector(input_to_select="in_report_output_folder", type_hint=File()), doc=OutputDocumentation(doc="the folder to store QC reports, by default it is named\n'QC', in the same folder as good_output_folder")), ToolOutput(tag="out_de_bubble_dir", output_type=Directory(optional=True), selector=InputSelector(input_to_select="in_de_bubble_dir", type_hint=File()), doc=OutputDocumentation(doc="specify the folder to store output of debubble\nalgorithm, default is debubble")), ToolOutput(tag="out_overlap_output_folder", output_type=Directory(optional=True), selector=InputSelector(input_to_select="in_overlap_output_folder", type_hint=File()), doc=OutputDocumentation(doc="the folder to store only overlapped bases of the good\nreads"))], container=None, version="v0.1.0")
if __name__ == "__main__":
# or "cwl"
After_Py_V0_1_0().translate("wdl", allow_empty_container=True)
from datetime import datetime
from typing import List, Optional, Dict, Any
from janis_core import *
from janis_core.types.common_data_types import Int, String, File
Afplot_Regions_Distance_V0_1_0 = CommandToolBuilder(tool="afplot_regions_distance", base_command=["afplot", "regions", "distance"], inputs=[ToolInput(tag="in_margin", input_type=Int(optional=True), prefix="--margin", doc=InputDocumentation(doc="Margin around regions to plot")), ToolInput(tag="in_region", input_type=String(optional=True), prefix="--region", doc=InputDocumentation(doc="Region string. Must be of format <contig:start-end>")), ToolInput(tag="in_region_file", input_type=File(optional=True), prefix="--region-file", doc=InputDocumentation(doc="Path to region file")), ToolInput(tag="in_name", input_type=String(optional=True), prefix="--name", doc=InputDocumentation(doc="Optional title for plot")), ToolInput(tag="in_output_dir", input_type=File(optional=True), prefix="--output-dir", doc=InputDocumentation(doc="Path to output directory [required]")), ToolInput(tag="in_vcf", input_type=File(optional=True), prefix="--vcf", doc=InputDocumentation(doc="Path to input VCF file [required]")), ToolInput(tag="in_color_palette", input_type=String(optional=True), prefix="--color-palette", doc=InputDocumentation(doc="The name of a color palette to pass to")), ToolInput(tag="in_seaborn_dot_set_palette", input_type=String(), position=0, doc=InputDocumentation(doc="--dpi INTEGER DPI for output PNGs (default: 300)"))], outputs=[ToolOutput(tag="out_output_dir", output_type=File(optional=True), selector=InputSelector(input_to_select="in_output_dir", type_hint=File()), doc=OutputDocumentation(doc="Path to output directory [required]"))], container=None, version="v0.1.0")
if __name__ == "__main__":
# or "cwl"
Afplot_Regions_Distance_V0_1_0().translate("wdl", allow_empty_container=True)
from datetime import datetime
from typing import List, Optional, Dict, Any
from janis_core import *
from janis_core.types.common_data_types import Int, String, Array, File, Boolean
Design_Py_Sliding_Window_Auto_From_Args_V0_1_0 = CommandToolBuilder(tool="design.py_sliding_window_auto_from_args", base_command=["design.py", "sliding-window", "auto-from-args"], inputs=[ToolInput(tag="in_guide_length", input_type=Int(optional=True), prefix="--guide-length", doc=InputDocumentation(doc="Length of guide to construct")), ToolInput(tag="in_obj", input_type=String(optional=True), prefix="--obj", doc=InputDocumentation(doc="Objective function to solve. 'maximize-activity'\nmaximizes the expected activity of the guide set of\nthe target genomes subject to soft and hard\nconstraints on the size of the guide set. 'minimize-\nguides' minimizes the number of guides in the guide\nset subject to coverage constraints across the target\ngenomes.")), ToolInput(tag="in_guide_mismatches", input_type=Int(optional=True), prefix="--guide-mismatches", doc=InputDocumentation(doc="Allow for this number of mismatches when determining\nwhether a guide covers a sequence")), ToolInput(tag="in_guide_cover_frac", input_type=String(optional=True), prefix="--guide-cover-frac", doc=InputDocumentation(doc="The fraction of all sequences that must be covered by\nthe guides.")), ToolInput(tag="in_soft_guide_constraint", input_type=Int(optional=True), prefix="--soft-guide-constraint", doc=InputDocumentation(doc="Soft constraint on the number of guides. There is no\npenalty for a number of guides <=\nSOFT_GUIDE_CONSTRAINT, and having a number of guides\nbeyond this is penalized. See --penalty-strength. This\nvalue must be <= HARD_GUIDE_CONSTRAINT.")), ToolInput(tag="in_hard_guide_constraint", input_type=Int(optional=True), prefix="--hard-guide-constraint", doc=InputDocumentation(doc="Hard constraint on the number of guides. The number of\nguides designed for a target will be <=\nHARD_GUIDE_CONSTRAINT.")), ToolInput(tag="in_penalty_strength", input_type=Int(optional=True), prefix="--penalty-strength", doc=InputDocumentation(doc="Importance of the penalty when the number of guides\nexceeds the soft guide constraint. Namely, for a guide\nset G, if the penalty strength is L and the soft guide\nconstraint is h, then the penalty in the objective\nfunction is L*max(0, |G|-h). Must be >= 0. The value\ndepends on the output of activity model and reflects a\ntolerance for more guides; for the default activity\nmodel reasonable values are in the range [0.1, 0.5].")), ToolInput(tag="in_maximization_algorithm", input_type=String(optional=True), prefix="--maximization-algorithm", doc=InputDocumentation(doc="Algorithm to use for solving submodular maximization\nproblem. 'greedy' is the canonical deterministic\ngreedy algorithm (Nemhauser 1978) for constrained\nmonotone submodular maximization, which may perform\nwell in practice but has poor theoretical guarantees\nhere because the function is not monotone (unless\n--penalty-strength is 0). 'random-greedy' is the\nrandomized greedy algorithm (Buchbinder 2014) for\nconstrained non-monotone submodular maximization that\nhas good worst-case theoretical guarantees.")), ToolInput(tag="in_missing_th_res", input_type=Int(optional=True), prefix="--missing-thres", doc=InputDocumentation(doc="MISSING_THRES MISSING_THRES\n<A> <B> <C>; parameters governing the threshold on\nwhich sites to ignore due to too much missing data.\nThe 3 values specify not to attempt to design guides\noverlapping sites where the fraction of sequences with\nmissing data is > min(A, max(B, C*m)) where m is the\nmedian fraction of sequences with missing data over\nthe alignment. Set a=1 and b=1 to not ignore sites due\nto missing data.")), ToolInput(tag="in_id_m", input_type=Int(optional=True), prefix="--id-m", doc=InputDocumentation(doc="Allow for this number of mismatches when determining\nwhether a guide 'hits' a sequence in a group/taxon\nother than the for which it is being designed; higher\nvalues correspond to more specificity.")), ToolInput(tag="in_id_frac", input_type=String(optional=True), prefix="--id-frac", doc=InputDocumentation(doc="Decide that a guide 'hits' a group/taxon if it 'hits'\na fraction of sequences in that group/taxon that\nexceeds this value; lower values correspond to more\nspecificity.")), ToolInput(tag="in_id_method", input_type=String(optional=True), prefix="--id-method", doc=InputDocumentation(doc="Choice of method to query for specificity. 'lshnn' for\nLSH near-neighbor approach. 'shard' for approach that\nshards k-mers across small tries.")), ToolInput(tag="in_specific_against_fast_as", input_type=Array(t=String(), optional=True), prefix="--specific-against-fastas", doc=InputDocumentation(doc="Path to one or more FASTA files giving sequences, such\nthat guides are designed to be specific against (i.e.,\nnot hit) these sequences, according to --id-m and\n--id-frac. This is equivalent to specifying the FASTAs\nin the main input (as positional inputs), except that,\nwhen provided here, guides are not designed for them\nand they do not need to be aligned.")), ToolInput(tag="in_specific_against_tax_a", input_type=File(optional=True), prefix="--specific-against-taxa", doc=InputDocumentation(doc="Path to TSV file giving giving taxonomies from which\nto download all genomes and ensure guides are specific\nagainst (i.e., not hit) these. The TSV file has 2\ncolumns: (1) a taxonomic ID; (2) segment label, or\n'None' if unsegmented")), ToolInput(tag="in_do_not_allow_gu_pairing", input_type=Boolean(optional=True), prefix="--do-not-allow-gu-pairing", doc=InputDocumentation(doc="When determining whether a guide binds to a region of\ntarget sequence, do not count G-U (wobble) base pairs\nas matching. Default is to tolerate G-U pairing:\nnamely, A in an output guide sequence matches G in the\ntarget and C in an output guide sequence matches T in\nthe target (since the synthesized guide is the reverse\ncomplement of the output guide sequence)")), ToolInput(tag="in_required_guides", input_type=File(optional=True), prefix="--required-guides", doc=InputDocumentation(doc="Path to a file that gives guide sequences that will be\nincluded in the guide cover and output for the windows\nin which they belong, e.g., if certain guide sequences\nare shown experimentally to perform well. The file\nmust have 3 columns: col 1 gives an identifier for the\nalignment that the guide covers, such that i\nrepresents the i'th FASTA given as input (0-based);\ncol 2 gives a guide sequence; col 3 gives the start\nposition of the guide (0-based) in the alignment")), ToolInput(tag="in_blacklisted_ranges", input_type=File(optional=True), prefix="--blacklisted-ranges", doc=InputDocumentation(doc="Path to a file that gives ranges in alignments from\nwhich guides will not be constructed. The file must\nhave 3 columns: col 1 gives an identifier for the\nalignment that the range corresponds to, such that i\nrepresents the i'th FASTA given as input (0-based);\ncol 2 gives the start position of the range\n(inclusive); col 3 gives the end position of the range\n(exclusive)")), ToolInput(tag="in_blacklisted_km_ers", input_type=Int(optional=True), prefix="--blacklisted-kmers", doc=InputDocumentation(doc="Path to a FASTA file that gives k-mers to blacklisted\nfrom guide sequences. No guide sequences will be\nconstructed that contain these k-mers. The k-mers make\nup the sequences in the FASTA file; the sequence names\nare ignored. k-mers should be long enough so that not\ntoo many guide sequences are deemed to be unsuitable,\nand should be at most the length of the guide")), ToolInput(tag="in_require_flanking_five", input_type=Int(optional=True), prefix="--require-flanking5", doc=InputDocumentation(doc="Require the given sequence on the 5' protospacer\nflanking site (PFS) of each designed guide; this\ntolerates ambiguity in the sequence (e.g., 'H'\nrequires 'A', 'C', or 'T', or, equivalently, avoids\nguides flanked by 'G'). Note that this is the 5' end\nin the target sequence (not the spacer sequence).")), ToolInput(tag="in_require_flanking_three", input_type=Int(optional=True), prefix="--require-flanking3", doc=InputDocumentation(doc="Require the given sequence on the 3' protospacer\nflanking site (PFS) of each designed guide; this\ntolerates ambiguity in the sequence (e.g., 'H'\nrequires 'A', 'C', or 'T', or, equivalently, avoids\nguides flanked by 'G'). Note that this is the 3' end\nin the target sequence (not the spacer sequence).")), ToolInput(tag="in_seed", input_type=String(optional=True), prefix="--seed", doc=InputDocumentation(doc="SEED will set the random seed, guaranteeing the same\noutput given the same inputs. If SEED is not set to\nthe same value, output may vary across different runs.")), ToolInput(tag="in_predict_activity_model_path", input_type=File(optional=True), prefix="--predict-activity-model-path", doc=InputDocumentation(doc="PREDICT_ACTIVITY_MODEL_PATH\nPaths to directories containing serialized models in\nTensorFlow's SavedModel format for predicting guide-\ntarget activity. There are two arguments: (1)\nclassification model to determine which guides are\nactive; (2) regression model, which is used to\ndetermine which guides (among active ones) are highly\nactive. The models/ directory contains example models.\nIf not set, ADAPT does not predict activities to use\nduring design.")), ToolInput(tag="in_predict_activity_th_res", input_type=Int(optional=True), prefix="--predict-activity-thres", doc=InputDocumentation(doc="PREDICT_ACTIVITY_THRES\nThresholds to use for decisions on output of\npredictive models. There are two arguments: (1)\nclassification threshold for deciding which guide-\ntarget pairs are active (in [0,1], where higher values\nhave higher precision but less recall); (2) regression\nthreshold for deciding which guide-target pairs are\nhighly active (>= 0, where higher values limit the\nnumber determined to be highly active). If not set but\n--predict-activity-model-path is set, then ADAPT uses\ndefault thresholds stored with the models.")), ToolInput(tag="in_use_simple_binary_activity_prediction", input_type=Boolean(optional=True), prefix="--use-simple-binary-activity-prediction", doc=InputDocumentation(doc="If set, predict activity using a simple binary\nprediction between guide and target according to their\ndistance, with the threshold determined based on\n--guide-mismatches. This is only applicable when OBJ\nis 'maxmimize-activity'. This does not use a\nserialized model for predicting activity, so\n--predict-activity-model-path should not be set when\nthis is set.")), ToolInput(tag="in_do_not_memoize_guide_computations", input_type=Boolean(optional=True), prefix="--do-not-memoize-guide-computations", doc=InputDocumentation(doc="If set, do not memoize computations during the search,\nincluding of guides identified at each site and of\nspecificity queries. This can be helpful for\nbenchmarking the improvement of memoization, or if\nthere is reason to believe memoization will slow the\nsearch (e.g., if possible amplicons rarely overlap).\nNote that activity predictions are still memoized.")), ToolInput(tag="in_debug", input_type=Boolean(optional=True), prefix="--debug", doc=InputDocumentation(doc="Debug output")), ToolInput(tag="in_verbose", input_type=Boolean(optional=True), prefix="--verbose", doc=InputDocumentation(doc="Verbose output")), ToolInput(tag="in_window_size", input_type=Int(optional=True), prefix="--window-size", doc=InputDocumentation(doc="Ensure that selected guides are all a window of this\nsize")), ToolInput(tag="in_window_step", input_type=String(optional=True), prefix="--window-step", doc=InputDocumentation(doc="Amount by which to increase the window start position\nfor every iteration")), ToolInput(tag="in_sort", input_type=Boolean(optional=True), prefix="--sort", doc=InputDocumentation(doc="If set, sort output TSV by number of guides\n(ascending) then by score (descending); default is to\nsort by window position")), ToolInput(tag="in_path_mafft_used", input_type=File(optional=True), prefix="--mafft-path", doc=InputDocumentation(doc="Path to mafft executable, used for generating\nalignments")), ToolInput(tag="in_prep_memoize_dir", input_type=File(optional=True), prefix="--prep-memoize-dir", doc=InputDocumentation(doc="Path to directory in which to memoize alignments and\nstatistics on them. If set to 's3://BUCKET/PATH', it\nwill save to the S3 bucket if boto3 and botocore are\ninstalled and access key information exists via\nAWS_ACCESS_KEY_ID and AWS_SECRET_ACCESS_KEY or via AWS\nCLI. If not set, this does not memoize this\ninformation.")), ToolInput(tag="in_sample_seqs", input_type=Int(optional=True), prefix="--sample-seqs", doc=InputDocumentation(doc="After fetching accessions, randomly select SAMPLE_SEQS\nof them with replacement from each taxonomy any move\nforward in the design with these. This is useful for\ntesting and measuring output growth as input size\ngrows, as well as assessing the dispersion in output\nassociated with some input sample.")), ToolInput(tag="in_prep_influenza", input_type=Boolean(optional=True), prefix="--prep-influenza", doc=InputDocumentation(doc="If set, fetch sequences using the NCBI Influenza\ndatabase; should only be used for Influenza A or B\nvirus taxonomies")), ToolInput(tag="in_cover_by_year_decay", input_type=Int(optional=True), prefix="--cover-by-year-decay", doc=InputDocumentation(doc="COVER_BY_YEAR_DECAY\n<A> <B>; if set, group input sequences by year and set\na desired partial cover for each year (fraction of\nsequences that must be covered by guides) as follows:\nAll years >= A receive a desired cover fraction of\nGUIDE_COVER_FRAC for guides (and PRIMER_COVER_FRAC for\nprimers). Each preceding year receives a desired cover\nfraction that decays by B -- i.e., year n is given\nB*(desired cover fraction of year n+1).")), ToolInput(tag="in_cluster_threshold", input_type=Int(optional=True), prefix="--cluster-threshold", doc=InputDocumentation(doc="Maximum inter-cluster distance to use when clustering\ninput sequences prior to alignment. Expressed as\naverage nucleotide dissimilarity (1-ANI, where ANI is\naverage nucleotide identity); higher values result in\nfewer clusters")), ToolInput(tag="in_use_accessions", input_type=File(optional=True), prefix="--use-accessions", doc=InputDocumentation(doc="If set, use specified accessions instead of fetching\nneighbors for the given taxonomic ID(s). This provides\na path to a TSV file with 3 columns: (1) a taxonomic\nID; (2) segment label, or 'None' if unsegmented; (3)\naccession. Each row specifies an accession to use in\nthe input, and values for columns 1 and 2 can appear\nin multiple rows.")), ToolInput(tag="in_use_fast_a", input_type=File(optional=True), prefix="--use-fasta", doc=InputDocumentation(doc="If set, use sequences in fasta instead of fetching\nneighbors for the given taxonomic ID(s). This provides\na path to a TSV file with 3 columns: (1) a taxonomic\nID; (2) segment label, or 'None' if unsegmented; (3)\npath to FASTA.")), ToolInput(tag="in_only_design_for", input_type=File(optional=True), prefix="--only-design-for", doc=InputDocumentation(doc="If set, only design for given taxonomies. This\nprovides a path to a TSV file with 2 columns: (1) a\ntaxonomic ID; (2) segment label, or 'None' if\nunsegmented")), ToolInput(tag="in_tax_a_to_ignore_for_specificity", input_type=File(optional=True), prefix="--taxa-to-ignore-for-specificity", doc=InputDocumentation(doc="If set, specify which taxa should be ignored when\nenforcing specificity while designing for other taxa.\nThis provides a path to a TSV file with 2 columns: (1)\na taxonomic ID A; (2) a taxonomic ID B such that B\nshould be ignored when determining specificity for A.\nWhen designing for A, this masks taxonomy B from all\nspecificity queries. This is useful, e.g., if B is a\nsubset of A.")), ToolInput(tag="in_ncbi_api_key", input_type=String(optional=True), prefix="--ncbi-api-key", doc=InputDocumentation(doc="API key to use for NCBI e-utils. Using this increases\nthe limit on requests/second and may prevent an IP\naddress from being blocked due to too many requests")), ToolInput(tag="in_aws_access_key_id", input_type=Int(optional=True), prefix="--aws-access-key-id", doc=InputDocumentation(doc="User Account Access Key for AWS. This is only\nnecessary if using S3 for memoization via\nPREP_MEMOIZE_DIR and AWS CLI is not installed and\nconfigured.")), ToolInput(tag="in_aws_secret_access_key", input_type=Int(optional=True), prefix="--aws-secret-access-key", doc=InputDocumentation(doc="User Account Secret Access Key for AWS. This is only\nnecessary if using S3 for memoization via\nPREP_MEMOIZE_DIR and AWS CLI is not installed and\nconfigured.")), ToolInput(tag="in_ref_accs", input_type=Array(t=String(), optional=True), prefix="--ref-accs", doc=InputDocumentation(doc="Accession(s) of reference sequence(s) to use for\ncuration (comma-separated). If not set, ADAPT will\nautomatically get accessions for reference sequences\nfrom NCBI based on the taxonomic ID")), ToolInput(tag="in_metadata_filter", input_type=Array(t=String(), optional=True), prefix="--metadata-filter", doc=InputDocumentation(doc="Only include accessions of specified taxonomic ID that\nmatch this metadata in the design. Metadata options\nare year, taxid, and country. Format as\n'metadata=value' or 'metadata!=value'. Separate\nmultiple values with commas and different metadata\nfilters with spaces (e.g. '--metadata-filter\nyear!=2020,2019 taxid=11060')")), ToolInput(tag="in_specific_against_metadata_filter", input_type=Array(t=String(), optional=True), prefix="--specific-against-metadata-filter", doc=InputDocumentation(doc="Only include accessions of the specified taxonomic ID\nthat do not match this metadata in the design, and be\nspecific against any accession that does match this\nmetadata. Metadata options are year, taxid, and\ncountry. Format as 'metadata=value' or\n'metadata!=value'. Separate multiple values with\ncommas and different metadata filters with spaces\n(e.g. '--specific-against-metadata-filter\nyear!=2020,2019 taxid=11060')")), ToolInput(tag="in_write_input_seqs", input_type=File(optional=True), prefix="--write-input-seqs", doc=InputDocumentation(doc="Path to a file to which to write the sequences\n(accession.version) being used as input for design")), ToolInput(tag="in_write_input_aln", input_type=Int(optional=True), prefix="--write-input-aln", doc=InputDocumentation(doc="Prefix of path to files to which to write the\nalignments being used as input for design; filenames\nare 'WRITE_INPUT_ALN.[cluster-number]'\n")), ToolInput(tag="in_var_48", input_type=String(), position=0, doc=InputDocumentation(doc="[--prep-memoize-dir PREP_MEMOIZE_DIR]")), ToolInput(tag="in_tax_id", input_type=String(), position=0, doc=InputDocumentation(doc="Taxonomic (e.g., species) ID from NCBI")), ToolInput(tag="in_segment", input_type=String(), position=1, doc=InputDocumentation(doc="Label of segment (e.g., 'S') if there is one, or\n'None' if unsegmented")), ToolInput(tag="in_out_tsv", input_type=String(), position=2, doc=InputDocumentation(doc="Path to output TSVs, with one per cluster; output TSVs\nare OUT_TSV.{cluster-number}"))], outputs=[], container="quay.io/biocontainers/adapt:1.2.0--py_0", version="v0.1.0")
if __name__ == "__main__":
# or "cwl"
Design_Py_Sliding_Window_Auto_From_Args_V0_1_0().translate("wdl")
from datetime import datetime
from typing import List, Optional, Dict, Any
from janis_core import *
from janis_core.types.common_data_types import String, Int, File
Advntr_Viewmodel_V0_1_0 = CommandToolBuilder(tool="advntr_viewmodel", base_command=["advntr", "viewmodel"], inputs=[ToolInput(tag="in_gene", input_type=String(optional=True), prefix="--gene", doc=InputDocumentation(doc="comma-separated list of Gene Names")), ToolInput(tag="in_pattern", input_type=Int(optional=True), prefix="--pattern", doc=InputDocumentation(doc="repeating pattern of VNTR in forward (5' to 3') direction")), ToolInput(tag="in_models", input_type=File(optional=True), prefix="--models", doc=InputDocumentation(doc="VNTR models file [vntr_data/hg19_selected_VNTRs_Illumina.db]"))], outputs=[], container=None, version="v0.1.0")
if __name__ == "__main__":
# or "cwl"
Advntr_Viewmodel_V0_1_0().translate("wdl", allow_empty_container=True)
from datetime import datetime
from typing import List, Optional, Dict, Any
from janis_core import *
from janis_core.types.common_data_types import Boolean, Int, File, String
Abyss_Fixmate_V0_1_0 = CommandToolBuilder(tool="abyss_fixmate", base_command=["abyss-fixmate"], inputs=[ToolInput(tag="in_no_qname", input_type=Boolean(optional=True), prefix="--no-qname", doc=InputDocumentation(doc="set the qname to * [default]")), ToolInput(tag="in_qname", input_type=Boolean(optional=True), prefix="--qname", doc=InputDocumentation(doc="do not alter the qname")), ToolInput(tag="in_all", input_type=Boolean(optional=True), prefix="--all", doc=InputDocumentation(doc="print all alignments")), ToolInput(tag="in_diff", input_type=Boolean(optional=True), prefix="--diff", doc=InputDocumentation(doc="print alignments that align to different\ncontigs [default]")), ToolInput(tag="in_min_align", input_type=Int(optional=True), prefix="--min-align", doc=InputDocumentation(doc="the minimal alignment size [1]")), ToolInput(tag="in_same", input_type=File(optional=True), prefix="--same", doc=InputDocumentation(doc="write properly-paired reads to this file")), ToolInput(tag="in_hist", input_type=File(optional=True), prefix="--hist", doc=InputDocumentation(doc="write the fragment size histogram to FILE")), ToolInput(tag="in_cov", input_type=File(optional=True), prefix="--cov", doc=InputDocumentation(doc="write the physical coverage to FILE")), ToolInput(tag="in_verbose", input_type=Boolean(optional=True), prefix="--verbose", doc=InputDocumentation(doc="display verbose output")), ToolInput(tag="in_db", input_type=File(optional=True), prefix="--db", doc=InputDocumentation(doc="specify path of database repository in FILE")), ToolInput(tag="in_library", input_type=String(optional=True), prefix="--library", doc=InputDocumentation(doc="specify library NAME for sqlite")), ToolInput(tag="in_strain", input_type=String(optional=True), prefix="--strain", doc=InputDocumentation(doc="specify strain NAME for sqlite")), ToolInput(tag="in_species", input_type=String(optional=True), prefix="--species", doc=InputDocumentation(doc="specify species NAME for sqlite"))], outputs=[], container=None, version="v0.1.0")
if __name__ == "__main__":
# or "cwl"
Abyss_Fixmate_V0_1_0().translate("wdl", allow_empty_container=True)
from datetime import datetime
from typing import List, Optional, Dict, Any
from janis_core import *
from janis_core.types.common_data_types import Boolean, File, Int, String
Abyss_Sealer_V0_1_0 = CommandToolBuilder(tool="abyss_sealer", base_command=["abyss-sealer"], inputs=[ToolInput(tag="in_print_flanks", input_type=Boolean(optional=True), prefix="--print-flanks", doc=InputDocumentation(doc="outputs flank files")), ToolInput(tag="in_input_scaffold", input_type=File(optional=True), prefix="--input-scaffold", doc=InputDocumentation(doc="load scaffold from FILE")), ToolInput(tag="in_flank_length", input_type=Int(optional=True), prefix="--flank-length", doc=InputDocumentation(doc="length of flanks to be used as pseudoreads [100]")), ToolInput(tag="in_max_gap_length", input_type=Int(optional=True), prefix="--max-gap-length", doc=InputDocumentation(doc="max gap size to fill in bp [800]; runtime increases\nexponentially with respect to this parameter")), ToolInput(tag="in_threads", input_type=Int(optional=True), prefix="--threads", doc=InputDocumentation(doc="use N parallel threads [1]")), ToolInput(tag="in_km_er", input_type=Int(optional=True), prefix="--kmer", doc=InputDocumentation(doc="the size of a k-mer")), ToolInput(tag="in_bloom_size", input_type=Int(optional=True), prefix="--bloom-size", doc=InputDocumentation(doc="size of Bloom filter (e.g. '40G'). Required\nwhen not using pre-built Bloom filter(s)\n(-i option)")), ToolInput(tag="in_dot_file", input_type=File(optional=True), prefix="--dot-file", doc=InputDocumentation(doc="write graph traversals to a DOT file")), ToolInput(tag="in_fix_errors", input_type=Boolean(optional=True), prefix="--fix-errors", doc=InputDocumentation(doc="find and fix single-base errors when reads\nhave no kmers in bloom filter [disabled]")), ToolInput(tag="in_max_cost", input_type=Int(optional=True), prefix="--max-cost", doc=InputDocumentation(doc="max edges to traverse during each graph search [100000]")), ToolInput(tag="in_input_bloom", input_type=File(optional=True), prefix="--input-bloom", doc=InputDocumentation(doc="load bloom filter from FILE")), ToolInput(tag="in_mask", input_type=Boolean(optional=True), prefix="--mask", doc=InputDocumentation(doc="mask new and changed bases as lower case")), ToolInput(tag="in_no_mask", input_type=Boolean(optional=True), prefix="--no-mask", doc=InputDocumentation(doc="do not mask bases [default]")), ToolInput(tag="in_chastity", input_type=Boolean(optional=True), prefix="--chastity", doc=InputDocumentation(doc="discard unchaste reads [default]")), ToolInput(tag="in_no_chastity", input_type=Boolean(optional=True), prefix="--no-chastity", doc=InputDocumentation(doc="do not discard unchaste reads")), ToolInput(tag="in_trim_masked", input_type=Boolean(optional=True), prefix="--trim-masked", doc=InputDocumentation(doc="trim masked bases from the ends of reads")), ToolInput(tag="in_no_trim_masked", input_type=Boolean(optional=True), prefix="--no-trim-masked", doc=InputDocumentation(doc="do not trim masked bases from the ends\nof reads [default]")), ToolInput(tag="in_flank_mismatches", input_type=Int(optional=True), prefix="--flank-mismatches", doc=InputDocumentation(doc="max mismatches between paths and flanks; use\n'nolimit' for no limit [nolimit]")), ToolInput(tag="in_max_mismatches", input_type=Int(optional=True), prefix="--max-mismatches", doc=InputDocumentation(doc="max mismatches between all alternate paths;\nuse 'nolimit' for no limit [nolimit]")), ToolInput(tag="in_no_limits", input_type=Boolean(optional=True), prefix="--no-limits", doc=InputDocumentation(doc="disable all limits; equivalent to\n'-B nolimit -m nolimit -M nolimit -P nolimit'")), ToolInput(tag="in_output_prefix", input_type=File(optional=True), prefix="--output-prefix", doc=InputDocumentation(doc="prefix of output FASTA files [required]")), ToolInput(tag="in_max_paths", input_type=Int(optional=True), prefix="--max-paths", doc=InputDocumentation(doc="merge at most N alternate paths; use 'nolimit'\nfor no limit [2]")), ToolInput(tag="in_trim_quality", input_type=String(optional=True), prefix="--trim-quality", doc=InputDocumentation(doc="trim bases from the ends of reads whose\nquality is less than the threshold")), ToolInput(tag="in_standard_quality", input_type=Boolean(optional=True), prefix="--standard-quality", doc=InputDocumentation(doc="zero quality is `!' (33)\ndefault for FASTQ and SAM files")), ToolInput(tag="in_illumina_quality", input_type=Boolean(optional=True), prefix="--illumina-quality", doc=InputDocumentation(doc="zero quality is `@' (64)\ndefault for qseq and export files")), ToolInput(tag="in_read_name", input_type=String(optional=True), prefix="--read-name", doc=InputDocumentation(doc="only process reads with names that contain STR")), ToolInput(tag="in_search_mem", input_type=Int(optional=True), prefix="--search-mem", doc=InputDocumentation(doc="mem limit for graph searches; multiply by the\nnumber of threads (-j) to get the total mem used\nfor graph traversal [500M]")), ToolInput(tag="in_gap_file", input_type=File(optional=True), prefix="--gap-file", doc=InputDocumentation(doc="write sealed gaps to FILE")), ToolInput(tag="in_trace_file", input_type=File(optional=True), prefix="--trace-file", doc=InputDocumentation(doc="write graph search stats to FILE")), ToolInput(tag="in_verbose", input_type=Boolean(optional=True), prefix="--verbose", doc=InputDocumentation(doc="display verbose output")), ToolInput(tag="in_max_branches", input_type=Int(optional=True), prefix="--max-branches", doc=InputDocumentation(doc="max branches in de Bruijn graph traversal;\nuse 'nolimit' for no limit [nolimit]")), ToolInput(tag="in_min_frag", input_type=Int(optional=True), prefix="--min-frag", doc=InputDocumentation(doc="min fragment size in base pairs")), ToolInput(tag="in_max_frag", input_type=Int(optional=True), prefix="--max-frag", doc=InputDocumentation(doc="max fragment size in base pairs")), ToolInput(tag="in_abyss_sealer_b", input_type=String(), position=0, doc=InputDocumentation(doc="")), ToolInput(tag="in_bloom_filter_size", input_type=Int(), position=1, doc=InputDocumentation(doc=""))], outputs=[], container="quay.io/biocontainers/abyss:2.3.0--ha4ec83a_0", version="v0.1.0")
if __name__ == "__main__":
# or "cwl"
Abyss_Sealer_V0_1_0().translate("wdl")
tag="in_cov",
input_type=File(optional=True),
prefix="--cov",
doc=InputDocumentation(doc="write the physical coverage to FILE")),
ToolInput(tag="in_verbose",
input_type=Boolean(optional=True),
prefix="--verbose",
doc=InputDocumentation(doc="display verbose output")),
ToolInput(tag="in_db",
input_type=File(optional=True),
prefix="--db",
doc=InputDocumentation(
doc="specify path of database repository in FILE")),
ToolInput(
tag="in_library",
input_type=String(optional=True),
prefix="--library",
doc=InputDocumentation(doc="specify library NAME for sqlite")),
ToolInput(
tag="in_strain",
input_type=String(optional=True),
prefix="--strain",
doc=InputDocumentation(doc="specify strain NAME for sqlite")),
ToolInput(
tag="in_species",
input_type=String(optional=True),
prefix="--species",
doc=InputDocumentation(doc="specify species NAME for sqlite"))
],
outputs=[],
container="quay.io/biocontainers/abyss:2.2.5--ha4ec83a_0",
from datetime import datetime
from typing import List, Optional, Dict, Any
from janis_core import *
from janis_core.types.common_data_types import Int, Boolean, String, File
Abyss_Bloom_V0_1_0 = CommandToolBuilder(tool="abyss_bloom", base_command=["abyss-bloom"], inputs=[ToolInput(tag="in_km_er", input_type=Int(optional=True), prefix="--kmer", doc=InputDocumentation(doc="the size of a k-mer [<=128]")), ToolInput(tag="in_verbose", input_type=Boolean(optional=True), prefix="--verbose", doc=InputDocumentation(doc="display verbose output")), ToolInput(tag="in_bloom_size", input_type=Int(optional=True), prefix="--bloom-size", doc=InputDocumentation(doc="size of bloom filter [500M]")), ToolInput(tag="in_buffer_size", input_type=Int(optional=True), prefix="--buffer-size", doc=InputDocumentation(doc="size of I/O buffer for each thread, in bytes [100000]")), ToolInput(tag="in_threads", input_type=Int(optional=True), prefix="--threads", doc=InputDocumentation(doc="use N parallel threads [1]")), ToolInput(tag="in_hash_seed", input_type=Int(optional=True), prefix="--hash-seed", doc=InputDocumentation(doc="seed for hash function (only works with\n`-t konnector') [0]")), ToolInput(tag="in_num_hashes", input_type=Int(optional=True), prefix="--num-hashes", doc=InputDocumentation(doc="number of hash functions (only works with\n`-t rolling-hash') [1]")), ToolInput(tag="in_levels", input_type=String(optional=True), prefix="--levels", doc=InputDocumentation(doc="build a cascading bloom filter with N levels\nand output the last level")), ToolInput(tag="in_in_it_level", input_type=Boolean(optional=True), prefix="--init-level", doc=InputDocumentation(doc="='N=FILE' initialize level N of cascading bloom filter\nfrom FILE")), ToolInput(tag="in_chastity", input_type=Boolean(optional=True), prefix="--chastity", doc=InputDocumentation(doc="discard unchaste reads [default]")), ToolInput(tag="in_no_chastity", input_type=Boolean(optional=True), prefix="--no-chastity", doc=InputDocumentation(doc="do not discard unchaste reads")), ToolInput(tag="in_trim_masked", input_type=Boolean(optional=True), prefix="--trim-masked", doc=InputDocumentation(doc="trim masked bases from the ends of reads")), ToolInput(tag="in_no_trim_masked", input_type=Boolean(optional=True), prefix="--no-trim-masked", doc=InputDocumentation(doc="do not trim masked bases from the ends\nof reads [default]")), ToolInput(tag="in_num_locks", input_type=Int(optional=True), prefix="--num-locks", doc=InputDocumentation(doc="number of write locks on bloom filter [1000]")), ToolInput(tag="in_trim_quality", input_type=String(optional=True), prefix="--trim-quality", doc=InputDocumentation(doc="trim bases from the ends of reads whose\nquality is less than the threshold")), ToolInput(tag="in_bloom_type", input_type=String(optional=True), prefix="--bloom-type", doc=InputDocumentation(doc="'konnector', 'rolling-hash', or 'counting' [konnector]")), ToolInput(tag="in_standard_quality", input_type=Boolean(optional=True), prefix="--standard-quality", doc=InputDocumentation(doc="zero quality is `!' (33)\ndefault for FASTQ and SAM files")), ToolInput(tag="in_illumina_quality", input_type=Boolean(optional=True), prefix="--illumina-quality", doc=InputDocumentation(doc="zero quality is `@' (64)\ndefault for qseq and export files")), ToolInput(tag="in_window", input_type=String(optional=True), prefix="--window", doc=InputDocumentation(doc="/N build a bloom filter for subwindow M of N")), ToolInput(tag="in_method", input_type=Boolean(optional=True), prefix="--method", doc=InputDocumentation(doc="=`String' choose distance calculation method\n[`jaccard'(default), `forbes', `czekanowski']")), ToolInput(tag="in_depth", input_type=String(optional=True), prefix="--depth", doc=InputDocumentation(doc="depth of neighbouring from --root [k]")), ToolInput(tag="in_root", input_type=String(optional=True), prefix="--root", doc=InputDocumentation(doc="root k-mer from graph traversal [required]")), ToolInput(tag="in_root_fast_a", input_type=File(optional=True), prefix="--root-fasta", doc=InputDocumentation(doc="get root k-mers from FASTA file")), ToolInput(tag="in_fast_a_attr", input_type=File(optional=True), prefix="--fasta-attr", doc=InputDocumentation(doc=":FILE, assign a node attribute (e.g. 'color=blue')")), ToolInput(tag="in_node_attr", input_type=File(optional=True), prefix="--node-attr", doc=InputDocumentation(doc=":FILE to k-mers in the given FASTA")), ToolInput(tag="in_bloom_attr", input_type=File(optional=True), prefix="--bloom-attr", doc=InputDocumentation(doc=":FILE assign a node attribute (e.g. 'color=blue')\nto k-mers in the given Bloom filter")), ToolInput(tag="in_inverse", input_type=Boolean(optional=True), prefix="--inverse", doc=InputDocumentation(doc="get k-mers that are *NOT* in the bloom filter")), ToolInput(tag="in_bed", input_type=Boolean(optional=True), prefix="--bed", doc=InputDocumentation(doc="output k-mers in BED format")), ToolInput(tag="in_fast_a", input_type=Boolean(optional=True), prefix="--fasta", doc=InputDocumentation(doc="output k-mers in FASTA format [default]")), ToolInput(tag="in_raw", input_type=Boolean(optional=True), prefix="--raw", doc=InputDocumentation(doc="output k-mers in raw format (one per line)"))], outputs=[], container=None, version="v0.1.0")
if __name__ == "__main__":
# or "cwl"
Abyss_Bloom_V0_1_0().translate("wdl", allow_empty_container=True)
