prefix="--frameshift",
doc=InputDocumentation(
doc=
"set this flag to search for frameshifts in VNTR instead of copy number.\nSupported VNTR IDs: [25561, 519759]"
)),
ToolInput(
tag="in_expansion",
input_type=Boolean(optional=True),
prefix="--expansion",
doc=InputDocumentation(
doc=
"set this flag to determine long expansion from PCR-free data")
),
ToolInput(
tag="in_coverage",
input_type=Float(optional=True),
prefix="--coverage",
doc=InputDocumentation(
doc="average sequencing coverage in PCR-free sequencing")),
ToolInput(tag="in_haploid",
input_type=Boolean(optional=True),
prefix="--haploid",
doc=InputDocumentation(
doc="set this flag if the organism is haploid")),
ToolInput(
tag="in_naive",
input_type=Boolean(optional=True),
prefix="--naive",
doc=InputDocumentation(doc="use naive approach for PacBio reads")),
ToolInput(
tag="in_working_directory",
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 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 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")