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
Abyss_Layout_V0_1_0 = CommandToolBuilder(tool="abyss_layout", base_command=["abyss-layout"], inputs=[ToolInput(tag="in_min_length", input_type=Int(optional=True), prefix="--min-length", doc=InputDocumentation(doc="minimum sequence length [0]")), ToolInput(tag="in_min_overlap", input_type=Int(optional=True), prefix="--min-overlap", doc=InputDocumentation(doc="minimum overlap [0]")), ToolInput(tag="in_km_er", input_type=Int(optional=True), prefix="--kmer", doc=InputDocumentation(doc="length of a k-mer")), 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_tred", input_type=Boolean(optional=True), prefix="--tred", doc=InputDocumentation(doc="remove transitive edges")), ToolInput(tag="in_no_tred", input_type=Boolean(optional=True), prefix="--no-tred", doc=InputDocumentation(doc="do not remove 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_verbose", input_type=Boolean(optional=True), prefix="--verbose", doc=InputDocumentation(doc="display verbose output")), ToolInput(tag="in_overlap", input_type=String(), position=0, doc=InputDocumentation(doc="the sequence overlap graph"))], outputs=[], container="quay.io/biocontainers/abyss:2.2.5--ha4ec83a_0", version="v0.1.0")
if __name__ == "__main__":
# or "cwl"
Abyss_Layout_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=None, version="v0.1.0")
if __name__ == "__main__":
# or "cwl"
Abyss_Map_Ssq_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
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")
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
Xtractore_V0_1_0 = CommandToolBuilder(tool="xtractore", base_command=["xtractore"], inputs=[ToolInput(tag="in_debug", input_type=Boolean(optional=True), prefix="--debug", doc=InputDocumentation(doc="print debugging output")), ToolInput(tag="in_id_file", input_type=Boolean(optional=True), prefix="--idfile", doc=InputDocumentation(doc=": FILE file containing a list of feature IDs (1 per line\nwith no spaces); if provided, only features with\nIDs in this file will be extracted")), ToolInput(tag="in_outfile", input_type=File(optional=True), prefix="--outfile", doc=InputDocumentation(doc=": FILE file to which output sequences will be written;\ndefault is terminal (stdout)")), ToolInput(tag="in_type", input_type=Boolean(optional=True), prefix="--type", doc=InputDocumentation(doc=": STRING feature type to extract; can be used multiple\ntimes to extract features of multiple types")), ToolInput(tag="in_verbose", input_type=Boolean(optional=True), prefix="--verbose", doc=InputDocumentation(doc="print verbose warning and error messages")), ToolInput(tag="in_width", input_type=Boolean(optional=True), prefix="--width", doc=InputDocumentation(doc=": INT width of each line of sequence in the Fasta\noutput; default is 80; set to 0 for no\nformatting\n")), ToolInput(tag="in_features_dot_gff_three", input_type=Int(), position=0, doc=InputDocumentation(doc="")), ToolInput(tag="in_sequences_dot_fast_a", input_type=String(), position=1, doc=InputDocumentation(doc=""))], outputs=[ToolOutput(tag="out_outfile", output_type=File(optional=True), selector=InputSelector(input_to_select="in_outfile", type_hint=File()), doc=OutputDocumentation(doc=": FILE file to which output sequences will be written;\ndefault is terminal (stdout)"))], container="quay.io/biocontainers/aegean:0.16.0--hc2cb157_0", version="v0.1.0")
if __name__ == "__main__":
# or "cwl"
Xtractore_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_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)
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, Directory, Int
Abritamr_V0_1_0 = CommandToolBuilder(tool="abriTAMR", base_command=["abriTAMR"], inputs=[ToolInput(tag="in_mdu_qc", input_type=Boolean(optional=True), prefix="--mduqc", doc=InputDocumentation(doc="Set if running on MDU QC data. If set please provide\nthe MDU QC .csv as further input and an additional\noutput suitable for lims input will be provided.\n(default: False)")), ToolInput(tag="in_qc", input_type=File(optional=True), prefix="--qc", doc=InputDocumentation(doc="Name of checked MDU QC file. (default:\nmdu_qc_checked.csv)")), ToolInput(tag="in_positive_control", input_type=File(optional=True), prefix="--positive_control", doc=InputDocumentation(doc="Path to positive control sequence - must be set if\nusing -m (default: )")), ToolInput(tag="in_singularity", input_type=Boolean(optional=True), prefix="--Singularity", doc=InputDocumentation(doc="If using singularity container for AMRfinderplus\n(default: False)")), ToolInput(tag="in_singularity_path", input_type=File(optional=True), prefix="--singularity_path", doc=InputDocumentation(doc="Path to the singularity container for AMRfinderplus,\nif empty will defualt to shub://phgenomics-\nsingularity/amrfinderplus (default: )")), ToolInput(tag="in_contigs", input_type=File(optional=True), prefix="--contigs", doc=InputDocumentation(doc="Tab-delimited file with sample ID as column 1 and path\nto assemblies as column 2 OR path to a contig file\n(used if only doing a single sample - should provide\nvalue for -pfx). (default: )")), ToolInput(tag="in_amr_finder_output", input_type=File(optional=True), prefix="--amrfinder_output", doc=InputDocumentation(doc="Tab-delimited file with sample ID as column 1 and path\nto amr_finder output files as column 2 OR path to a\namrfinder ouptu file (used if only doing a single\nsample - should provide value for -pfx). (default: )")), ToolInput(tag="in_prefix", input_type=File(optional=True), prefix="--prefix", doc=InputDocumentation(doc="If using abriTAMR on single file please provide a\nprefix (default: )")), ToolInput(tag="in_workdir", input_type=Directory(optional=True), prefix="--workdir", doc=InputDocumentation(doc="Working directory, default is current directory\n(default: /)")), ToolInput(tag="in_resources", input_type=Directory(optional=True), prefix="--resources", doc=InputDocumentation(doc="Directory where templates are stored (default:\n/usr/local/lib/python3.7/site-packages/abritamr)")), ToolInput(tag="in_species_detect", input_type=Boolean(optional=True), prefix="--species_detect", doc=InputDocumentation(doc="Set if you would like to use point mutations.\n(default: False)")), ToolInput(tag="in_jobs", input_type=Int(optional=True), prefix="--jobs", doc=InputDocumentation(doc="Number of AMR finder jobs to run in parallel.\n(default: 16)")), ToolInput(tag="in_keep", input_type=Boolean(optional=True), prefix="--keep", doc=InputDocumentation(doc="If you would like to keep intermediate files and\nsnakemake log. Default is to remove (default: False)\n")), ToolInput(tag="in_v", input_type=Boolean(optional=True), prefix="-v", doc=InputDocumentation(doc=""))], outputs=[ToolOutput(tag="out_amr_finder_output", output_type=File(optional=True), selector=InputSelector(input_to_select="in_amr_finder_output", type_hint=File()), doc=OutputDocumentation(doc="Tab-delimited file with sample ID as column 1 and path\nto amr_finder output files as column 2 OR path to a\namrfinder ouptu file (used if only doing a single\nsample - should provide value for -pfx). (default: )"))], container="quay.io/biocontainers/abritamr:0.2.2--py_0", version="v0.1.0")
if __name__ == "__main__":
# or "cwl"
Abritamr_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, File, String
Abyss_Bloom_Dbg_V0_1_0 = CommandToolBuilder(tool="abyss_bloom_dbg", base_command=["abyss-bloom-dbg"], inputs=[ToolInput(tag="in___assemblyfasta", input_type=Int(optional=True), prefix="-G", doc=InputDocumentation(doc="[options] <FASTQ> [FASTQ]... > assembly.fasta")), ToolInput(tag="in_bloom_size", input_type=Int(optional=True), prefix="--bloom-size", doc=InputDocumentation(doc="overall memory budget for the assembly in bytes.\nUnit suffixes 'k' (kilobytes), 'M' (megabytes),\nor 'G' (gigabytes) may be used. [required]")), 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_graph", input_type=File(optional=True), prefix="--graph", doc=InputDocumentation(doc="write de Bruijn graph to FILE (GraphViz)")), ToolInput(tag="in_num_hashes", input_type=Int(optional=True), prefix="--num-hashes", doc=InputDocumentation(doc="number of Bloom filter hash functions [1]")), ToolInput(tag="in_threads", input_type=Int(optional=True), prefix="--threads", doc=InputDocumentation(doc="use N parallel threads [1]")), 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_km_er", input_type=Int(optional=True), prefix="--kmer", doc=InputDocumentation(doc="the size of a k-mer [required]")), ToolInput(tag="in_kc", input_type=Int(optional=True), prefix="--kc", doc=InputDocumentation(doc="use a cascading Bloom filter with N levels,\ninstead of a counting Bloom filter [2]")), ToolInput(tag="in_out", input_type=File(optional=True), prefix="--out", doc=InputDocumentation(doc="write the contigs to FILE [STDOUT]")), 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_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), typically\nfor FASTQ and SAM files [default]")), ToolInput(tag="in_illumina_quality", input_type=Boolean(optional=True), prefix="--illumina-quality", doc=InputDocumentation(doc="zero quality is `@' (64), typically\nfor qseq and export files")), ToolInput(tag="in_trim_length", input_type=Boolean(optional=True), prefix="--trim-length", doc=InputDocumentation(doc="max branch length to trim, in k-mers [k]")), ToolInput(tag="in_verbose", input_type=Boolean(optional=True), prefix="--verbose", doc=InputDocumentation(doc="display verbose output")), ToolInput(tag="in_single_km_er", input_type=Int(optional=True), prefix="--single-kmer", doc=InputDocumentation(doc="use a spaced seed that consists of two k-mers\nseparated by a gap. K must be chosen such that\nK <= k/2")), ToolInput(tag="in_qr_seed", input_type=Int(optional=True), prefix="--qr-seed", doc=InputDocumentation(doc="use a spaced seed than consists of two mirrored\nQR seeds separated by a gap. The following must\nhold: (a) N must be prime, (b) N >= 11,\n(c) N <= k/2")), ToolInput(tag="in_spaced_seed", input_type=String(optional=True), prefix="--spaced-seed", doc=InputDocumentation(doc="bitmask indicating k-mer positions to be\nignored during hashing. The pattern must be\nsymmetric")), ToolInput(tag="in_cov_track", input_type=File(optional=True), prefix="--cov-track", doc=InputDocumentation(doc="WIG track with 0/1 indicating k-mers with\ncoverage above the -c threshold. A reference\nmust also be specified with -R.")), ToolInput(tag="in_trace_file", input_type=File(optional=True), prefix="--trace-file", doc=InputDocumentation(doc="write debugging info about extension of\neach read to FILE")), ToolInput(tag="in_ref", input_type=File(optional=True), prefix="--ref", doc=InputDocumentation(doc="specify a reference genome. FILE may be\nFASTA, FASTQ, SAM, or BAM and may be gzipped."))], outputs=[], container=None, version="v0.1.0")
if __name__ == "__main__":
# or "cwl"
Abyss_Bloom_Dbg_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, String
Abyss_Longseqdist_V0_1_0 = CommandToolBuilder(tool="abyss_longseqdist", base_command=["abyss-longseqdist"], inputs=[ToolInput(tag="in_km_er", input_type=Int(optional=True), prefix="--kmer", doc=InputDocumentation(doc="length of a k-mer")), ToolInput(tag="in_min_gap", input_type=Int(optional=True), prefix="--min-gap", doc=InputDocumentation(doc="minimum scaffold gap length to output [200]")), ToolInput(tag="in_verbose", input_type=Boolean(optional=True), prefix="--verbose", doc=InputDocumentation(doc="display verbose output")), ToolInput(tag="in_sam", input_type=String(), position=0, doc=InputDocumentation(doc="BWA-MEM alignments of long sequences to the assembly")), ToolInput(tag="in_dist", input_type=String(), position=1, doc=InputDocumentation(doc="estimates of the distance between contigs"))], outputs=[], container=None, version="v0.1.0")
if __name__ == "__main__":
# or "cwl"
Abyss_Longseqdist_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, File, Int, Float
Abyss_Paired_Dbg_Mpi_V0_1_0 = CommandToolBuilder(tool="abyss_paired_dbg_mpi", base_command=["abyss-paired-dbg-mpi"], 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_Paired_Dbg_Mpi_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, 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 GFA 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_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=None, version="v0.1.0")
if __name__ == "__main__":
# or "cwl"
Abyss_Todot_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, Boolean, File
Abyss_Kaligner_V0_1_0 = CommandToolBuilder(tool="abyss_kaligner", base_command=["abyss-kaligner"], inputs=[ToolInput(tag="in_kmer_size_alignment", input_type=Int(optional=True), prefix="--kmer", doc=InputDocumentation(doc="k-mer size and minimum alignment length")), ToolInput(tag="in_section", input_type=Int(optional=True), prefix="--section", doc=InputDocumentation(doc="/N split the target into N sections and align\nreads to section S [1/1]")), ToolInput(tag="in_ignore_multimap", input_type=String(optional=True), prefix="--ignore-multimap", doc=InputDocumentation(doc="duplicate k-mer in the target\n[default]")), ToolInput(tag="in_multimap", input_type=Boolean(optional=True), prefix="--multimap", doc=InputDocumentation(doc="allow duplicate k-mer in the target")), ToolInput(tag="in_no_multimap", input_type=Boolean(optional=True), prefix="--no-multimap", doc=InputDocumentation(doc="disallow duplicate k-mer in the target")), ToolInput(tag="in_threads", input_type=File(optional=True), prefix="--threads", doc=InputDocumentation(doc="use N threads [2] up to one per query file\nor if N is 0 use one thread per query file")), ToolInput(tag="in_verbose", input_type=Boolean(optional=True), prefix="--verbose", doc=InputDocumentation(doc="display verbose output")), ToolInput(tag="in_no_sam", input_type=Boolean(optional=True), prefix="--no-sam", doc=InputDocumentation(doc="output the results in KAligner format")), ToolInput(tag="in_sam", input_type=Boolean(optional=True), prefix="--sam", doc=InputDocumentation(doc="output the results in SAM format")), ToolInput(tag="in_seq", input_type=Boolean(optional=True), prefix="--seq", doc=InputDocumentation(doc="print the sequence with the alignments")), ToolInput(tag="in_k_aligner", input_type=String(), position=0, doc=InputDocumentation(doc="")), ToolInput(tag="in_var_11", input_type=String(), 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_Kaligner_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, String
Pathoverlap_V0_1_0 = CommandToolBuilder(tool="PathOverlap", base_command=["PathOverlap"], inputs=[ToolInput(tag="in_km_er", input_type=Int(optional=True), prefix="--kmer", doc=InputDocumentation(doc="k-mer size")), ToolInput(tag="in_graph", input_type=File(optional=True), prefix="--graph", doc=InputDocumentation(doc="write the contig adjacency graph to FILE")), ToolInput(tag="in_repeats", input_type=File(optional=True), prefix="--repeats", doc=InputDocumentation(doc="write repeat contigs to FILE")), ToolInput(tag="in_overlap", input_type=Boolean(optional=True), prefix="--overlap", doc=InputDocumentation(doc="find overlapping paths [default]")), ToolInput(tag="in_assemble", input_type=Boolean(optional=True), prefix="--assemble", doc=InputDocumentation(doc="assemble overlapping paths")), ToolInput(tag="in_trim", input_type=Boolean(optional=True), prefix="--trim", doc=InputDocumentation(doc="trim overlapping paths")), 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_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 GFA 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 [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 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_contig_adjacency_graph", input_type=String(), position=0, doc=InputDocumentation(doc="contig adjacency graph")), 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"
Pathoverlap_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
Agat_Convert_Bed2Gff_Pl_V0_1_0 = CommandToolBuilder(tool="agat_convert_bed2gff.pl", base_command=["agat_convert_bed2gff.pl"], inputs=[ToolInput(tag="in_bed", input_type=Boolean(optional=True), prefix="--bed", doc=InputDocumentation(doc="Input bed file that will be convert.")), ToolInput(tag="in_source", input_type=Boolean(optional=True), prefix="--source", doc=InputDocumentation(doc="The source informs about the tool used to produce the data and\nis stored in 2nd field of a gff file. Example:\nStringtie,Maker,Augustus,etc. [default: data]")), ToolInput(tag="in_primary_tag", input_type=Boolean(optional=True), prefix="--primary_tag", doc=InputDocumentation(doc="The primary_tag corresponf to the data type and is stored in 3rd\nfield of a gff file. Example: gene,mRNA,CDS,etc. [default: gene]")), ToolInput(tag="in_inflate_off", input_type=Boolean(optional=True), prefix="--inflate_off", doc=InputDocumentation(doc="By default we inflate the block fields (blockCount, blockSizes,\nblockStarts) to create subfeatures of the main feature\n(primary_tag). Type of subfeature created based on the\ninflate_type parameter. If you don't want this inflating\nbehaviour you can deactivate it by using the option\n--inflate_off.")), ToolInput(tag="in_inflate_type", input_type=Boolean(optional=True), prefix="--inflate_type", doc=InputDocumentation(doc="Feature type (3rd column in gff) created when inflate parameter\nactivated [default: exon].")), ToolInput(tag="in_verbose", input_type=Boolean(optional=True), prefix="--verbose", doc=InputDocumentation(doc="add verbosity")), ToolInput(tag="in_outfile", input_type=File(optional=True), prefix="--outfile", doc=InputDocumentation(doc="Output GFF file. If no output file is specified, the output will\nbe written to STDOUT.")), ToolInput(tag="in_agat_convert_bed_two_gff_do_tpl", input_type=Int(), position=0, doc=InputDocumentation(doc="Description:"))], outputs=[ToolOutput(tag="out_outfile", output_type=File(optional=True), selector=InputSelector(input_to_select="in_outfile", type_hint=File()), doc=OutputDocumentation(doc="Output GFF file. If no output file is specified, the output will\nbe written to STDOUT."))], container=None, version="v0.1.0")
if __name__ == "__main__":
# or "cwl"
Agat_Convert_Bed2Gff_Pl_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
Mergecontigs_V0_1_0 = CommandToolBuilder(tool="MergeContigs", base_command=["MergeContigs"], inputs=[ToolInput(tag="in_km_er", input_type=Int(optional=True), prefix="--kmer", doc=InputDocumentation(doc="k-mer size")), ToolInput(tag="in_out", input_type=File(optional=True), prefix="--out", doc=InputDocumentation(doc="output the merged contigs to FILE [stdout]")), ToolInput(tag="in_graph", input_type=File(optional=True), prefix="--graph", doc=InputDocumentation(doc="write the contig overlap graph to FILE")), ToolInput(tag="in_merged", input_type=Boolean(optional=True), prefix="--merged", doc=InputDocumentation(doc="output only merged contigs")), ToolInput(tag="in_adj", input_type=Boolean(optional=True), prefix="--adj", doc=InputDocumentation(doc="output the graph in adj format")), ToolInput(tag="in_dot", input_type=Boolean(optional=True), prefix="--dot", doc=InputDocumentation(doc="output the graph in dot format [default]")), 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_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")), 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_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="contig overlap graph")), ToolInput(tag="in_path", input_type=File(), position=2, doc=InputDocumentation(doc="sequences of contig IDs"))], outputs=[ToolOutput(tag="out_out", output_type=File(optional=True), selector=InputSelector(input_to_select="in_out", type_hint=File()), doc=OutputDocumentation(doc="output the merged contigs to FILE [stdout]"))], container="quay.io/biocontainers/abyss:2.2.5--ha4ec83a_0", version="v0.1.0")
if __name__ == "__main__":
# or "cwl"
Mergecontigs_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="quay.io/biocontainers/abyss:2.2.5--ha4ec83a_0", version="v0.1.0")
if __name__ == "__main__":
# or "cwl"
Abyss_Dida_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, Boolean
Qpwave_V0_1_0 = CommandToolBuilder(tool="qpWave", base_command=["qpWave"], inputs=[ToolInput(tag="in_use_parameters_file", input_type=File(optional=True), prefix="-p", doc=InputDocumentation(doc="... use parameters from <file> .")), ToolInput(tag="in_print_version_exit", input_type=Boolean(optional=True), prefix="-v", doc=InputDocumentation(doc="... print version and exit.")), ToolInput(tag="in_toggle_verbose_mode", input_type=Boolean(optional=True), prefix="-V", doc=InputDocumentation(doc="... toggle verbose mode ON.")), ToolInput(tag="in_file", input_type=File(), position=0, doc=InputDocumentation(doc=""))], outputs=[], container=None, version="v0.1.0")
if __name__ == "__main__":
# or "cwl"
Qpwave_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 File, Boolean
Qpf4Ratio_V0_1_0 = CommandToolBuilder(tool="qpF4ratio", base_command=["qpF4ratio"], inputs=[ToolInput(tag="in_use_parameters_file", input_type=File(optional=True), prefix="-p", doc=InputDocumentation(doc="... use parameters from <file> .")), ToolInput(tag="in_print_version_exit", input_type=Boolean(optional=True), prefix="-v", doc=InputDocumentation(doc="... print version and exit.")), ToolInput(tag="in_toggle_verbose_mode", input_type=Boolean(optional=True), prefix="-V", doc=InputDocumentation(doc="... toggle verbose mode ON.")), ToolInput(tag="in_file", input_type=File(), 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"
Qpf4Ratio_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, 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:2.2.5--ha4ec83a_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 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:2.2.5--ha4ec83a_0", version="v0.1.0")
if __name__ == "__main__":
# or "cwl"
Abyss_Scaffold_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, String
Parsealigns_V0_1_0 = CommandToolBuilder(tool="ParseAligns", base_command=["ParseAligns"], inputs=[ToolInput(tag="in_min_align", input_type=Int(optional=True), prefix="--min-align", doc=InputDocumentation(doc="minimum alignment length")), ToolInput(tag="in_dist", input_type=File(optional=True), prefix="--dist", doc=InputDocumentation(doc="write distance estimates to this file")), ToolInput(tag="in_frag", input_type=File(optional=True), prefix="--frag", doc=InputDocumentation(doc="write fragment sizes 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_sam", input_type=Boolean(optional=True), prefix="--sam", doc=InputDocumentation(doc="alignments are in SAM format")), ToolInput(tag="in_k_aligner", input_type=Boolean(optional=True), prefix="--kaligner", doc=InputDocumentation(doc="alignments are in KAligner format")), ToolInput(tag="in_cover", input_type=String(optional=True), prefix="--cover", doc=InputDocumentation(doc="coverage cut-off for distance estimates")), ToolInput(tag="in_verbose", input_type=Boolean(optional=True), prefix="--verbose", doc=InputDocumentation(doc="display verbose output")), ToolInput(tag="in_k", input_type=Boolean(optional=True), prefix="-k", doc=InputDocumentation(doc="")), ToolInput(tag="in_km_er", input_type=String(), position=0, doc=InputDocumentation(doc=""))], outputs=[], container="quay.io/biocontainers/abyss:2.3.0--ha4ec83a_0", version="v0.1.0")
if __name__ == "__main__":
# or "cwl"
Parsealigns_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
Abruijn_V0_1_0 = CommandToolBuilder(tool="abruijn", base_command=["abruijn"], inputs=[ToolInput(tag="in_debug", input_type=Boolean(optional=True), prefix="--debug", doc=InputDocumentation(doc="enable debug output")), ToolInput(tag="in_resume", input_type=Boolean(optional=True), prefix="--resume", doc=InputDocumentation(doc="try to resume previous assembly")), ToolInput(tag="in_threads", input_type=Int(optional=True), prefix="--threads", doc=InputDocumentation(doc="number of parallel threads (default: 1)")), ToolInput(tag="in_iterations", input_type=Int(optional=True), prefix="--iterations", doc=InputDocumentation(doc="number of polishing iterations (default: 1)")), ToolInput(tag="in_platform", input_type=String(optional=True), prefix="--platform", doc=InputDocumentation(doc="sequencing platform (default: pacbio)")), ToolInput(tag="in_km_er_size", input_type=Int(optional=True), prefix="--kmer-size", doc=InputDocumentation(doc="kmer size (default: auto)")), ToolInput(tag="in_min_overlap", input_type=Int(optional=True), prefix="--min-overlap", doc=InputDocumentation(doc="minimum overlap between reads (default: 5000)")), ToolInput(tag="in_min_coverage", input_type=Int(optional=True), prefix="--min-coverage", doc=InputDocumentation(doc="minimum kmer coverage (default: auto)")), ToolInput(tag="in_max_coverage", input_type=Int(optional=True), prefix="--max-coverage", doc=InputDocumentation(doc="maximum kmer coverage (default: auto)")), ToolInput(tag="in_reads", input_type=String(), position=0, doc=InputDocumentation(doc="path to reads file (FASTA format)")), ToolInput(tag="in_out_dir", input_type=String(), position=1, doc=InputDocumentation(doc="output directory"))], outputs=[], container=None, version="v0.1.0")
if __name__ == "__main__":
# or "cwl"
Abruijn_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, 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=None, version="v0.1.0")
if __name__ == "__main__":
# or "cwl"
Dassembler_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 File, Int, String, Boolean, Directory
Adam_Shell_V0_1_0 = CommandToolBuilder(tool="adam_shell", base_command=["adam-shell"], inputs=[ToolInput(tag="in_preload_file_enforcing", input_type=File(optional=True), prefix="-I", doc=InputDocumentation(doc="preload <file>, enforcing line-by-line interpretation")), ToolInput(tag="in_master", input_type=Int(optional=True), prefix="--master", doc=InputDocumentation(doc="spark://host:port, mesos://host:port, yarn,\nk8s://https://host:port, or local (Default: local[*]).")), ToolInput(tag="in_deploy_mode", input_type=String(optional=True), prefix="--deploy-mode", doc=InputDocumentation(doc="Whether to launch the driver program locally ('client') or\non one of the worker machines inside the cluster ('cluster')\n(Default: client).")), ToolInput(tag="in_class", input_type=String(optional=True), prefix="--class", doc=InputDocumentation(doc="Your application's main class (for Java / Scala apps).")), ToolInput(tag="in_name", input_type=String(optional=True), prefix="--name", doc=InputDocumentation(doc="A name of your application.")), ToolInput(tag="in_jars", input_type=String(optional=True), prefix="--jars", doc=InputDocumentation(doc="Comma-separated list of jars to include on the driver\nand executor classpaths.")), ToolInput(tag="in_packages", input_type=Boolean(optional=True), prefix="--packages", doc=InputDocumentation(doc="Comma-separated list of maven coordinates of jars to include\non the driver and executor classpaths. Will search the local\nmaven repo, then maven central and any additional remote\nrepositories given by --repositories. The format for the\ncoordinates should be groupId:artifactId:version.")), ToolInput(tag="in_exclude_packages", input_type=Boolean(optional=True), prefix="--exclude-packages", doc=InputDocumentation(doc="Comma-separated list of groupId:artifactId, to exclude while\nresolving the dependencies provided in --packages to avoid\ndependency conflicts.")), ToolInput(tag="in_repositories", input_type=Boolean(optional=True), prefix="--repositories", doc=InputDocumentation(doc="Comma-separated list of additional remote repositories to\nsearch for the maven coordinates given with --packages.")), ToolInput(tag="in_py_files", input_type=String(optional=True), prefix="--py-files", doc=InputDocumentation(doc="Comma-separated list of .zip, .egg, or .py files to place\non the PYTHONPATH for Python apps.")), ToolInput(tag="in_files", input_type=File(optional=True), prefix="--files", doc=InputDocumentation(doc="Comma-separated list of files to be placed in the working\ndirectory of each executor. File paths of these files\nin executors can be accessed via SparkFiles.get(fileName).")), ToolInput(tag="in_conf", input_type=String(optional=True), prefix="--conf", doc=InputDocumentation(doc="=VALUE Arbitrary Spark configuration property.")), ToolInput(tag="in_properties_file", input_type=File(optional=True), prefix="--properties-file", doc=InputDocumentation(doc="Path to a file from which to load extra properties. If not\nspecified, this will look for conf/spark-defaults.conf.")), ToolInput(tag="in_driver_memory", input_type=Int(optional=True), prefix="--driver-memory", doc=InputDocumentation(doc="Memory for driver (e.g. 1000M, 2G) (Default: 1024M).")), ToolInput(tag="in_driver_java_options", input_type=Boolean(optional=True), prefix="--driver-java-options", doc=InputDocumentation(doc="Extra Java options to pass to the driver.")), ToolInput(tag="in_driver_library_path", input_type=Boolean(optional=True), prefix="--driver-library-path", doc=InputDocumentation(doc="Extra library path entries to pass to the driver.")), ToolInput(tag="in_driver_class_path", input_type=Boolean(optional=True), prefix="--driver-class-path", doc=InputDocumentation(doc="Extra class path entries to pass to the driver. Note that\njars added with --jars are automatically included in the\nclasspath.")), ToolInput(tag="in_executor_memory", input_type=Int(optional=True), prefix="--executor-memory", doc=InputDocumentation(doc="Memory per executor (e.g. 1000M, 2G) (Default: 1G).")), ToolInput(tag="in_proxy_user", input_type=String(optional=True), prefix="--proxy-user", doc=InputDocumentation(doc="User to impersonate when submitting the application.\nThis argument does not work with --principal / --keytab.")), ToolInput(tag="in_verbose", input_type=Boolean(optional=True), prefix="--verbose", doc=InputDocumentation(doc="Print additional debug output.")), ToolInput(tag="in_driver_cores", input_type=Int(optional=True), prefix="--driver-cores", doc=InputDocumentation(doc="Number of cores used by the driver, only in cluster mode\n(Default: 1).")), ToolInput(tag="in_supervise", input_type=Boolean(optional=True), prefix="--supervise", doc=InputDocumentation(doc="If given, restarts the driver on failure.")), ToolInput(tag="in_kill", input_type=String(optional=True), prefix="--kill", doc=InputDocumentation(doc="If given, kills the driver specified.")), ToolInput(tag="in_status", input_type=String(optional=True), prefix="--status", doc=InputDocumentation(doc="If given, requests the status of the driver specified.")), ToolInput(tag="in_total_executor_cores", input_type=Int(optional=True), prefix="--total-executor-cores", doc=InputDocumentation(doc="Total cores for all executors.")), ToolInput(tag="in_executor_cores", input_type=Int(optional=True), prefix="--executor-cores", doc=InputDocumentation(doc="Number of cores per executor. (Default: 1 in YARN mode,\nor all available cores on the worker in standalone mode)")), ToolInput(tag="in_queue", input_type=String(optional=True), prefix="--queue", doc=InputDocumentation(doc="The YARN queue to submit to (Default: 'default').")), ToolInput(tag="in_num_executors", input_type=Int(optional=True), prefix="--num-executors", doc=InputDocumentation(doc="Number of executors to launch (Default: 2).\nIf dynamic allocation is enabled, the initial number of\nexecutors will be at least NUM.")), ToolInput(tag="in_archives", input_type=Directory(optional=True), prefix="--archives", doc=InputDocumentation(doc="Comma separated list of archives to be extracted into the\nworking directory of each executor.")), ToolInput(tag="in_principal", input_type=String(optional=True), prefix="--principal", doc=InputDocumentation(doc="Principal to be used to login to KDC, while running on\nsecure HDFS.")), ToolInput(tag="in_keytab", input_type=File(optional=True), prefix="--keytab", doc=InputDocumentation(doc="The full path to the file that contains the keytab for the\nprincipal specified above. This keytab will be copied to\nthe node running the Application Master via the Secure\nDistributed Cache, for renewing the login tickets and the\ndelegation tokens periodically.\n"))], outputs=[], container=None, version="v0.1.0")
if __name__ == "__main__":
# or "cwl"
Adam_Shell_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, String
Locuspocus_V0_1_0 = CommandToolBuilder(tool="locuspocus", base_command=["locuspocus"], inputs=[ToolInput(tag="in_debug", input_type=Boolean(optional=True), prefix="--debug", doc=InputDocumentation(doc="print detailed debugging messages to terminal\n(standard error)")), ToolInput(tag="in_delta", input_type=Boolean(optional=True), prefix="--delta", doc=InputDocumentation(doc=": INT when parsing interval loci, use the following\ndelta to extend gene loci and include potential\nregulatory regions; default is 500")), ToolInput(tag="in_skip_ends", input_type=Boolean(optional=True), prefix="--skipends", doc=InputDocumentation(doc="when enumerating interval loci, exclude\nunannotated (and presumably incomplete) iLoci at\neither end of the sequence")), ToolInput(tag="in_ends_only", input_type=Boolean(optional=True), prefix="--endsonly", doc=InputDocumentation(doc="report only incomplete iLocus fragments at the\nunannotated ends of sequences (complement of\n--skipends)")), ToolInput(tag="in_skip_ii_loci", input_type=Boolean(optional=True), prefix="--skipiiloci", doc=InputDocumentation(doc="do not report intergenic iLoci")), ToolInput(tag="in_refine", input_type=Boolean(optional=True), prefix="--refine", doc=InputDocumentation(doc="by default genes are grouped in the same iLocus\nif they have any overlap; 'refine' mode allows\nfor a more nuanced handling of overlapping genes")), ToolInput(tag="in_cds", input_type=Boolean(optional=True), prefix="--cds", doc=InputDocumentation(doc="use CDS rather than UTRs for determining gene\noverlap; implies 'refine' mode")), ToolInput(tag="in_min_overlap", input_type=Boolean(optional=True), prefix="--minoverlap", doc=InputDocumentation(doc=": INT the minimum number of nucleotides two genes must\noverlap to be grouped in the same iLocus; default\nis 1")), ToolInput(tag="in_name_fmt", input_type=Boolean(optional=True), prefix="--namefmt", doc=InputDocumentation(doc=": STR provide a printf-style format string to override\nthe default ID format for newly created loci;\ndefault is 'locus%lu' (locus1, locus2, etc) for\nloci and 'iLocus%lu' (iLocus1, iLocus2, etc) for\ninterval loci; note the format string should\ninclude a single %lu specifier to be filled in\nwith a long unsigned integer value")), ToolInput(tag="in_i_lens", input_type=Boolean(optional=True), prefix="--ilens", doc=InputDocumentation(doc=": FILE create a file with the lengths of each intergenic")), ToolInput(tag="in_outfile", input_type=File(optional=True), prefix="--outfile", doc=InputDocumentation(doc=": FILE name of file to which results will be written;\ndefault is terminal (standard output)")), ToolInput(tag="in_retain_ids", input_type=Boolean(optional=True), prefix="--retainids", doc=InputDocumentation(doc="retain original feature IDs from input files;\nconflicts will arise if input contains duplicated\nID values")), ToolInput(tag="in_transmap", input_type=Boolean(optional=True), prefix="--transmap", doc=InputDocumentation(doc=": FILE print a mapping from each transcript annotation\nto its corresponding locus to the given file")), ToolInput(tag="in_verbose", input_type=Boolean(optional=True), prefix="--verbose", doc=InputDocumentation(doc="include all locus subfeatures (genes, RNAs, etc)\nin the GFF3 output; default includes only locus\nfeatures")), ToolInput(tag="in_filter", input_type=Boolean(optional=True), prefix="--filter", doc=InputDocumentation(doc=": TYPE comma-separated list of feature types to use in\nconstructing loci/iLoci; default is 'gene'")), ToolInput(tag="in_parent", input_type=Boolean(optional=True), prefix="--parent", doc=InputDocumentation(doc=": CT:PT if a feature of type $CT exists without a parent,\ncreate a parent for this feature with type $PT;\nfor example, mRNA:gene will create a gene feature\nas a parent for any top-level mRNA feature;\nthis option can be specified multiple times")), ToolInput(tag="in_pseudo", input_type=Boolean(optional=True), prefix="--pseudo", doc=InputDocumentation(doc="correct erroneously labeled pseudogenes")), ToolInput(tag="in_i_locus", input_type=String(), position=0, doc=InputDocumentation(doc="-g|--genemap: FILE print a mapping from each gene annotation to its"))], outputs=[ToolOutput(tag="out_outfile", output_type=File(optional=True), selector=InputSelector(input_to_select="in_outfile", type_hint=File()), doc=OutputDocumentation(doc=": FILE name of file to which results will be written;\ndefault is terminal (standard output)"))], container="quay.io/biocontainers/aegean:0.16.0--hc2cb157_0", version="v0.1.0")
if __name__ == "__main__":
# or "cwl"
Locuspocus_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, File, String
Abyss_Fixmate_Ssq_V0_1_0 = CommandToolBuilder(tool="abyss_fixmate_ssq", base_command=["abyss-fixmate-ssq"], 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")), ToolInput(tag="in_abyss_fix_mate", input_type=String(), position=0, doc=InputDocumentation(doc=""))], outputs=[], container="quay.io/biocontainers/abyss:2.3.0--ha4ec83a_0", version="v0.1.0")
if __name__ == "__main__":
# or "cwl"
Abyss_Fixmate_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, String, Boolean, File
Design_Naively_Py_V0_1_0 = CommandToolBuilder(tool="design_naively.py", base_command=["design_naively.py"], inputs=[ToolInput(tag="in_window_size", input_type=Int(optional=True), prefix="--window-size", doc=InputDocumentation(doc="Output guide(s) within each window (sliding along the\nalignment) of this length")), ToolInput(tag="in_guide_length", input_type=Int(optional=True), prefix="--guide-length", doc=InputDocumentation(doc="Length of guide to construct")), 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_best_n", input_type=String(optional=True), prefix="--best-n", doc=InputDocumentation(doc="Find the best BEST_N guides in each window")), 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_skip_gaps", input_type=String(optional=True), prefix="--skip-gaps", doc=InputDocumentation(doc="If this fraction or more of sequences at a position\ncontain a gap character, do not design a guide there")), ToolInput(tag="in_ref_seq", input_type=File(optional=True), prefix="--ref-seq", doc=InputDocumentation(doc="The label used in the FASTA file of the reference\nsequence to design guides based on sequence diversity;\nrequired for diversity method")), ToolInput(tag="in_no_consensus", input_type=Boolean(optional=True), prefix="--no-consensus", doc=InputDocumentation(doc="If set, do not use the consensus method to determine\nguides; otherwise, will use the consensus method")), ToolInput(tag="in_no_mode", input_type=Boolean(optional=True), prefix="--no-mode", doc=InputDocumentation(doc="If set, do not use the mode method to determine\nguides; otherwise, will use the mode method")), ToolInput(tag="in_diversity", input_type=String(optional=True), prefix="--diversity", doc=InputDocumentation(doc="A string of which diversity method to use to determine\nguides ('entropy'); None (default) to not use a\ndiversity method. 'entropy' will calculate the average\nper position entropy of each potential guide, then\nreturn the guides at the positions with the lowest\nentropy; nucleotides are determined by the reference\nsequence")), 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_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_in_fast_a", input_type=String(), position=0, doc=InputDocumentation(doc="Path to input FASTA (aligned)")), ToolInput(tag="in_out_tsv", input_type=String(), position=1, doc=InputDocumentation(doc="Path to TSV file to which to write the output"))], outputs=[], container="quay.io/biocontainers/adapt:1.2.0--py_0", version="v0.1.0")
if __name__ == "__main__":
# or "cwl"
Design_Naively_Py_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_Ssq_V0_1_0 = CommandToolBuilder(tool="DistanceEst_ssq", base_command=["DistanceEst-ssq"], 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="quay.io/biocontainers/abyss:2.3.1--hd403d74_0", version="v0.1.0")
if __name__ == "__main__":
# or "cwl"
Distanceest_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, Boolean, String
Simplegraph_V0_1_0 = CommandToolBuilder(tool="SimpleGraph", base_command=["SimpleGraph"], inputs=[ToolInput(tag="in_km_er", input_type=Int(optional=True), prefix="--kmer", doc=InputDocumentation(doc="k-mer size")), ToolInput(tag="in_n_pairs", input_type=Int(optional=True), prefix="--npairs", doc=InputDocumentation(doc="minimum number of pairs [0]")), ToolInput(tag="in_seed_length", input_type=Int(optional=True), prefix="--seed-length", doc=InputDocumentation(doc="minimum seed contig length [0]")), ToolInput(tag="in_dist_error", input_type=Int(optional=True), prefix="--dist-error", doc=InputDocumentation(doc="acceptable error of a distance estimate\ndefault is 6 bp")), ToolInput(tag="in_max_cost", input_type=Int(optional=True), prefix="--max-cost", doc=InputDocumentation(doc="maximum computational cost")), ToolInput(tag="in_out", input_type=File(optional=True), prefix="--out", doc=InputDocumentation(doc="write result to FILE")), ToolInput(tag="in_threads", input_type=Int(optional=True), prefix="--threads", doc=InputDocumentation(doc="use THREADS parallel threads [1]")), ToolInput(tag="in_extend", input_type=Boolean(optional=True), prefix="--extend", doc=InputDocumentation(doc="extend unambiguous paths")), ToolInput(tag="in_no_extend", input_type=Boolean(optional=True), prefix="--no-extend", doc=InputDocumentation(doc="do not extend unambiguous paths [default]")), ToolInput(tag="in_scaffold", input_type=Boolean(optional=True), prefix="--scaffold", doc=InputDocumentation(doc="join contigs with Ns [default]")), ToolInput(tag="in_no_scaffold", input_type=Boolean(optional=True), prefix="--no-scaffold", doc=InputDocumentation(doc="do not scaffold")), 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_adj", input_type=String(), position=0, doc=InputDocumentation(doc="adjacency of the contigs")), ToolInput(tag="in_dist", input_type=String(), position=1, doc=InputDocumentation(doc="distance estimates between the contigs"))], outputs=[], container=None, version="v0.1.0")
if __name__ == "__main__":
# or "cwl"
Simplegraph_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
Abyss_Gapfill_V0_1_0 = CommandToolBuilder(
tool="abyss_gapfill",
base_command=["abyss-gapfill"],
inputs=[
ToolInput(
tag="in_min_align",
input_type=Int(optional=True),
prefix="--min-align",
doc=InputDocumentation(doc="the minimal alignment size [1]")),
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_Gapfill_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_in_crm_nt", input_type=Boolean(optional=True), prefix="--incrmnt", doc=InputDocumentation(doc="FILE incrementally align sequences to an existing graph/MSA [Null]\ngraph could be in GFA or MSA format generated by abPOA")), 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:1.1.0--hed695b0_0", version="v0.1.0")
if __name__ == "__main__":
# or "cwl"
Abpoa_V0_1_0().translate("wdl")