def get_parser():
p = get_gather_pbparser(
Constants.TOOL_ID,
Constants.VERSION,
"Dev Alignments Gather",
"General Chunk Alignments Gather",
Constants.DRIVER,
is_distributed=False,
)
p.add_input_file_type(FileTypes.CHUNK, "cjson_in", "GCHUNK Json", "Gathered CHUNK Json with AlignmentSet chunk key")
p.add_output_file_type(
FileTypes.DS_ALIGN, "ds_out", "AlignmentSet", "Gathered AlignmentSet", "gathered.alignmentset.xml"
)
# XXX moved this functionality to pbalign
# p.add_boolean(Constants.CONSOLIDATE_ID, "consolidate",
# default=False,
# name="Consolidate .bam",
# description="Merge chunked/gathered .bam files")
# p.add_int(Constants.N_FILES_ID, "consolidate_n_files",
# default=1,
# name="Number of .bam files",
# description="Number of .bam files to create in consolidate mode")
return p
def get_contract_parser():
driver = "python -m pbfalcon.tasks.gather1_run_daligner_jobs --resolved-tool-contract "
p = get_gather_pbparser(TOOL_ID,
"0.1.3",
"Gather Daligner",
"Gather Daligner Jobs",
driver,
is_distributed=False)
p.add_input_file_type(FileTypes.CHUNK, "cjson_in", "Gather ChunkJson",
"Fasta Gather Chunk JSON")
p.add_output_file_type(FileTypes.FOFN, "fofn_out",
"FOFN of .las files, stage-1", "FOFN Not Sure Yet",
"file_gathered")
# FIXME. There's an a bit of friction between the TC and the argrunning
# layer here. For nproc and nchunks, chunk-key, the values are a bit
# different between the two backends.
p.arg_parser.add_str(
"pbsmrtpipe.task_options.task_falcon_run_daligner_job_scatter_chunk_key",
"chunk_key", "$chunk.daligner_job_id", "Chunk key",
"Chunk key to use (format $chunk:{chunk-key}")
return p
def get_parser():
driver = "python -m pbcommand.cli.examples.dev_gather_fasta_app --resolved-tool-contract "
desc = "Gather a fasta resources in a Chunk.json file"
p = get_gather_pbparser(TOOL_ID, __version__, "Fasta Chunk Gather",
desc, driver, is_distributed=False)
p.add_input_file_type(FileTypes.CHUNK, "chunk_json", "Chunk JSON", "Chunked Fasta JSON Out")
p.add_output_file_type(FileTypes.FASTA, "output", "Chunk JSON", "Output Fasta", "gathered")
return p
def get_parser():
driver = "python -m pbcommand.cli.examples.dev_gather_fasta_app --resolved-tool-contract "
desc = "Gather a fasta resources in a Chunk.json file"
p = get_gather_pbparser(TOOL_ID, __version__, "Fasta Chunk Gather",
desc, driver, is_distributed=False)
p.add_input_file_type(FileTypes.CHUNK, "chunk_json", "Chunk JSON", "Chunked Fasta JSON Out")
p.add_output_file_type(FileTypes.FASTA, "output", "Chunk JSON", "Output Fasta", "gathered")
return p
def get_parser():
p = get_gather_pbparser(Constants.TOOL_ID,
Constants.VERSION,
"LAA JSON gather",
"Gather task for LAA subreads JSON output",
Constants.DRIVER,
is_distributed=False)
p.add_input_file_type(FileTypes.CHUNK, "cjson_in", "GCHUNK Json",
"Gathered CHUNK Json with JSON chunk key")
p.add_output_file_type(FileTypes.JSON, "json_out", "JSON",
"Gathered JSON",
default_name="amplicon_analysis_subreads")
return p
def get_parser():
p = get_gather_pbparser(
Constants.TOOL_ID, Constants.VERSION, "Dev CCS Gather", __doc__, Constants.DRIVER, is_distributed=False
)
p.add_input_file_type(
FileTypes.CHUNK, "cjson_in", "GCHUNK Json", "Gathered CHUNK Json with ConsensusReadSet chunk key"
)
p.add_output_file_type(
FileTypes.DS_CCS, "ds_out", "ConsensusReadSet", "Gathered ConsensusReadSet", default_name="gathered"
)
return p
def get_parser():
p = get_gather_pbparser(Constants.TOOL_ID,
Constants.VERSION,
"Dev SubreadSet Gather",
"General Chunk SubreadSet Gather",
Constants.DRIVER,
is_distributed=False)
p.add_input_file_type(FileTypes.CHUNK, "cjson_in", "GCHUNK Json",
"Gathered CHUNK Json with SubreadSet chunk key")
p.add_output_file_type(FileTypes.DS_SUBREADS, "ds_out", "SubreadSet",
"Gathered SubreadSet", default_name="gathered")
return p
def get_parser():
p = get_gather_pbparser(Constants.TOOL_ID,
Constants.VERSION,
"Dev SubreadSet Gather",
"General Chunk SubreadSet Gather",
Constants.DRIVER,
is_distributed=False)
p.add_input_file_type(FileTypes.CHUNK, "cjson_in", "GCHUNK Json",
"Gathered CHUNK Json with SubreadSet chunk key")
p.add_output_file_type(FileTypes.DS_SUBREADS, "ds_out", "SubreadSet",
"Gathered SubreadSet",
"gathered_subreads.dataset.xml")
return p
def get_contract_parser():
"""Return contract parser.
input idx 0: chunk json
output idx 0: combined consensus isoforms contigset from all cluster bins
"""
p = get_gather_pbparser(Constants.TOOL_ID,
Constants.VERSION,
"Gather consensus isoforms ContigSets",
"Chunk ContigSet Gather for Consensus Isoforms",
Constants.DRIVER,
is_distributed=True)
p.add_input_file_type(FileTypes.CHUNK, "cjson_in", "Gather CHUNK Json",
"Gathered CHUNK Json with ContigSet chunk key")
p.add_output_file_type(FileTypes.DS_CONTIG, "consensus_isoforms_out", "ContigSet",
"Combined ContigSet", "Combined ContigSet")
return p
def get_parser():
p = get_gather_pbparser(Constants.TOOL_ID,
Constants.VERSION,
"Dev Gff Gather",
"General Chunk Gff Gather",
Constants.DRIVER,
is_distributed=False)
p.add_input_file_type(FileTypes.CHUNK, "cjson_in", "GCHUNK Json",
"Gathered CHUNK Json with Gff chunk key")
p.add_output_file_type(FileTypes.GFF, "gff_out", "Gff", "Gathered Gff",
"gathered.gff")
p.arg_parser.add_str(Constants.OPT_CHUNK_KEY, "chunk_key", "$chunk.gff_id",
"Chunk key",
"Chunk key to use (format $chunk:{chunk-key}")
return p
def get_contract_parser():
driver = "python -m pbcoretools.tasks.gather_fastq --resolved-tool-contract "
p = get_gather_pbparser(Constants.TOOL_ID, "0.1.3", "Gather Fastq",
"Gather Fastq", driver, is_distributed=True)
p.add_input_file_type(FileTypes.CHUNK, "cjson_in", "Gather ChunkJson",
"Fastq Gather Chunk JSON")
p.add_output_file_type(FileTypes.FASTQ, "fastq_out", "Fastq Gathered",
"Fastq Gathered",
default_name="gathered")
p.add_str(Constants.CHUNK_KEY_ID, "chunk_key",
"$chunk:fastq_id", "Chunk key", "Chunk key to use (format $chunk:{chunk-key}")
return p
def get_parser():
p = get_gather_pbparser(Constants.TOOL_ID,
Constants.VERSION,
"Dev JSON Gather",
"General Chunk JSON Statistics Gather",
Constants.DRIVER,
is_distributed=True)
p.add_input_file_type(FileTypes.CHUNK, "cjson_in", "GCHUNK Json",
"Gathered CHUNK Json with Json chunk key")
p.add_output_file_type(FileTypes.JSON, "json_out", "JSON", "Gathered JSON",
"gathered")
# Only need to add to argparse layer for the commandline
p.arg_parser.add_str(Constants.OPT_CHUNK_KEY, "chunk_key",
Constants.CHUNK_KEY, "Chunk key",
"Chunk key to use (format $chunk.{chunk-key}")
return p
def get_parser():
p = get_gather_pbparser(Constants.TOOL_ID,
Constants.VERSION,
"Dev Gff Gather",
"General Chunk Gff Gather",
Constants.DRIVER,
is_distributed=False)
p.add_input_file_type(FileTypes.CHUNK, "cjson_in", "GCHUNK Json",
"Gathered CHUNK Json with Gff chunk key")
p.add_output_file_type(FileTypes.GFF, "gff_out", "Gff", "Gathered Gff", "gathered.gff")
p.arg_parser.add_str(Constants.OPT_CHUNK_KEY,
"chunk_key",
"$chunk.gff_id",
"Chunk key", "Chunk key to use (format $chunk:{chunk-key}")
return p
def get_contract_parser():
driver = "python -m pbsmrtpipe.tools_dev.gather_fastq --resolved-tool-contract "
p = get_gather_pbparser(TOOL_ID, "0.1.3", "Gather Fastq",
"Gather Fastq", driver, is_distributed=False)
p.add_input_file_type(FileTypes.CHUNK, "cjson_in", "Gather ChunkJson",
"Fastq Gather Chunk JSON")
p.add_output_file_type(FileTypes.FASTQ, "fastq_out", "Fastq Gathered",
"Fastq Gathered",
"file_gathered.fastq")
p.add_str("pbsmrtpipe.task_options.dev_scatter_chunk_key", "chunk_key",
"$chunk:fastq_id", "Chunk key", "Chunk key to use (format $chunk:{chunk-key}")
return p
def get_parser():
p = get_gather_pbparser(Constants.TOOL_ID,
Constants.VERSION,
"Dev CCS Gather",
__doc__,
Constants.DRIVER,
is_distributed=False)
p.add_input_file_type(
FileTypes.CHUNK, "cjson_in", "GCHUNK Json",
"Gathered CHUNK Json with ConsensusReadSet chunk key")
p.add_output_file_type(FileTypes.DS_CCS, "ds_out", "ConsensusReadSet",
"Gathered ConsensusReadSet",
"gathered_consensus_reads.dataset.xml.")
return p
def get_contract_parser():
driver = "python -m pbsmrtpipe.tools_dev.gather_fastq --resolved-tool-contract "
p = get_gather_pbparser(TOOL_ID, "0.1.3", "Gather Fastq",
"Gather Fastq", driver, is_distributed=False)
p.add_input_file_type(FileTypes.CHUNK, "cjson_in", "Gather ChunkJson",
"Fastq Gather Chunk JSON")
p.add_output_file_type(FileTypes.FASTQ, "fastq_out", "Fastq Gathered",
"Fastq Gathered",
"file_gathered.fastq")
p.add_str("pbsmrtpipe.task_options.dev_scatter_chunk_key", "chunk_key",
"$chunk:fastq_id", "Chunk key", "Chunk key to use (format $chunk:{chunk-key}")
return p
def get_contract_parser():
"""Return contract parser.
input idx 0: chunk json
output idx 0: concatenated SAM file.
"""
p = get_gather_pbparser(Constants.TOOL_ID,
Constants.VERSION,
"Gather GMAP SAM",
"Chunk Gather for GMAP SAM",
Constants.DRIVER,
is_distributed=True)
p.add_input_file_type(FileTypes.CHUNK, "cjson_in", "Gather CHUNK Json",
"Gathered CHUNK Json with chunk key")
p.add_output_file_type(FileTypes.SAM, "sam_out", "SAM",
"Gathered SAM", "Gathered SAM")
return p
def get_parser():
p = get_gather_pbparser(Constants.TOOL_ID,
Constants.VERSION,
"Dev Alignments Gather",
"General Chunk ConsensusAlignments Gather",
Constants.DRIVER,
is_distributed=False)
p.add_input_file_type(
FileTypes.CHUNK, "cjson_in", "GCHUNK Json",
"Gathered CHUNK Json with ConsensusAlignmentSet chunk key")
p.add_output_file_type(FileTypes.DS_ALIGN_CCS, "ds_out", "AlignmentSet",
"Gathered AlignmentSet",
"gathered.consensusalignmentset.xml")
return p
def get_contract_parser():
"""Return contract parser.
input idx 0: chunk json
output idx 0: concatenated SAM file.
"""
p = get_gather_pbparser(Constants.TOOL_ID,
Constants.VERSION,
"Gather GMAP SAM",
"Chunk Gather for GMAP SAM",
Constants.DRIVER,
is_distributed=True)
p.add_input_file_type(FileTypes.CHUNK, "cjson_in", "Gather CHUNK Json",
"Gathered CHUNK Json with chunk key")
p.add_output_file_type(FileTypes.SAM, "sam_out", "SAM",
"Gathered SAM", "Gathered SAM")
return p
def get_parser():
p = get_gather_pbparser(Constants.TOOL_ID,
Constants.VERSION,
"Dev Pickle Gather",
"General Chunk Pickle Gather",
Constants.DRIVER,
is_distributed=True)
p.add_input_file_type(FileTypes.CHUNK, "cjson_in", "GCHUNK Json",
"Gathered CHUNK Json with Pickle chunk key")
p.add_output_file_type(FileTypes.PICKLE, "pickle_out", "Pickle",
"Gathered Pickle", "gathered")
p.arg_parser.add_str(Constants.OPT_CHUNK_KEY,
"chunk_key",
default=Constants.CHUNK_KEY,
name="Chunk key",
description="Chunk key to use (format $chunk:{chunk-key}")
return p
def get_parser():
p = get_gather_pbparser(Constants.TOOL_ID,
Constants.VERSION,
"Dev Alignments Gather",
"General Chunk ConsensusAlignments Gather",
Constants.DRIVER,
is_distributed=False)
p.add_input_file_type(FileTypes.CHUNK, "cjson_in", "GCHUNK Json",
"Gathered CHUNK Json with ConsensusAlignmentSet chunk key")
p.add_output_file_type(FileTypes.DS_ALIGN_CCS,
"ds_out",
"AlignmentSet",
"Gathered AlignmentSet",
default_name="gathered")
return p
def get_parser():
p = get_gather_pbparser(Constants.TOOL_ID,
Constants.VERSION,
"Dev Alignments Gather",
"General Chunk Alignments Gather",
Constants.DRIVER,
is_distributed=False)
p.add_input_file_type(FileTypes.CHUNK, "cjson_in", "GCHUNK Json",
"Gathered CHUNK Json with AlignmentSet chunk key")
p.add_output_file_type(FileTypes.DS_ALIGN,
"ds_out",
"AlignmentSet",
"Gathered AlignmentSet",
"gathered_alignments.dataset.xml.")
return p
def get_parser():
p = get_gather_pbparser(Constants.TOOL_ID,
Constants.VERSION,
"Dev Alignments Gather",
"General Chunk Alignments Gather",
Constants.DRIVER,
is_distributed=True)
p.add_input_file_type(FileTypes.CHUNK, "cjson_in", "GCHUNK Json",
"Gathered CHUNK Json with AlignmentSet chunk key")
p.add_output_file_type(FileTypes.DS_ALIGN,
"ds_out",
"AlignmentSet",
"Gathered AlignmentSet",
default_name="gathered")
return p
def get_parser():
p = get_gather_pbparser(Constants.TOOL_ID,
Constants.VERSION,
"Dev Pickle Gather",
"General Chunk Pickle Gather",
Constants.DRIVER,
is_distributed=True)
p.add_input_file_type(FileTypes.CHUNK, "cjson_in", "GCHUNK Json",
"Gathered CHUNK Json with Pickle chunk key")
p.add_output_file_type(FileTypes.PICKLE, "pickle_out", "Pickle",
"Gathered Pickle", "gathered")
p.arg_parser.add_str(
Constants.OPT_CHUNK_KEY,
"chunk_key",
default=Constants.CHUNK_KEY,
name="Chunk key",
description="Chunk key to use (format $chunk:{chunk-key}")
return p
def get_parser():
p = get_gather_pbparser(Constants.TOOL_ID,
Constants.VERSION,
"Dev ContigSet Gather",
"General Chunk ContigSet Gather",
Constants.DRIVER,
is_distributed=True)
p.add_input_file_type(FileTypes.CHUNK, "cjson_in", "GCHUNK Json",
"Gathered CHUNK Json with ContigSet chunk key")
p.add_output_file_type(FileTypes.DS_CONTIG, "contigset", "ContigSet",
"Gathered ContigSet", "gathered")
p.arg_parser.add_str(Constants.OPT_CHUNK_KEY, "chunk_key",
Constants.CHUNK_KEY, "Chunk key",
"Chunk key to use (format $chunk:{chunk-key}")
return p
def get_contract_parser():
driver = "python -m pbcoretools.tasks.gather_fasta --resolved-tool-contract "
p = get_gather_pbparser(TOOL_ID, "0.1.3", "Gather Fasta",
"Gather Fasta", driver, is_distributed=True)
p.add_input_file_type(FileTypes.CHUNK, "cjson_in", "Gather ChunkJson",
"Fasta Gather Chunk JSON")
p.add_output_file_type(FileTypes.FASTA, "fasta_out", "Fasta Gathered",
"Fasta Gathered",
"gathered")
# FIXME. There's an a bit of friction between the TC and the argrunning
# layer here. For nproc and nchunks, chunk-key, the values are a bit
# different between the two backends.
p.arg_parser.add_str("pbcoretools.task_options.dev_scatter_chunk_key", "chunk_key",
"$chunk.fasta_id", "Chunk key", "Chunk key to use (format $chunk:{chunk-key}")
return p
def get_contract_parser():
driver = "python -m pbfalcon.tasks.gather1_run_daligner_jobs --resolved-tool-contract "
p = get_gather_pbparser(TOOL_ID, "0.1.3", "Gather Daligner",
"Gather Daligner Jobs", driver, is_distributed=False)
p.add_input_file_type(FileTypes.CHUNK, "cjson_in", "Gather ChunkJson",
"Fasta Gather Chunk JSON")
p.add_output_file_type(FileTypes.FOFN, "fofn_out", "FOFN LAS maybe?",
"FOFN Not Sure Yet",
"file_gathered.fofn")
# FIXME. There's an a bit of friction between the TC and the argrunning
# layer here. For nproc and nchunks, chunk-key, the values are a bit
# different between the two backends.
p.arg_parser.add_str("pbsmrtpipe.task_options.task_falcon_run_daligner_job_scatter_chunk_key", "chunk_key",
"$chunk.daligner_job_id", "Chunk key", "Chunk key to use (format $chunk:{chunk-key}")
return p
def get_parser():
p = get_gather_pbparser(Constants.TOOL_ID,
Constants.VERSION,
"Dev text Gather",
"General Chunk text Gather",
Constants.DRIVER,
is_distributed=False)
p.add_input_file_type(FileTypes.CHUNK, "cjson_in", "GCHUNK Json",
"Gathered CHUNK Json with text chunk key")
p.add_output_file_type(FileTypes.TXT, "txt_out", "Text", "Gathered text",
"gathered")
# Only need to add to argparse layer for the commandline
p.arg_parser.add_str(Constants.OPT_CHUNK_KEY, "chunk_key", "$chunk.txt_id",
"Chunk key",
"Chunk key to use (format $chunk.{chunk-key}")
return p
def get_parser():
p = get_gather_pbparser(Constants.TOOL_ID,
Constants.VERSION,
"Dev JSON Gather",
"General Chunk JSON Statistics Gather",
Constants.DRIVER,
is_distributed=True)
p.add_input_file_type(FileTypes.CHUNK, "cjson_in", "GCHUNK Json",
"Gathered CHUNK Json with Json chunk key")
p.add_output_file_type(FileTypes.JSON, "json_out",
"JSON",
"Gathered JSON", "gathered")
# Only need to add to argparse layer for the commandline
p.arg_parser.add_str(Constants.OPT_CHUNK_KEY,
"chunk_key",
Constants.CHUNK_KEY,
"Chunk key",
"Chunk key to use (format $chunk.{chunk-key}")
return p
def get_parser():
p = get_gather_pbparser(Constants.TOOL_ID,
Constants.VERSION,
"Dev BigWig Gather",
"General Chunk BigWig Gather",
Constants.DRIVER,
is_distributed=True)
p.add_input_file_type(FileTypes.CHUNK, "cjson_in", "GCHUNK Json",
"Gathered CHUNK Json with BigWig chunk key")
p.add_output_file_type(FileTypes.BIGWIG, "bigwig_out", "BigWig file",
"Gathered BigWig file", "gathered")
# Only need to add to argparse layer for the commandline
p.arg_parser.add_str(Constants.OPT_CHUNK_KEY, "chunk_key", "$chunk.bw_id",
"Chunk key",
"Chunk key to use (format $chunk.{chunk-key}")
return p
def get_parser():
p = get_gather_pbparser(Constants.TASK_ID,
Constants.VERSION,
"Dev Kinetics HDF5 Gather",
"General Chunk Kinetics HDF5 Gather",
Constants.DRIVER_EXE,
is_distributed=True,
default_level=logging.INFO)
p.add_input_file_type(FileTypes.CHUNK, "cjson_in", "GCHUNK Json",
"Gathered CHUNK Json with BigWig chunk key")
p.add_output_file_type(FileTypes.H5, "h5_out", "Kinetics HDF5 file",
"Gathered HDF5 file", "gathered")
# Only need to add to argparse layer for the commandline
p.arg_parser.add_str(Constants.OPT_CHUNK_KEY, "chunk_key",
Constants.CHUNK_KEY, "Chunk key",
"Chunk key to use (format $chunk.{chunk-key}")
return p
def get_parser():
p = get_gather_pbparser(Constants.TOOL_ID,
Constants.VERSION,
"Dev BigWig Gather",
"General Chunk BigWig Gather",
Constants.DRIVER,
is_distributed=True)
p.add_input_file_type(FileTypes.CHUNK, "cjson_in", "GCHUNK Json",
"Gathered CHUNK Json with BigWig chunk key")
p.add_output_file_type(FileTypes.BIGWIG, "bigwig_out",
"BigWig file",
"Gathered BigWig file", "gathered")
# Only need to add to argparse layer for the commandline
p.arg_parser.add_str(Constants.OPT_CHUNK_KEY,
"chunk_key",
"$chunk.bw_id",
"Chunk key",
"Chunk key to use (format $chunk.{chunk-key}")
return p
def get_parser():
p = get_gather_pbparser(Constants.TOOL_ID,
Constants.VERSION,
"Dev CSV Gather",
"General Chunk CSV Gather",
Constants.DRIVER,
is_distributed=False)
p.add_input_file_type(FileTypes.CHUNK, "cjson_in", "GCHUNK Json",
"Gathered CHUNK Json with CSV chunk key")
p.add_output_file_type(FileTypes.CSV, "csv_out",
"CSV",
"Gathered CSV", "gathered.csv")
# Only need to add to argparse layer for the commandline
p.arg_parser.add_str(Constants.OPT_CHUNK_KEY,
"chunk_key",
"$chunk.csv_id",
"Chunk key",
"Chunk key to use (format $chunk.{chunk-key}")
return p
def get_parser():
p = get_gather_pbparser(Constants.TOOL_ID,
Constants.VERSION,
"Dev ContigSet Gather",
"General Chunk ContigSet Gather",
Constants.DRIVER,
is_distributed=True)
p.add_input_file_type(FileTypes.CHUNK, "cjson_in", "GCHUNK Json",
"Gathered CHUNK Json with ContigSet chunk key")
p.add_output_file_type(FileTypes.DS_CONTIG,
"contigset",
"ContigSet",
"Gathered ContigSet",
"gathered")
p.arg_parser.add_str(Constants.OPT_CHUNK_KEY,
"chunk_key",
Constants.CHUNK_KEY,
"Chunk key", "Chunk key to use (format $chunk:{chunk-key}")
return p
def get_parser():
p = get_gather_pbparser(Constants.TASK_ID,
Constants.VERSION,
"Dev Kinetics HDF5 Gather",
"General Chunk Kinetics HDF5 Gather",
Constants.DRIVER_EXE,
is_distributed=True,
default_level=logging.INFO)
p.add_input_file_type(FileTypes.CHUNK, "cjson_in", "GCHUNK Json",
"Gathered CHUNK Json with BigWig chunk key")
p.add_output_file_type(FileTypes.H5, "h5_out",
"Kinetics HDF5 file",
"Gathered HDF5 file", "gathered")
# Only need to add to argparse layer for the commandline
p.arg_parser.add_str(Constants.OPT_CHUNK_KEY,
"chunk_key",
Constants.CHUNK_KEY,
"Chunk key",
"Chunk key to use (format $chunk.{chunk-key}")
return p
def get_contract_parser():
driver = "python -m pbsmrtpipe.tools_dev.gather_fasta --resolved-tool-contract "
p = get_gather_pbparser(TOOL_ID,
"0.1.3",
"Gather Fasta",
"Gather Fasta",
driver,
is_distributed=False)
p.add_input_file_type(FileTypes.CHUNK, "cjson_in", "Gather ChunkJson",
"Fasta Gather Chunk JSON")
p.add_output_file_type(FileTypes.FASTA, "fasta_out", "Fasta Gathered",
"Fasta Gathered", "file_gathered.fasta")
# FIXME. There's an a bit of friction between the TC and the argrunning
# layer here. For nproc and nchunks, chunk-key, the values are a bit
# different between the two backends.
p.arg_parser.add_str("pbsmrtpipe.task_options.dev_scatter_chunk_key",
"chunk_key", "$chunk.fasta_id", "Chunk key",
"Chunk key to use (format $chunk:{chunk-key}")
return p
def get_parser():
p = get_gather_pbparser(Constants.TOOL_ID,
Constants.VERSION,
"Dev Alignments Gather",
"General Chunk Alignments Gather",
Constants.DRIVER,
is_distributed=False)
p.add_input_file_type(FileTypes.CHUNK, "cjson_in", "GCHUNK Json",
"Gathered CHUNK Json with AlignmentSet chunk key")
p.add_output_file_type(FileTypes.DS_ALIGN, "ds_out", "AlignmentSet",
"Gathered AlignmentSet",
"gathered.alignmentset.xml")
# XXX moved this functionality to pbalign
# p.add_boolean(Constants.CONSOLIDATE_ID, "consolidate",
# default=False,
# name="Consolidate .bam",
# description="Merge chunked/gathered .bam files")
# p.add_int(Constants.N_FILES_ID, "consolidate_n_files",
# default=1,
# name="Number of .bam files",
# description="Number of .bam files to create in consolidate mode")
return p
