def get_contract_parser():
p = get_pbparser(
Constants.TOOL_ID,
__version__,
spec.title,
__doc__,
Constants.DRIVER_EXE,
is_distributed=True)
add_base_options_pbcommand(p, "Top Variants Report")
p.add_input_file_type(FileTypes.GFF,
file_id="gff",
name="GFF file",
description="variants.gff (can be gzip'ed)")
p.add_input_file_type(FileTypes.DS_REF,
file_id="reference",
name="Reference dataset",
description="ReferenceSet or FASTA")
# p.add_output_file_type(FileTypes.REPORT, "report",
# "JSON report", "JSON report", "report.json")
p.add_int(Constants.HOW_MANY_ID, "how_many",
default=Constants.HOW_MANY_DEFAULT,
name="Number of variants",
description="number of top variants to show (default=100)")
p.add_int(Constants.BATCH_SORT_SIZE_ID, "batch_sort_size",
default=Constants.BATCH_SORT_SIZE_DEFAULT,
name="Batch sort size",
description="Intermediate sort size parameter (default=10000)")
# XXX do we need a flag for minor variants?
return p
def get_contract_parser():
p = get_pbparser(Constants.TOOL_ID,
__version__,
meta_rpt.title,
__doc__,
Constants.DRIVER_EXE,
is_distributed=True)
add_base_options_pbcommand(p, "Top Variants Report")
p.add_input_file_type(FileTypes.GFF,
file_id="gff",
name="GFF file",
description="variants.gff (can be gzip'ed)")
p.add_input_file_type(FileTypes.DS_REF,
file_id="reference",
name="Reference dataset",
description="ReferenceSet or FASTA")
# p.add_output_file_type(FileTypes.REPORT, "report",
# "JSON report", "JSON report", "report.json")
p.add_int(Constants.HOW_MANY_ID,
"how_many",
default=Constants.HOW_MANY_DEFAULT,
name="Number of variants",
description="number of top variants to show (default=100)")
p.add_int(Constants.BATCH_SORT_SIZE_ID,
"batch_sort_size",
default=Constants.BATCH_SORT_SIZE_DEFAULT,
name="Batch sort size",
description="Intermediate sort size parameter (default=10000)")
# XXX do we need a flag for minor variants?
return p
def get_parser():
p = get_pbparser(
Constants.TOOL_ID,
__version__,
"Modifications Report",
__doc__,
Constants.DRIVER_EXE,
is_distributed=True)
p.add_input_file_type(FileTypes.H5, "basemods_h5", "HDF5 file",
"HDF5 file of base modifications from ipdSummary")
add_base_options_pbcommand(p, "Basemods report")
return p
def _add_options_to_parser(p):
desc = spec.description
p = add_base_options_pbcommand(p, spec.title)
p.add_input_file_type(FileTypes.DS_ALIGN,
file_id="alignment_file",
name="AlignmentSet",
description="AlignmentSet XML or aligned .bam file")
p.add_input_file_type(FileTypes.REPORT,
file_id="var_rpt",
name="Variant report JSON",
description="The variants report - i.e., variants_report.json")
p.add_input_file_type(FileTypes.REPORT,
file_id="mapping_stats_rpt",
name="Mapping statistics JSON",
description="The mapping statistics report - i.e., "
"mapping_stats_report.json")
return p
def _add_options_to_parser(p):
desc = 'Generates the SAT metric performance attributes'
p = add_base_options_pbcommand(p)
p.add_input_file_type(FileTypes.DS_ALIGN,
file_id="alignment_file",
name="AlignmentSet",
description="AlignmentSet XML or aligned .bam file")
p.add_input_file_type(FileTypes.REPORT,
file_id="var_rpt",
name="Variant report JSON",
description="The variants report - i.e., variants_report.json")
p.add_input_file_type(FileTypes.REPORT,
file_id="mapping_stats_rpt",
name="Mapping statistics JSON",
description="The mapping statistics report - i.e., "
"mapping_stats_report.json")
return p
def _add_options_to_parser(p):
desc = meta_rpt.description
p = add_base_options_pbcommand(p, meta_rpt.title)
p.add_input_file_type(FileTypes.DS_ALIGN,
file_id="alignment_file",
name="AlignmentSet",
description="AlignmentSet XML or aligned .bam file")
p.add_input_file_type(
FileTypes.REPORT,
file_id="var_rpt",
name="Variant report JSON",
description="The variants report - i.e., variants_report.json")
p.add_input_file_type(FileTypes.REPORT,
file_id="mapping_stats_rpt",
name="Mapping statistics JSON",
description="The mapping statistics report - i.e., "
"mapping_stats_report.json")
return p
def _add_options_to_parser(p):
p = add_base_options_pbcommand(p)
p.add_input_file_type(FileTypes.DS_REF,
file_id="reference",
name="Reference dataset",
description="ReferenceSet or FASTA")
p.add_input_file_type(FileTypes.GFF,
file_id="aln_summ_gff",
name="Alignment summary GFF",
description="Alignment summary GFF")
p.add_input_file_type(FileTypes.GFF,
file_id="variants_gff",
name="Variants GFF",
description="Variants GFF")
p.add_int(Constants.MAX_CONTIGS_ID, "maxContigs",
default=Constants.MAX_CONTIGS_DEFAULT,
name="Max contigs",
description="Max number of contigs to plot. Defaults to 25.")
return p
def _add_options_to_parser(p):
p = add_base_options_pbcommand(p, meta_rpt.title)
p.add_input_file_type(FileTypes.DS_REF,
file_id="reference",
name="Reference dataset",
description="ReferenceSet or FASTA")
p.add_input_file_type(FileTypes.GFF,
file_id="aln_summ_gff",
name="Alignment summary GFF",
description="Alignment summary GFF")
p.add_input_file_type(FileTypes.GFF,
file_id="variants_gff",
name="Variants GFF",
description="Variants GFF")
p.add_int(Constants.MAX_CONTIGS_ID, "maxContigs",
default=Constants.MAX_CONTIGS_DEFAULT,
name="Max contigs",
description="Max number of contigs to plot. Defaults to 25.")
return p
