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