Mercurial > repos > greg > pima_report

comparison pima_report.py @ 23:d89b7d47a85a draft

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Uploaded
author greg
date Thu, 20 Apr 2023 16:45:57 +0000
parents 13a9c8ecd30e
children 803e5965ed20
comparison
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22:13a9c8ecd30e 23:d89b7d47a85a
879 parser.add_argument('--kraken2_version', action='store', dest='kraken2_version', default=None, help='kraken2 version string') 879 parser.add_argument('--kraken2_version', action='store', dest='kraken2_version', default=None, help='kraken2 version string')
880 parser.add_argument('--minimap2_version', action='store', dest='minimap2_version', default=None, help='minimap2 version string') 880 parser.add_argument('--minimap2_version', action='store', dest='minimap2_version', default=None, help='minimap2 version string')
881 parser.add_argument('--mutation_regions_bed_file', action='store', dest='mutation_regions_bed_file', help='AMR mutation regions BRD file') 881 parser.add_argument('--mutation_regions_bed_file', action='store', dest='mutation_regions_bed_file', help='AMR mutation regions BRD file')
882 parser.add_argument('--mutation_regions_dir', action='store', dest='mutation_regions_dir', help='Directory of mutation regions TSV files') 882 parser.add_argument('--mutation_regions_dir', action='store', dest='mutation_regions_dir', help='Directory of mutation regions TSV files')
883 parser.add_argument('--pima_css', action='store', dest='pima_css', help='PIMA css stypesheet') 883 parser.add_argument('--pima_css', action='store', dest='pima_css', help='PIMA css stypesheet')
884 parser.add_argument('--plasmids_file', action='store', dest='plasmids_file', help='pChunks plasmids TSV file') 884 parser.add_argument('--plasmids_file', action='store', dest='plasmids_file', default=None, help='pChunks plasmids TSV file')
885 parser.add_argument('--quast_report_file', action='store', dest='quast_report_file', help='Quast report tabular file') 885 parser.add_argument('--quast_report_file', action='store', dest='quast_report_file', help='Quast report tabular file')
886 parser.add_argument('--read_type', action='store', dest='read_type', help='Sample read type (ONT or Illumina)') 886 parser.add_argument('--read_type', action='store', dest='read_type', help='Sample read type (ONT or Illumina)')
887 parser.add_argument('--reference_insertions_file', action='store', dest='reference_insertions_file', help='Reference insertions BED file') 887 parser.add_argument('--reference_insertions_file', action='store', dest='reference_insertions_file', help='Reference insertions BED file')
888 parser.add_argument('--samtools_version', action='store', dest='samtools_version', default=None, help='Samtools version string') 888 parser.add_argument('--samtools_version', action='store', dest='samtools_version', default=None, help='Samtools version string')
889 parser.add_argument('--varscan_version', action='store', dest='varscan_version', default=None, help='Varscan version string') 889 parser.add_argument('--varscan_version', action='store', dest='varscan_version', default=None, help='Varscan version string')