Mercurial > repos > greg > pima_report
changeset 23:d89b7d47a85a draft
Uploaded
| author | greg |
|---|---|
| date | Thu, 20 Apr 2023 16:45:57 +0000 |
| parents | 13a9c8ecd30e |
| children | 803e5965ed20 |
| files | pima_report.py pima_report.xml |
| diffstat | 2 files changed, 2 insertions(+), 2 deletions(-) [+] |
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--- a/pima_report.py Thu Apr 13 18:33:19 2023 +0000 +++ b/pima_report.py Thu Apr 20 16:45:57 2023 +0000 @@ -881,7 +881,7 @@ parser.add_argument('--mutation_regions_bed_file', action='store', dest='mutation_regions_bed_file', help='AMR mutation regions BRD file') parser.add_argument('--mutation_regions_dir', action='store', dest='mutation_regions_dir', help='Directory of mutation regions TSV files') parser.add_argument('--pima_css', action='store', dest='pima_css', help='PIMA css stypesheet') -parser.add_argument('--plasmids_file', action='store', dest='plasmids_file', help='pChunks plasmids TSV file') +parser.add_argument('--plasmids_file', action='store', dest='plasmids_file', default=None, help='pChunks plasmids TSV file') parser.add_argument('--quast_report_file', action='store', dest='quast_report_file', help='Quast report tabular file') parser.add_argument('--read_type', action='store', dest='read_type', help='Sample read type (ONT or Illumina)') parser.add_argument('--reference_insertions_file', action='store', dest='reference_insertions_file', help='Reference insertions BED file')
--- a/pima_report.xml Thu Apr 13 18:33:19 2023 +0000 +++ b/pima_report.xml Thu Apr 20 16:45:57 2023 +0000 @@ -152,7 +152,7 @@ <option value="illumina">Short reads - Illumina</option> </param> <param name="reference_insertions_file" type="data" format="bed" label="Reference insertions BED file"/> - <param name="plasmids_file" type="data" format="tsv" label="pChunks plasmids TSV file"/> + <param name="plasmids_file" type="data" format="tsv" optional="true" label="pChunks plasmids TSV file" help="Optional, ignored if not selected"/> <param name="samtools_pileup_file" type="data" format="pileup" label="Samtools pileup file"/> <param name="varscan_vcf_file" type="data" format="vcf" label="Varscan VCF file"/> </inputs>