# HG changeset patch
# User greg
# Date 1682009157 0
# Node ID d89b7d47a85a5fbc688660269c4d4bbc1d3056e3
# Parent  13a9c8ecd30e03e5a29d65debbc84b7f57a54410
Uploaded

diff -r 13a9c8ecd30e -r d89b7d47a85a pima_report.py
--- 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')
diff -r 13a9c8ecd30e -r d89b7d47a85a pima_report.xml
--- 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>