# HG changeset patch
# User iuc
# Date 1610615324 0
# Node ID 5b6d2f69bbc5cca5e39893549fa40050d977fbaa
# Parent  2e4b9161ce40f66a6b2fb72da3f2ac966918c2ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit a80e3713d10fafef22e964198d59251adf955812"

diff -r 2e4b9161ce40 -r 5b6d2f69bbc5 vsnp_add_zero_coverage.xml
--- a/vsnp_add_zero_coverage.xml	Thu Dec 10 15:24:20 2020 +0000
+++ b/vsnp_add_zero_coverage.xml	Thu Jan 14 09:08:44 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="vsnp_add_zero_coverage" name="vSNP: add zero coverage" version="@WRAPPER_VERSION@.1" profile="@PROFILE@">
+<tool id="vsnp_add_zero_coverage" name="vSNP: add zero coverage" version="@WRAPPER_VERSION@.2" profile="@PROFILE@">
     <description></description>
     <macros>
         <import>macros.xml</import>
@@ -37,7 +37,7 @@
             <when value="cached">
                 <param name="reference" type="select" label="Using reference genome">
                     <options from_data_table="fasta_indexes">
-                        <filter type="data_meta" column="dbkey" key="dbkey" ref="bam_input"/>
+                        <filter type="data_meta" column="1" key="dbkey" ref="bam_input"/>
                         <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected BAM file"/>
                     </options>
                 </param>
diff -r 2e4b9161ce40 -r 5b6d2f69bbc5 vsnp_determine_ref_from_data.py
--- a/vsnp_determine_ref_from_data.py	Thu Dec 10 15:24:20 2020 +0000
+++ b/vsnp_determine_ref_from_data.py	Thu Jan 14 09:08:44 2021 +0000
@@ -197,12 +197,12 @@
 if __name__ == '__main__':
     parser = argparse.ArgumentParser()
 
-    parser.add_argument('--dnaprint_fields', action='append', dest='dnaprint_fields', nargs=2, required=False, default=None, help="List of dnaprints data table value, name and path fields")
-    parser.add_argument('--read1', action='store', dest='read1', required=True, default=None, help='Required: single read')
+    parser.add_argument('--dnaprint_fields', action='append', dest='dnaprint_fields', nargs=2, help="List of dnaprints data table value, name and path fields")
+    parser.add_argument('--read1', action='store', dest='read1', help='Required: single read')
     parser.add_argument('--read2', action='store', dest='read2', required=False, default=None, help='Optional: paired read')
-    parser.add_argument('--gzipped', action='store_true', dest='gzipped', default=False, help='Input files are gzipped')
-    parser.add_argument('--output_dbkey', action='store', dest='output_dbkey', required=True, default=None, help='Output reference file')
-    parser.add_argument('--output_metrics', action='store', dest='output_metrics', required=True, default=None, help='Output metrics file')
+    parser.add_argument('--gzipped', action='store_true', dest='gzipped', help='Input files are gzipped')
+    parser.add_argument('--output_dbkey', action='store', dest='output_dbkey', help='Output reference file')
+    parser.add_argument('--output_metrics', action='store', dest='output_metrics', help='Output metrics file')
 
     args = parser.parse_args()