Mercurial > repos > dfornika > pick_plasmids_containing_genes

diff pick_plasmids_containing_genes.xml @ 2:2dd1a0ed7cce draft

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"planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/pick_plasmids_containing_genes commit 9cb01222a76ffdf89fa8d7b69f32df7c2b1f860a-dirty"
author dfornika
date Sat, 02 Nov 2019 01:32:22 -0400
parents a938371b3bfd
children 50640b06fca5
line wrap: on
line diff
--- a/pick_plasmids_containing_genes.xml	Sat Nov 02 00:34:49 2019 -0400
+++ b/pick_plasmids_containing_genes.xml	Sat Nov 02 01:32:22 2019 -0400
@@ -4,20 +4,17 @@
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         '$__tool_directory__/pick_plasmids_containing_genes.py'
-        --plasmids 
+        --plasmids
         #for $plasmid in $plasmids:
           '${plasmid}'
         #end for
-        --abricate_reports
-        #for $abricate_report in $abricate_reports:
-          '${abricate_report}'
-        #end for
+        --concatenated_abricate_reports '${concatenated_abricate_reports}'
         --abricate_report_screening_file '${screening_file.fields.path}'
         --outdir outdir
     ]]></command>
     <inputs>
         <param name="plasmids" type="data_collection" collection_type="list" format="fasta" />
-        <param name="abricate_reports" type="data_collection" collection_type="list" format="tabular" />
+        <param name="concatenated_abricate_reports" type="data_collection" collection_type="list" format="tabular,txt" />
         <param name="screening_file" type="select" format="tabular">
 	    <options from_data_table="abricate_report_screening_files">
 	        <validator type="no_options" message="No abricate report screening files are available" />