# HG changeset patch
# User jjohnson
# Date 1521509495 14400
# Node ID 5e2cfbb37c9e5c8b1a8ddd7072bc6cabf2729b75
# Parent  da1ac511a473f32edc7a5f469ec5a3064ab93538
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/metagene_annotator commit 0b34e8f3ef8f834cf45a0964b681243a39bee497-dirty

diff -r da1ac511a473 -r 5e2cfbb37c9e metagene_annotator.xml
--- a/metagene_annotator.xml	Mon Mar 19 20:47:09 2018 -0400
+++ b/metagene_annotator.xml	Mon Mar 19 21:31:35 2018 -0400
@@ -5,13 +5,14 @@
         <requirement type="package">python</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
+        #set $output_list = str($output_formats).split(',')
         mga $input $multiple_species > mga_output
-        #if 'tsv' in $output_formats or 'bed' in $output_formats:
+        #if 'tsv' in $output_list or 'bed' in $output_list:
             && python '$__tool_directory__/convert_mga.py' -v mga_output
-            #if 'tsv' in $output_formats
+            #if 'tsv' in $output_list
                 --tsv '$mga_tsv'
             #end if
-            #if 'bed' in $output_formats
+            #if 'bed' in $output_list
                 --bed '$mga_bed'
             #end if
         #end if
@@ -20,14 +21,14 @@
         <param name="input" type="data" format="fasta" label="prokaryote DNA sequences"/>
         <param name="multiple_species" type="boolean" truevalue="-m" falsevalue="-s" checked="true" 
                label="MetaGenomic - Sequences are from multiple organisms" />
-        <param name="output_formats" type="select" multiple="true" label="output formats">
-            <option value="txt">MetaGeneAnnotator text report</option>
+        <param name="output_formats" type="select" multiple="true" display="checkboxes" label="output formats">
+            <option value="txt" selected="true">MetaGeneAnnotator text report</option>
             <option value="tsv">MetaGeneAnnotator tabular report with sequence columns</option>
             <option value="bed">MetaGeneAnnotator in BED format</option>
         </param>
     </inputs>
     <outputs>
-        <data name="mga_txt" format="text" from_work_dir="mga_output" label="${tool.name} on ${on_string} ${input.name} mga report">
+        <data name="mga_txt" format="txt" from_work_dir="mga_output" label="${tool.name} on ${on_string} ${input.name} mga report">
             <filter>'txt' in output_formats</filter>
         </data>
         <data name="mga_tsv" format="tabular" label="${tool.name} on ${on_string} ${input.name} mga table">
@@ -39,6 +40,10 @@
         </data>
         <data name="mga_bed" format="bed" label="${tool.name} on ${on_string} ${input.name} mga bed">
             <filter>'bed' in output_formats</filter>
+            <actions>
+                <action name="column_names" type="metadata" 
+                 default="chrom,chromStart,chromEnd,name,score,strand,thickStart,thickEnd,itemRgb,blockCount,blockSizes,blockStarts"/>
+            </actions>
         </data>
     </outputs>
     <tests>