Mercurial > repos > iuc > bedtools

diff sortBed.xml @ 11:7308cc546a36 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
author iuc
date Mon, 17 Oct 2016 10:13:35 -0400
parents 607c0576c6ab
children 95a3b2c25bd1
line wrap: on
line diff
--- a/sortBed.xml	Mon Oct 03 07:36:08 2016 -0400
+++ b/sortBed.xml	Mon Oct 17 10:13:35 2016 -0400
@@ -7,14 +7,14 @@
     <expand macro="stdio" />
     <command>
 <![CDATA[
-        sortBed 
-            -i $input 
-            $option 
-            > $output
+        sortBed
+            -i '$input'
+            $option
+            > '$output'
 ]]>
     </command>
     <inputs>
-        <param format="bed" name="input" type="data" label="Sort the following BED file"/>
+        <param format="bed,gff,gff3,vcf" name="input" type="data" label="Sort the following BED file"/>
         <param name="option" type="select" label="Sort by">
             <!-- sort -k 1,1 -k2,2 -n a.bed -->
             <option value="">chromosome, then by start position (asc)</option>
@@ -27,7 +27,7 @@
         </param>
     </inputs>
     <outputs>
-        <data format="bed" name="output" metadata_source="input" label="${input.name} (as BED)"/>
+        <data format_source="input" name="output" metadata_source="input" label="SortBed on ${input.name}"/>
     </outputs>
     <tests>
         <test>