Mercurial > repos > iuc > bedtools

diff multiCov.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 c78cf6fe3018
children 95a3b2c25bd1
line wrap: on
line diff
--- a/multiCov.xml	Mon Oct 03 07:36:08 2016 -0400
+++ b/multiCov.xml	Mon Oct 17 10:13:35 2016 -0400
@@ -13,10 +13,10 @@
         #end for
 
         bedtools multicov
-            -bed $input
+            -bed '$input'
             -bams
             #for $i, $bam in enumerate( $bams ):
-                ${i}.bam
+                '${i}.bam'
             #end for
             $strand
             -f $overlap
@@ -26,7 +26,7 @@
             $duplicate
             $failed
             $proper
-            > $output
+            > '$output'
 ]]>
     </command>
     <inputs>
@@ -43,7 +43,7 @@
             label="Include duplicate reads"
             help="Default counts non-duplicates only. (-D)" />
         <param name="failed" type="boolean" checked="false" truevalue="-F" falsevalue=""
-            label="Include failed-QC reads" 
+            label="Include failed-QC reads"
             help="Default counts pass-QC reads only (-F)"/>
         <param name="proper" type="boolean" checked="false" truevalue="-p" falsevalue=""
             label="Only count proper pairs"