diff multiCov.xml @ 26:c0fbce5dc84a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811

--- a/multiCov.xml	Wed Sep 14 17:29:56 2016 -0400
+++ b/multiCov.xml	Mon Oct 17 10:13:20 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"
@@ -55,7 +55,7 @@
     <tests>
         <test>
             <param name="input" value="multiCov1.bed" ftype="bed" />
-            <param name="bams" value="srma_in3.bam,srma_in3.bam" ftpye="bam"/>
+            <param name="bams" value="srma_in3.bam,srma_in3.bam" ftype="bam"/>
             <param name="q" value="1"/>
             <param name="split" value="False"/>
             <output name="output" file="multiCovBed_result1.bed" ftype="bed" />