Mercurial > repos > iuc > bedtools
diff multiCov.xml @ 26:c0fbce5dc84a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
author | iuc |
---|---|
date | Mon, 17 Oct 2016 10:13:20 -0400 |
parents | a2d4c30ba2f9 |
children | d279800f4ff9 |
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--- 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" />