Mercurial > repos > yufei-luo > s_mart
diff SMART/galaxy/CompareOverlappingAdapt.xml @ 60:90f4b29d884f
Uploaded
author | m-zytnicki |
---|---|
date | Fri, 21 Feb 2014 08:32:36 -0500 |
parents | 169d364ddd91 |
children | 783e6ed4eb66 |
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--- a/SMART/galaxy/CompareOverlappingAdapt.xml Mon Feb 10 03:39:09 2014 -0500 +++ b/SMART/galaxy/CompareOverlappingAdapt.xml Fri Feb 21 08:32:36 2014 -0500 @@ -4,45 +4,15 @@ <requirement type="set_environment">PYTHONPATH</requirement> </requirements> <command interpreter="python"> - ../Java/Python/CompareOverlappingAdapt.py -i $formatType.inputFileName1 - #if $formatType.FormatInputFileName1 == 'bed': - -f bed - #elif $formatType.FormatInputFileName1 == 'gff': - -f gff - #elif $formatType.FormatInputFileName1 == 'gff2': - -f gff2 - #elif $formatType.FormatInputFileName1 == 'gff3': - -f gff3 - #elif $formatType.FormatInputFileName1 == 'sam': - -f sam - #elif $formatType.FormatInputFileName1 == 'gtf': - -f gtf - #end if - -j $formatType2.inputFileName2 - #if $formatType2.FormatInputFileName2 == 'bed': - -g bed - #elif $formatType2.FormatInputFileName2 == 'gff': - -g gff - #elif $formatType2.FormatInputFileName2 == 'gff2': - -g gff2 - #elif $formatType2.FormatInputFileName2 == 'gff3': - -g gff3 - #elif $formatType2.FormatInputFileName2 == 'sam': - -g sam - #elif $formatType2.FormatInputFileName2 == 'gtf': - -g gtf - #end if - -o $outputFileGff + ../Java/Python/CompareOverlappingAdapt.py -i $formatType.inputFileName1 -f $formatType.FormatInputFileName1 -j $formatType2.inputFileName2 -g $formatType2.FormatInputFileName2 -o $outputFileGff $InvertMatch $NotOverlapping -m $NbOverlap #if $OptionDistance.Dist == 'Yes': -d $OptionDistance.distance #end if - #if $OptionCollinearOrAntiSens.OptionCA == 'Collinear': + #if $OptionCA == 'Collinear': -c - #elif $OptionCollinearOrAntiSens.OptionCA == 'AntiSens': + #elif $OptionCA == 'AntiSense': -a #end if - $InvertMatch - $NotOverlapping </command> <inputs> @@ -114,21 +84,14 @@ <when value="No"> </when> </conditional> - <conditional name="OptionCollinearOrAntiSens"> - <param name="OptionCA" type="select" label="Collinear or anti-sens"> - <option value="Collinear">Collinear</option> - <option value="AntiSens">AntiSens</option> - <option value="NONE" selected="true">NONE</option> - </param> - <when value="Collinear"> - </when> - <when value="AntiSens"> - </when> - <when value="NONE"> - </when> - </conditional> + <param name="OptionCA" type="select" label="Collinear or anti-sense features only"> + <option value="Collinear">Collinear</option> + <option value="AntiSense">AntiSense</option> + <option value="All" selected="true">All</option> + </param> <param name="InvertMatch" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Invert match: the output file will contain all query elements which do NOT overlap"/> <param name="NotOverlapping" type="boolean" truevalue="-O" falsevalue="" checked="false" label="Also report the query data which do not overlap, with the nbOverlaps tag set to 0."/> + <param name="NbOverlap" type="integer" value="1" label="Min. # of overlapping nt. to declare an overlap."/> </inputs> <outputs>