Mercurial > repos > yufei-luo > s_mart
view SMART/galaxy/getNb.xml @ 10:c081f25e1572
Updated CompareOverlappingSmallRef.py
author | m-zytnicki |
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date | Thu, 14 Mar 2013 05:25:40 -0400 |
parents | 769e306b7933 |
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<tool id="getNumber" name="get number"> <description>Get the distribution of exons per transcripts, or mapping per read, or transcript per cluster.</description> <command interpreter="python"> ../Java/Python/getNb.py -i $formatType.inputFileName #if $formatType.FormatInputFileName == 'bed': -f bed #elif $formatType.FormatInputFileName == 'gff': -f gff #elif $formatType.FormatInputFileName == 'gff2': -f gff2 #elif $formatType.FormatInputFileName == 'gff3': -f gff3 #elif $formatType.FormatInputFileName == 'sam': -f sam #elif $formatType.FormatInputFileName == 'gtf': -f gtf #end if -o $outputFilePNG -q $query $barPlot #if $optionXMAX.XMAX == 'Yes': -x $optionXMAX.xMaxValue #end if </command> <inputs> <conditional name="formatType"> <param name="FormatInputFileName" type="select" label="Input File Format"> <option value="bed">bed</option> <option value="gff">gff</option> <option value="gff2">gff2</option> <option value="gff3">gff3</option> <option value="sam">sam</option> <option value="gtf">gtf</option> </param> <when value="bed"> <param name="inputFileName" format="bed" type="data" label="Input File"/> </when> <when value="gff"> <param name="inputFileName" format="gff" type="data" label="Input File"/> </when> <when value="gff2"> <param name="inputFileName" format="gff2" type="data" label="Input File"/> </when> <when value="gff3"> <param name="inputFileName" format="gff3" type="data" label="Input File"/> </when> <when value="sam"> <param name="inputFileName" format="sam" type="data" label="Input File"/> </when> <when value="gtf"> <param name="inputFileName" format="gtf" type="data" label="Input File"/> </when> </conditional> <param name="query" type="text" value="None" label="compulsory option, choice (exon, transcript, cluster)" /> <param name="barPlot" type="boolean" truevalue="-b" falsevalue="" checked="false" label="use barplot representation"/> <conditional name="optionXMAX"> <param name="XMAX" type="select" label="maximum value on the x-axis to plot "> <option value="Yes">Yes</option> <option value="No" selected="true">No</option> </param> <when value="Yes"> <param name="xMaxValue" type="integer" value="0" /> </when> <when value="No"> </when> </conditional> </inputs> <outputs> <data name="outputFilePNG" format="png" label="[getNB]out file"/> </outputs> </tool>