Mercurial > repos > yufei-luo > s_mart
view SMART/galaxy/restrictTranscriptList.xml @ 45:e454402ba9d9
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author | m-zytnicki |
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date | Wed, 18 Sep 2013 08:51:22 -0400 |
parents | 2c0c0a89fad7 |
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<tool id="restrictTranscriptList" name="restrict transcript list"> <description>Select the features which are located in a given locus.</description> <requirements> <requirement type="set_environment">PYTHONPATH</requirement> </requirements> <command interpreter="python"> ../Java/Python/restrictTranscriptList.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 #if $OptionChrom.Chrom == "Yes": -c $OptionChrom.ChromName #end if #if $OptionStart.start == "Yes": -s $OptionStart.startValue #end if #if $OptionEnd.end == "Yes": -e $OptionEnd.endValue #end if -o $outputFile </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> <conditional name="OptionChrom"> <param name="Chrom" type="select" label="chromosome name"> <option value="Yes">Yes</option> <option value="No" selected="true">No</option> </param> <when value="Yes"> <param name="ChromName" type="text" value="None"/> </when> <when value="No"> </when> </conditional> <conditional name="OptionStart"> <param name="start" type="select" label="start region of the locus"> <option value="Yes">Yes</option> <option value="No" selected="true">No</option> </param> <when value="Yes"> <param name="startValue" type="integer" value="0"/> </when> <when value="No"> </when> </conditional> <conditional name="OptionEnd"> <param name="end" type="select" label="end region of the locus"> <option value="Yes">Yes</option> <option value="No" selected="true">No</option> </param> <when value="Yes"> <param name="endValue" type="integer" value="0"/> </when> <when value="No"> </when> </conditional> </inputs> <outputs> <data format="gff3" name="outputFile" label="[restrict transcript list] output file"/> </outputs> <help> Reads a list of genomic coordinates and outputs those which on a given chromosome and / or between two given positions. </help> <tests> <test> <param name="FormatInputFileName" value="gtf" /> <param name="inputFileName" value="genes.gtf" /> <param name="Chrom" value="Yes"/> <param name="ChromName" value="I"/> <param name="start" value="No" /> <param name="end" value="No" /> <output name="outputFile" file="exp_restrictTranscriptList.gff3" /> </test> </tests> </tool>