Mercurial > repos > yufei-luo > s_mart
view SMART/galaxy/getExons.xml @ 58:5f5c9b74c2dd
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author | m-zytnicki |
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date | Fri, 07 Feb 2014 11:53:36 -0500 |
parents | 2c0c0a89fad7 |
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<tool id="getExons" name="get exons"> <description>Get the exons of a set of transcripts.</description> <requirements> <requirement type="set_environment">PYTHONPATH</requirement> </requirements> <command interpreter="python"> ../Java/Python/getExons.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 $optionSelect.Value == "Yes": -s $optionSelect.selectValue #end if -o $outputFileGff </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="optionSelect"> <param name="Value" type="select" label="select some of the exons (like '1,2,5..-3,-1')"> <option value="Yes">Yes</option> <option value="No" selected="true">No</option> </param> <when value="Yes"> <param name="selectValue" type="text" value="None" label="select option" help="like '1,2,5..-3,-1'"/> </when> <when value="No"> </when> </conditional> </inputs> <outputs> <data format="gff3" name="outputFileGff" label="[get exons] output file"/> </outputs> <tests> <test> <param name="FormatInputFileName" value="gtf" /> <param name="inputFileName" value="genes.gtf" /> <param name="Value" value="No"/> <output name="outputFileGff" file="exp_getExons.gff3" /> </test> </tests> <help> Provide all the exons of an annotation file. </help> </tool>