Mercurial > repos > yufei-luo > s_mart
view SMART/galaxy/ConvertTranscriptFile.xml @ 10:c081f25e1572
Updated CompareOverlappingSmallRef.py
author | m-zytnicki |
---|---|
date | Thu, 14 Mar 2013 05:25:40 -0400 |
parents | 769e306b7933 |
children | 440ceca58672 |
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<tool id="ConvertTranscriptFile" name="Convert transcript file"> <description>Convert a file from a format to another.</description> <command interpreter="python"> ../Java/Python/convertTranscriptFile.py -i $inputFormatType.inputFileName #if $inputFormatType.FormatInputFileName == 'gff3': -f gff3 #elif $inputFormatType.FormatInputFileName == 'bed': -f bed #elif $inputFormatType.FormatInputFileName == 'gff2': -f gff2 #elif $inputFormatType.FormatInputFileName == 'bam': -f blast #elif $inputFormatType.FormatInputFileName == 'sam': -f sam #elif $inputFormatType.FormatInputFileName == 'gtf': -f gtf #end if -g $outputFormatType.outFormat #if $optionSequence.choose == 'Yes': -s $optionSequence.value #end if -n $name $strand -o $outputFile </command> <inputs> <conditional name="inputFormatType"> <param name="FormatInputFileName" type="select" label="Input File Format"> <option value="gff3">GFF3</option> <option value="bed">BED</option> <option value="gff2">GFF2</option> <option value="bam">BAM</option> <option value="sam">SAM</option> <option value="gtf">GTF</option> </param> <when value="gff3"> <param name="inputFileName" format="gff3" type="data" label="Input File"/> </when> <when value="bed"> <param name="inputFileName" format="bed" type="data" label="Input File"/> </when> <when value="gff2"> <param name="inputFileName" format="gff2" type="data" label="Input File"/> </when> <when value="bam"> <param name="inputFileName" format="bam" 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="outputFormatType"> <param name="outFormat" type="select" label="Please choose the format that you want to convert to (corresponding to your input file format)."> <option value="gff3">GFF3</option> <option value="bed">BED</option> <option value="gff2">GFF2</option> <option value="wig">WIG</option> <option value="sam">SAM</option> <option value="csv">CSV</option> <option value="gtf">GTF</option> </param> <when value="gff3"> </when> <when value="bed"> </when> <when value="gff2"> </when> <when value="wig"> </when> <when value="sam"> </when> <when value="csv"> </when> <when value="gtf"> </when> </conditional> <param name="name" type="text" value="SMART" label="name for the transcripts"/> <conditional name="optionSequence"> <param name="choose" type="select" label="give the corresponding Multi-Fasta file (useful for EMBL format)"> <option value="Yes">Yes</option> <option value="No" selected="true">No</option> </param> <when value="Yes"> <param name="value" type="data" format="mfa" /> </when> <when value="No"> </when> </conditional> <param name="strand" type="boolean" truevalue="-t" falsevalue="" checked="false" label="consider the 2 strands as different (only useful for writing WIG files)"/> </inputs> <outputs> <data name="outputFile" format="gff3" label="$inputFormatType.FormatInputFileName to $outputFormatType.outFormat"> <change_format> <when input="outputFormatType.outFormat" value="bed" format="bed" /> <when input="outputFormatType.outFormat" value="gff2" format="gff2" /> <when input="outputFormatType.outFormat" value="wig" format="wig" /> <when input="outputFormatType.outFormat" value="sam" format="sam" /> <when input="outputFormatType.outFormat" value="csv" format="csv" /> <when input="outputFormatType.outFormat" value="gtf" format="gtf" /> </change_format> </data> </outputs> <help> </help> </tool>