Mercurial > repos > yufei-luo > s_mart
view SMART/galaxy/coordinatesToSequence.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="coordinatesToSequence" name="coordinates to sequence"> <description>Coordinates to Sequences: Extract the sequences from a list of coordinates.</description> <command interpreter="python"> ../Java/Python/coordinatesToSequence.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 -s $sequence -o $outputFileFasta </command> <inputs> <conditional name="formatType"> <param name="FormatInputFileName1" 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="inputFileName1" format="bed" type="data" label="Input File"/> </when> <when value="gff"> <param name="inputFileName1" format="gff" type="data" label="Input File"/> </when> <when value="gff2"> <param name="inputFileName1" format="gff2" type="data" label="Input File"/> </when> <when value="gff3"> <param name="inputFileName1" format="gff3" type="data" label="Input File"/> </when> <when value="sam"> <param name="inputFileName1" format="sam" type="data" label="Input File"/> </when> <when value="gtf"> <param name="inputFileName1" format="gtf" type="data" label="Input File"/> </when> </conditional> <param name="sequence" type="data" label="Reference fasta File" format="fasta"/> </inputs> <outputs> <data name="outputFileFasta" format="fasta" label="coordinates to sequences output"/> </outputs> </tool>