Mercurial > repos > yufei-luo > s_mart
view SMART/galaxy/compareOverlapping.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="CompareOverlapping" name="Compare Overlapping"> <description>Print all the transcripts from a first file which overlap with the transcripts from a second file.</description> <command interpreter="python"> ../Java/Python/CompareOverlapping.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 -j $formatType2.inputFileName2 #if $formatType2.FormatInputFileName2 == 'bed': -g bed #elif $formatType2.FormatInputFileName2 == 'gff': -g gff #elif $formatType2.FormatInputFileName2 == 'gff2': -g gff2 #elif $formatType2.FormatInputFileName2 == 'gff3': -g gff3 #elif $formatType2.FormatInputFileName2 == 'sam': -g sam #elif $formatType2.FormatInputFileName2 == 'gtf': -g gtf #end if -o $outputFileGff #if $optionNFirstFile1.NFirstForFile1 == 'Yes': -S $optionNFirstFile1.firstNtFile1 #end if #if $optionNFirstFile2.NFirstForFile2 == 'Yes': -s $optionNFirstFile2.firstNtFile2 #end if #if $optionNLastFile1.NLastForFile1 == 'Yes': -U $optionNLastFile1.lastNtFile1 #end if #if $optionNLastFile2.NLastForFile2 == 'Yes': -u $optionNLastFile2.lastNtFile2 #end if #if $optionExtentionCinqFile1.extentionFile1 == 'Yes': -E $optionExtentionCinqFile1.extention51 #end if #if $optionExtentionCinqFile2.extentionFile2 == 'Yes': -e $optionExtentionCinqFile2.extention52 #end if #if $optionExtentionTroisFile1.extentionFile1 == 'Yes': -N $optionExtentionTroisFile1.extention31 #end if #if $optionExtentionTroisFile2.extentionFile2 == 'Yes': -n $optionExtentionTroisFile2.extention32 #end if #if $OptionColinearOrAntiSens.OptionCA == 'Colinear': -c #elif $OptionColinearOrAntiSens.OptionCA == 'AntiSens': -a #end if #if $OptionDistance.Dist == 'Yes': -d $OptionDistance.distance #end if #if $OptionMinOverlap.MO == 'Yes': -m $OptionMinOverlap.minOverlap #end if $InvertMatch $ReportIntron $NotOverlapping </command> <inputs> <conditional name="formatType"> <param name="FormatInputFileName1" type="select" label="Input File Format 1"> <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 1"/> </when> <when value="gff"> <param name="inputFileName1" format="gff" type="data" label="Input File 1"/> </when> <when value="gff2"> <param name="inputFileName1" format="gff2" type="data" label="Input File 1"/> </when> <when value="gff3"> <param name="inputFileName1" format="gff3" type="data" label="Input File 1"/> </when> <when value="sam"> <param name="inputFileName1" format="sam" type="data" label="Input File 1"/> </when> <when value="gtf"> <param name="inputFileName1" format="gtf" type="data" label="Input File 1"/> </when> </conditional> <conditional name="formatType2"> <param name="FormatInputFileName2" type="select" label="Input File Format 2"> <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="inputFileName2" format="bed" type="data" label="Input File 2"/> </when> <when value="gff"> <param name="inputFileName2" format="gff" type="data" label="Input File 2"/> </when> <when value="gff2"> <param name="inputFileName2" format="gff2" type="data" label="Input File 2"/> </when> <when value="gff3"> <param name="inputFileName2" format="gff3" type="data" label="Input File 2"/> </when> <when value="sam"> <param name="inputFileName2" format="sam" type="data" label="Input File 2"/> </when> <when value="gtf"> <param name="inputFileName2" format="gtf" type="data" label="Input File 2"/> </when> </conditional> <conditional name="optionNFirstFile1"> <param name="NFirstForFile1" type="select" label="NFirst for file 1" help="only consider the n first nucleotides of the transcripts in file 1"> <option value="Yes">Yes</option> <option value="No" selected="true">No</option> </param> <when value="Yes"> <param name="firstNtFile1" type="integer" value="1" label="n first nucleotides for input file 1" /> </when> <when value="No"> </when> </conditional> <conditional name="optionNFirstFile2"> <param name="NFirstForFile2" type="select" label="NFirst for file 2" help="only consider the n first nucleotides of the transcripts in file 2"> <option value="Yes">Yes</option> <option value="No" selected="true">No</option> </param> <when value="Yes"> <param name="firstNtFile2" type="integer" value="1" label="n first nucleotides for input file 1" /> </when> <when value="No"> </when> </conditional> <conditional name="optionNLastFile1"> <param name="NLastForFile1" type="select" label="NLast for file 1"> <option value="Yes">Yes</option> <option value="No" selected="true">No</option> </param> <when value="Yes"> <param name="lastNtFile1" type="integer" value="1" label="n last nucleotides for input file 1" help="only consider the n last nucleotides of the transcripts in file 1"/> </when> <when value="No"> </when> </conditional> <conditional name="optionNLastFile2"> <param name="NLastForFile2" type="select" label="NLast for file 2"> <option value="Yes">Yes</option> <option value="No" selected="true">No</option> </param> <when value="Yes"> <param name="lastNtFile2" type="integer" value="1" label="n last nucleotides for input file 2" help="only consider the n last nucleotides of the transcripts in file 2"/> </when> <when value="No"> </when> </conditional> <conditional name="optionExtentionCinqFile1"> <param name="extentionFile1" type="select" label="Extension towards 5 for file 1"> <option value="Yes">Yes</option> <option value="No" selected="true">No</option> </param> <when value="Yes"> <param name="extention51" type="integer" value="1" label="in file 1" /> </when> <when value="No"> </when> </conditional> <conditional name="optionExtentionCinqFile2"> <param name="extentionFile2" type="select" label="Extension towards 5 for file 2"> <option value="Yes">Yes</option> <option value="No" selected="true">No</option> </param> <when value="Yes"> <param name="extention52" type="integer" value="1" label="in file 2"/> </when> <when value="No"> </when> </conditional> <conditional name="optionExtentionTroisFile1"> <param name="extentionFile1" type="select" label="Extension towards 3 for file 1"> <option value="Yes">Yes</option> <option value="No" selected="true">No</option> </param> <when value="Yes"> <param name="extention31" type="integer" value="1" label="in file 1" /> </when> <when value="No"> </when> </conditional> <conditional name="optionExtentionTroisFile2"> <param name="extentionFile2" type="select" label="Extension towards 3 for file 2"> <option value="Yes">Yes</option> <option value="No" selected="true">No</option> </param> <when value="Yes"> <param name="extention32" type="integer" value="1" label="in file 2" /> </when> <when value="No"> </when> </conditional> <conditional name="OptionColinearOrAntiSens"> <param name="OptionCA" type="select" label="Colinear or anti-sens"> <option value="Colinear">Colinear</option> <option value="AntiSens">AntiSens</option> <option value="NONE" selected="true">NONE</option> </param> <when value="Colinear"> </when> <when value="AntiSens"> </when> <when value="NONE"> </when> </conditional> <conditional name="OptionDistance"> <param name="Dist" type="select" label="Maximum Distance between two reads"> <option value="Yes">Yes</option> <option value="No" selected="true">No</option> </param> <when value="Yes"> <param name="distance" type="integer" value="0"/> </when> <when value="No"> </when> </conditional> <conditional name="OptionMinOverlap"> <param name="MO" type="select" label="Minimum number of overlapping between two reads"> <option value="Yes">Yes</option> <option value="No" selected="true">No</option> </param> <when value="Yes"> <param name="minOverlap" type="integer" value="1"/> </when> <when value="No"> </when> </conditional> <param name="InvertMatch" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Invert match"/> <param name="ReportIntron" type="boolean" truevalue="-t" falsevalue="" checked="false" label="Report intron"/> <param name="NotOverlapping" type="boolean" truevalue="-O" falsevalue="" checked="false" label="When there is no overlapping, the number of Overlapping will be set to 0 by defalt."/> </inputs> <outputs> <data name="outputFileGff" format="gff3"/> </outputs> </tool>