Mercurial > repos > yufei-luo > s_mart
view SMART/galaxy/getDistance.xml @ 12:5a054da77808
Updated CompareOverlappingSmallRef.xml
author | m-zytnicki |
---|---|
date | Thu, 14 Mar 2013 05:37:35 -0400 |
parents | 769e306b7933 |
children | 440ceca58672 |
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<tool id="GetDistance" name="get distance"> <description>Give the distances between every data from the first input set and the data from the second input set</description> <command interpreter="python"> ../Java/Python/getDistance.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 $absolute $proportion #if $OptionColinearOrAntiSens.OptionCA == "Colinear": -c #elif $OptionColinearOrAntiSens.OptionCA == 'AntiSens': -a #end if #if $OptionFirstNucl5.FirstNu5 == "Yes": -s $OptionFirstNucl5.first5File1 -S $OptionFirstNucl5.first5File2 #end if #if $OptionFirstNucl3.FirstNu3 == "Yes": -e $OptionFirstNucl3.first3File1 -E $OptionFirstNucl3.first3File2 #end if #if $OptionMinDistance.MinD == "Yes": -m $OptionMinDistance.minDistance #end if #if $OptionMaxDistance.MaxD == "Yes": -M $OptionMaxDistance.maxDistance #end if $fivePrime $threePrime $spearMan #if $OptionBuckets.OBuckets == "Yes": -u $OptionBuckets.buckets #end if #if $OptionMinXaxis.MinX == "Yes": -x $OptionMinXaxis.minXaxis #end if #if $OptionMaxXaxis.MaxX == "Yes": -X $OptionMaxXaxis.maxXaxis #end if #if $OptionTitle.OTitle == "Yes": -t $OptionTitle.title #end if -o $outputFilePng $outputDistance $outputFileDistance </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> <param name="outputDistance" type="boolean" truevalue="-O" falsevalue="" checked="false" label="distance option" help="This option create a GFF3 output file containing the distance for each element of the query."/> <param name="absolute" type="boolean" truevalue="-b" falsevalue="" checked="false" label="absolute value option" help="This option gives the absolute value of the distance."/> <param name="proportion" type="boolean" truevalue="-p" falsevalue="" checked="false" label="proportion option" help="This option gives the proportion on the y-axis instead of the number of distances."/> <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="OptionFirstNucl5"> <param name="FirstNu5" type="select" label="only consider the n first 5' nucleotides for input files"> <option value="Yes">Yes</option> <option value="No" selected="true">No</option> </param> <when value="Yes"> <param name="first5File1" type="integer" value="1" label="in file 1" help="Be Careful! The value must be upper than 0"/> <param name="first5File2" type="integer" value="1" label="in file 2" help="Be Careful! The value must be upper than 0"/> </when> <when value="No"> </when> </conditional> <conditional name="OptionFirstNucl3"> <param name="FirstNu3" type="select" label="only consider the n first 3' nucleotides for input files"> <option value="Yes">Yes</option> <option value="No" selected="true">No</option> </param> <when value="Yes"> <param name="first3File1" type="integer" value="1" label="in file 1" help="Be Careful! The value must be upper than 0"/> <param name="first3File2" type="integer" value="1" label="in file 2" help="Be Careful! The value must be upper than 0"/> </when> <when value="No"> </when> </conditional> <conditional name="OptionMinDistance"> <param name="MinD" type="select" label="minimum distance considered between two transcripts"> <option value="Yes">Yes</option> <option value="No" selected="true">No</option> </param> <when value="Yes"> <param name="minDistance" type="integer" value="1"/> </when> <when value="No"> </when> </conditional> <conditional name="OptionMaxDistance"> <param name="MaxD" type="select" label="maximum distance considered between two transcripts"> <option value="Yes">Yes</option> <option value="No" selected="true">No</option> </param> <when value="Yes"> <param name="maxDistance" type="integer" value="1000"/> </when> <when value="No"> </when> </conditional> <param name="fivePrime" type="boolean" truevalue="-5" falsevalue="" checked="false" label="five prime option" help="Consider the elements from input file 1 which are upstream of elements of input file 2"/> <param name="threePrime" type="boolean" truevalue="-3" falsevalue="" checked="false" label="three prime option" help="Consider the elements from input file1 which are downstream of elements of input file 2"/> <param name="spearMan" type="boolean" truevalue="-r" falsevalue="" checked="false" label="spearman option" help="Compute Spearman rho."/> <conditional name="OptionBuckets"> <param name="OBuckets" type="select" label="Plots histogram instead of line plot with given interval size."> <option value="Yes">Yes</option> <option value="No" selected="true">No</option> </param> <when value="Yes"> <param name="buckets" type="integer" value="1" label="Interval size"/> </when> <when value="No"> </when> </conditional> <conditional name="OptionMinXaxis"> <param name="MinX" type="select" label="Minimum value on the x-axis to plot."> <option value="Yes">Yes</option> <option value="No" selected="true">No</option> </param> <when value="Yes"> <param name="minXaxis" type="integer" value="1"/> </when> <when value="No"> </when> </conditional> <conditional name="OptionMaxXaxis"> <param name="MaxX" type="select" label="Maximum value on the x-axis to plot."> <option value="Yes">Yes</option> <option value="No" selected="true">No</option> </param> <when value="Yes"> <param name="maxXaxis" type="integer" value="1"/> </when> <when value="No"> </when> </conditional> <conditional name="OptionTitle"> <param name="OTitle" type="select" label="Title for the graph."> <option value="Yes">Yes</option> <option value="No" selected="true">No</option> </param> <when value="Yes"> <param name="title" type="text" value=""/> </when> <when value="No"> </when> </conditional> </inputs> <outputs> <data name="outputFilePng" format="png"/> <data name="outputFileDistance" format="gff3"> <filter>outputDistance</filter> </data> </outputs> </tool>