Mercurial > repos > yufei-luo > s_mart
diff smart_toolShed/SMART/galaxy/getDistance.xml @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/smart_toolShed/SMART/galaxy/getDistance.xml Thu Jan 17 10:52:14 2013 -0500 @@ -0,0 +1,275 @@ +<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>