Mercurial > repos > alermine > nebula
view [APliBio]Nebula tools suite/Nebula/MakeTSSdist/makeTSSdist_wrapper.xml @ 4:0b8b39c2ce01 draft default tip
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author | alermine |
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date | Wed, 14 Nov 2012 06:04:04 -0500 |
parents | 2ec3ba0e9e70 |
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<tool id="makeTSSdist" name="MakeTSSdist" version="1.0"> <description>Get peak distribution around TSS</description> <command interpreter="bash"> #if str( $if_PDF ) == '0' and $use_reg.use_reg_selector == "no" and $use_control.use_control_selector == "no" #makeTSSdist_wrapper.sh -f $inputfile -l $left -o $outputPNG -r $right -u $stats -v $input_organism.version -p 0 #elif str( $if_PDF ) == '1' and $use_reg.use_reg_selector == "no" and $use_control.use_control_selector == "no" #makeTSSdist_wrapper.sh -f $inputfile -l $left -o $outputPDF -r $right -u $stats -v $input_organism.version -p 1 #elif str( $if_PDF ) == '0' and $use_reg.use_reg_selector == "no" and $use_control.use_control_selector == "yes" # makeTSSdist_wrapper.sh -f $inputfile -c $controlfile -o $outputPNG -l $left -r $right -u $stats -v $input_organism.version -p 0 #elif str( $if_PDF ) == '1' and $use_reg.use_reg_selector == "no" and $use_control.use_control_selector == "yes" # makeTSSdist_wrapper.sh -f $inputfile -c $controlfile -o $outputPDF -l $left -r $right -u $stats -v $input_organism.version -p 1 #elif str( $if_PDF ) == '0' and $use_reg.use_reg_selector == "yes" and $use_control.use_control_selector == "no" # makeTSSdist_wrapper.sh -f $inputfile -e $regfile -l $left -o $outputPNG -r $right -u $stats -v $input_organism.version -p 0 #elif str( $if_PDF ) == '1' and $use_reg.use_reg_selector == "yes" and $use_control.use_control_selector == "no" # makeTSSdist_wrapper.sh -f $inputfile -e $regfile -l $left -o $outputPDF -r $right -u $stats -v $input_organism.version -p 1 #elif str( $if_PDF ) == '0' and $use_reg.use_reg_selector == "yes" and $use_control.use_control_selector == "yes" #makeTSSdist_wrapper.sh -f $inputfile -c $controlfile -l $left -o $outputPNG -r $right -u $stats -v $input_organism.version -e $regfile -p 0 #else # makeTSSdist_wrapper.sh -f $inputfile -c $controlfile -l $left -o $outputPDF -r $right -u $stats -v $input_organism.version -e $regfile -p 1 #end if </command> <inputs> <param name="inputfile" type="data" label="ChIP peaks" value="ChIP peaks File" format="bed"/> <conditional name="use_control"> <param name="use_control_selector" type="select" label="Use control data"> <option value="no" selected="true">No</option> <option value="yes">Yes</option> </param> <when value="yes"> <param name="controlfile" type="data" label="Control peaks" value="Control peaks File" format="bed"/> </when> </conditional> <param name="left" type="integer" label="Step (bp)" value="1000"/> <param name="right" type="integer" label="length of the region +-TSS to consider (bp)" value="50000"/> <conditional name="input_organism"> <param name="input_organism_selector" type="select" label="Select organism"> <option value="Human" selected="true">Homo sapiens</option> <option value="Mouse">Mus musculus</option> <option value="Zebrafish">Zebrafish (Danio rerio)</option> <option value="XTropicalis">X.Tropicalis</option> <option value="Bacteria/MycoTube">M. tuberculosis</option> </param> <when value="Human"> <param name="version" type="select" label="Select genome vesion"> <option value="hg19" selected="true">hg19</option> <option value="hg18">hg18</option> </param> </when> <when value="Mouse"> <param name="version" type="select" label="Select genome vesion"> <option value="mm8" >mm8</option> <option value="mm9" selected="true">mm9</option> <option value="mm10" >mm10</option> </param> </when> <when value="Zebrafish"> <param name="version" type="select" label="Select genome vesion"> <option value="zv9" selected="true">zv9</option> </param> </when> <when value="XTropicalis"> <param name="version" type="select" label="Select genome vesion"> <option value="xenTro2" >xenTro2</option> <option value="xenTro3" selected="true">xenTro3</option> </param> </when> <when value="Bacteria/MycoTube"> <param name="version" type="select" label="Select genome vesion"> <option value="H37Rv" selected="true">H37Rv</option> </param> </when> </conditional> <conditional name="use_reg"> <param name="use_reg_selector" type="select" label="Use transcriptomic data (up- and down- regulated genes)"> <option value="no" selected="true">No</option> <option value="yes">Yes</option> </param> <when value="yes"> <param name="regfile" type="data" label="File with information about gene regulation" value="Regulation data" format="txt"/> </when> </conditional> <param name="if_PDF" type="boolean" label="Do you want to have a PDF image (default PNG)?" truevalue="1" falsevalue="0" checked="False"/> </inputs> <outputs> <data name="outputPNG" format="png" label="Peak location distribution (png)"> <filter>(if_PDF == 0)</filter> </data> <data name="outputPDF" format="pdf" label="Peak location distribution (pdf)"> <filter>(if_PDF == True)</filter> </data> <data name="stats" format="tabular" label="Peak location distribution (stats)"/> </outputs> <help> **What it does** This tool creates a .png file with distribution of peaks around gene TSS </help> </tool>