Mercurial > repos > alermine > nebula
diff [APliBio]Nebula tools suite/Nebula/MakeStatsCHiPSeq/makeStatsChIPSeq_wrapper.xml @ 0:2ec3ba0e9e70 draft
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author | alermine |
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date | Thu, 25 Oct 2012 08:18:25 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/[APliBio]Nebula tools suite/Nebula/MakeStatsCHiPSeq/makeStatsChIPSeq_wrapper.xml Thu Oct 25 08:18:25 2012 -0400 @@ -0,0 +1,36 @@ +<tool id="makeStatsChIPSeq" name="MakeStatsChIPSeq" version="1.0"> + <description>Get peak height distribution</description> + <command interpreter="bash"> +#if str( $ifPDF ) == 'Yes' #makeStatsChIPSeq_wrapper.sh -f $inputfile -c $controlfile -m $minHeight -o $outputPDF -s $maxHeight -u $stats -p 1 #else # makeStatsChIPSeq_wrapper.sh -f $inputfile -c $controlfile -m $minHeight -o $outputPNG -s $maxHeight -u $stats -p 0 #end if + </command> + <inputs> + + <param name="inputfile" type="data" label="ChIP: File with peaks" value="ChIP-Seq File" format="txt"/> + <param name="controlfile" type="data" label="Control: File with peaks" value="Control File" format="txt"/> + <param name="minHeight" type="integer" label="Minimal peak height to consider" value="3"/> + <param name="maxHeight" type="integer" label="Maximal peak height to consider" value="50"/> + + <param name="ifPDF" type="select" label="Do you want to have a PDF image (default PNG)?"> + <option value="No" selected="true">No</option> + <option value="Yes">Yes</option> + </param> + </inputs> + <outputs> + + <data name="stats" format="tabular" label="Peak height distribution (stats)"/> + + <data name="outputPNG" format="png" label="Peak height distribution (png)"> + <filter>(ifPDF == "No")</filter> + </data> + <data name="outputPDF" format="pdf" label="Peak height distribution (pdf)"> + <filter>(ifPDF == "Yes")</filter> + </data> + + </outputs> + <help> +**What it does** + +This tool creates a .png (or .pdf) file with distribution of peaks heights for ChIP and Control sample + + </help> +</tool>