0
|
1 <tool id="makeStatsChIPSeq" name="MakeStatsChIPSeq" version="1.0">
|
|
2 <description>Get peak height distribution</description>
|
|
3 <command interpreter="bash">
|
|
4 #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
|
|
5 </command>
|
|
6 <inputs>
|
|
7
|
|
8 <param name="inputfile" type="data" label="ChIP: File with peaks" value="ChIP-Seq File" format="txt"/>
|
|
9 <param name="controlfile" type="data" label="Control: File with peaks" value="Control File" format="txt"/>
|
|
10 <param name="minHeight" type="integer" label="Minimal peak height to consider" value="3"/>
|
|
11 <param name="maxHeight" type="integer" label="Maximal peak height to consider" value="50"/>
|
|
12
|
|
13 <param name="ifPDF" type="select" label="Do you want to have a PDF image (default PNG)?">
|
|
14 <option value="No" selected="true">No</option>
|
|
15 <option value="Yes">Yes</option>
|
|
16 </param>
|
|
17 </inputs>
|
|
18 <outputs>
|
|
19
|
|
20 <data name="stats" format="tabular" label="Peak height distribution (stats)"/>
|
|
21
|
|
22 <data name="outputPNG" format="png" label="Peak height distribution (png)">
|
|
23 <filter>(ifPDF == "No")</filter>
|
|
24 </data>
|
|
25 <data name="outputPDF" format="pdf" label="Peak height distribution (pdf)">
|
|
26 <filter>(ifPDF == "Yes")</filter>
|
|
27 </data>
|
|
28
|
|
29 </outputs>
|
|
30 <help>
|
|
31 **What it does**
|
|
32
|
|
33 This tool creates a .png (or .pdf) file with distribution of peaks heights for ChIP and Control sample
|
|
34
|
|
35 </help>
|
|
36 </tool>
|