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comparison findPeaks.xml @ 6:d8e7cd329afb draft

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author kevyin
date Thu, 13 Dec 2012 23:43:26 -0500
parents 74c1fc7bb164
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5:8cfd322a5907 6:d8e7cd329afb
1 <tool id="homer_findPeaks" name="homer_findPeaks" version="0.1.0">
2 <requirements>
3 <requirement type="package">homer</requirement>
4 </requirements>
5 <description>Homer's peakcaller. Requires tag directories (see makeTagDirectory)</description>
6 <!--<version_command></version_command>-->
7 <command>
8 findPeaks $tagDir.extra_files_path $options -o $outputPeakFile
9
10 #if $control_tagDir:
11 -i $control_tagDir.extra_files_path
12 #end if
13
14 2&gt; $out_log || echo "Error running findPeaks." >&amp;2
15 </command>
16 <inputs>
17 <param format="homerTagDirectory" name="tagDir" type="data" label="tag directory" />
18 <param format="homerTagDirectory" name="control_tagDir" type="data" optional="True" label="Control tag directory" />
19 <param type="text" name="options" label="Extra options" value="" >
20 <sanitizer>
21 <valid initial="string.printable">
22 <remove value="&apos;"/>
23 </valid>
24 <mapping initial="none">
25 <add source="&apos;" target="__sq__"/>
26 </mapping>
27 </sanitizer>
28 </param>
29 </inputs>
30 <outputs>
31 <!--<data format="html" name="html_outfile" label="index" />-->
32 <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />-->
33 <data format="txt" name="outputPeakFile" label="${tool.name} on #echo os.path.splitext(str($tagDir.name))[0]#.txt" />
34 <data format="txt" name="out_log" label="${tool.name} on #echo os.path.splitext(str($tagDir.name))[0]#.log" />
35 </outputs>
36 <tests>
37 <test>
38 <!--<param name="input_file" value="extract_genomic_dna.fa" />-->
39 <!--<output name="html_file" file="sample_output.html" ftype="html" />-->
40 </test>
41 </tests>
42
43 <help>
44
45 .. class:: infomark
46
47 **Homer findPeaks**
48 http://biowhat.ucsd.edu/homer/ngs/peaks.html
49
50 </help>
51 </tool>
52