Mercurial > repos > kevyin > homer
comparison findPeaks.xml @ 12:4356089c8e7f draft
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author | kevyin |
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date | Mon, 17 Dec 2012 00:25:28 -0500 |
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11:83dffd6d7733 | 12:4356089c8e7f |
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1 <tool id="homer_findPeaks" name="homer_findPeaks" version="0.1.2"> | |
2 <requirements> | |
3 <requirement type="package" version="4.1">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> $out_log || echo "Error running findPeaks." >&2 | |
15 </command> | |
16 <inputs> | |
17 <param format="homerTagDirectory" name="tagDir" type="data" label="tag directory" help="Must be made with homer_makeTagDirectory" /> | |
18 <param format="homerTagDirectory" name="control_tagDir" type="data" optional="True" label="Control tag directory" help="Must be made with homer_makeTagDirectory" /> | |
19 <param type="text" name="options" label="Extra options" value="" help="Go to link below for more options"> | |
20 <sanitizer> | |
21 <valid initial="string.printable"> | |
22 <remove value="'"/> | |
23 <remove value="/"/> | |
24 </valid> | |
25 <mapping initial="none"> | |
26 <add source="'" target="__sq__"/> | |
27 </mapping> | |
28 </sanitizer> | |
29 </param> | |
30 </inputs> | |
31 <outputs> | |
32 <!--<data format="html" name="html_outfile" label="index" />--> | |
33 <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />--> | |
34 <data format="txt" name="outputPeakFile" label="${tool.name} on #echo os.path.splitext(str($tagDir.name))[0]#.txt" /> | |
35 <data format="txt" name="out_log" label="${tool.name} on #echo os.path.splitext(str($tagDir.name))[0]#.log" /> | |
36 </outputs> | |
37 <tests> | |
38 <test> | |
39 <!--<param name="input_file" value="extract_genomic_dna.fa" />--> | |
40 <!--<output name="html_file" file="sample_output.html" ftype="html" />--> | |
41 </test> | |
42 </tests> | |
43 | |
44 <help> | |
45 | |
46 .. class:: infomark | |
47 | |
48 **Homer findPeaks** | |
49 | |
50 For more options, look under: "Command line options for findPeaks" | |
51 | |
52 http://biowhat.ucsd.edu/homer/ngs/peaks.html | |
53 | |
54 TIP: use homer_bed2pos and homer_pos2bed to convert between the homer peak positions and the BED format. | |
55 | |
56 </help> | |
57 </tool> | |
58 |