Mercurial > repos > kevyin > homer
comparison makeTagDirectory.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_makeTagDirectory" name="homer_makeTagDirectory" version="1.0.1"> | |
2 <requirements> | |
3 <requirement type="package" version="4.1">homer</requirement> | |
4 </requirements> | |
5 <description>Simple wrapper for makeTagDirectory. Used by findPeaks</description> | |
6 <!--<version_command></version_command>--> | |
7 <command interpreter="python">makeTagDirectory.py ${tagDir.files_path} | |
8 #for $alignF in $alignmentFiles | |
9 $alignF.file -f $alignF.file.ext | |
10 #end for | |
11 -o $tagDir | |
12 2> $out_log || echo "Error running homer_makeTagDirectory." >&2 | |
13 | |
14 </command> | |
15 <inputs> | |
16 <param name="title" label="Name for the output tag directory" type="text" default="Homer TagDirectory" /> | |
17 <param type="text" name="options" label="Extra options" value="" help="Go to link below for more options"> | |
18 <sanitizer> | |
19 <valid initial="string.printable"> | |
20 <remove value="'"/> | |
21 <remove value="/"/> | |
22 </valid> | |
23 <mapping initial="none"> | |
24 <add source="'" target="__sq__"/> | |
25 </mapping> | |
26 </sanitizer> | |
27 </param> | |
28 <repeat name="alignmentFiles" title="Alignment Files"> | |
29 <param name="file" label="Add file" type="data" format="sam,bed" /> | |
30 </repeat> | |
31 </inputs> | |
32 <outputs> | |
33 <!--<data format="homerTagDirectory" name="tagDir" label="${title} tag directory" />--> | |
34 <data format="html" name="tagDir" label="${title} tag directory" /> | |
35 <data format="txt" name="out_log" label="${title}.log" /> | |
36 <!--<data format="html" name="html_outfile" label="index" />--> | |
37 <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />--> | |
38 </outputs> | |
39 | |
40 | |
41 <tests> | |
42 <!--<test>--> | |
43 <!--<param name="input_file" value="extract_genomic_dna.fa" />--> | |
44 <!--<output name="html_file" file="sample_output.html" ftype="html" />--> | |
45 <!--</test>--> | |
46 </tests> | |
47 | |
48 <help> | |
49 | |
50 .. class:: infomark | |
51 | |
52 **Homer makeTagDirectory** | |
53 | |
54 For more options, look under: "Command line options" | |
55 | |
56 http://biowhat.ucsd.edu/homer/ngs/tagDir.html | |
57 | |
58 | |
59 </help> | |
60 </tool> | |
61 |