comparison annotatePeaks.xml @ 12:4356089c8e7f draft

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author kevyin
date Mon, 17 Dec 2012 00:25:28 -0500
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11:83dffd6d7733 12:4356089c8e7f
1 <tool id="homer_annotatePeaks" name="homer_annotatePeaks" version="0.0.4">
2 <requirements>
3 <requirement type="package" version="4.1">homer</requirement>
4 </requirements>
5 <description></description>
6 <!--<version_command></version_command>-->
7 <command>
8 annotatePeaks.pl $input_bed $genome_selector 1&gt; $out_annotated
9 2&gt; $out_log || echo "Error running annotatePeaks." >&amp;2
10 </command>
11 <inputs>
12 <param format="tabular,bed" name="input_bed" type="data" label="Homer peaks OR BED format"/>
13 <param name="genome_selector" type="select" label="Genome version">
14 <option value="hg19" selected="true">hg19</option>
15 </param>
16 <param type="text" name="options" label="Extra options" value="" help="Go to link below for more options">
17 <sanitizer>
18 <valid initial="string.printable">
19 <remove value="&apos;"/>
20 <remove value="/"/>
21 </valid>
22 <mapping initial="none">
23 <add source="&apos;" target="__sq__"/>
24 </mapping>
25 </sanitizer>
26 </param>
27 </inputs>
28 <outputs>
29 <!--<data format="html" name="html_outfile" label="index" />-->
30 <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />-->
31 <data format="csv" name="out_annotated" label="${tool.name} on #echo os.path.splitext(str($input_bed.name))[0]#_genome_${genome_selector}" />
32 <data format="txt" name="out_log" label="${tool.name} on #echo os.path.splitext(str($input_bed.name))[0]#_genome_${genome_selector}.log" />
33 </outputs>
34 <tests>
35 <test>
36 <!--<param name="input_file" value="extract_genomic_dna.fa" />-->
37 <!--<output name="html_file" file="sample_output.html" ftype="html" />-->
38 </test>
39 </tests>
40
41 <help>
42
43 .. class:: infomark
44
45 **Homer annoatePeaks**
46
47 More information on accepted formats and options
48
49 http://biowhat.ucsd.edu/homer/ngs/annotation.html
50
51 TIP: use homer_bed2pos and homer_pos2bed to convert between the homer peak positions and the BED format.
52
53 </help>
54 </tool>
55