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comparison annotatePeaks.xml @ 0:2103c773690f draft

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author kevyin
date Fri, 09 Nov 2012 00:53:35 -0500
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1 <tool id="homer_annotatePeaks" name="homer_annotatePeaks" version="0.0.2">
2 <requirements>
3 <requirement type="package">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; $out_log || echo "Error running annotatePeaks." >&amp;2
10 </command>
11 <inputs>
12 <param format="tabular,bed" name="input_bed" type="data" label="Homer peak positions or BED format" />
13 <param name="genome_selector" type="select" label="Genome version">
14 <option value="hg19" selected="true">hg19</option>
15 </param>
16 </inputs>
17 <outputs>
18 <!--<data format="html" name="html_outfile" label="index" />-->
19 <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />-->
20 <data format="csv" name="out_annotated" label="${tool.name} on #echo os.path.splitext(str($input_bed.name))[0]#_genome_${genome_selector}" />
21 <data format="txt" name="out_log" label="${tool.name} on #echo os.path.splitext(str($input_bed.name))[0]#_genome_${genome_selector}.log" />
22 </outputs>
23 <tests>
24 <test>
25 <!--<param name="input_file" value="extract_genomic_dna.fa" />-->
26 <!--<output name="html_file" file="sample_output.html" ftype="html" />-->
27 </test>
28 </tests>
29
30 <help>
31
32 .. class:: infomark
33
34 **Homer annoatePeaks**
35 More information on accepted formats
36 http://biowhat.ucsd.edu/homer/ngs/annotation.html
37
38
39 </help>
40 </tool>
41