annotate annotatePeaks.xml @ 0:2103c773690f draft

Uploaded
author kevyin
date Fri, 09 Nov 2012 00:53:35 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
2103c773690f Uploaded
kevyin
parents:
diff changeset
1 <tool id="homer_annotatePeaks" name="homer_annotatePeaks" version="0.0.2">
2103c773690f Uploaded
kevyin
parents:
diff changeset
2 <requirements>
2103c773690f Uploaded
kevyin
parents:
diff changeset
3 <requirement type="package">homer</requirement>
2103c773690f Uploaded
kevyin
parents:
diff changeset
4 </requirements>
2103c773690f Uploaded
kevyin
parents:
diff changeset
5 <description></description>
2103c773690f Uploaded
kevyin
parents:
diff changeset
6 <!--<version_command></version_command>-->
2103c773690f Uploaded
kevyin
parents:
diff changeset
7 <command>
2103c773690f Uploaded
kevyin
parents:
diff changeset
8 annotatePeaks.pl $input_bed $genome_selector 1&gt; $out_annotated
2103c773690f Uploaded
kevyin
parents:
diff changeset
9 2&gt; $out_log || echo "Error running annotatePeaks." >&amp;2
2103c773690f Uploaded
kevyin
parents:
diff changeset
10 </command>
2103c773690f Uploaded
kevyin
parents:
diff changeset
11 <inputs>
2103c773690f Uploaded
kevyin
parents:
diff changeset
12 <param format="tabular,bed" name="input_bed" type="data" label="Homer peak positions or BED format" />
2103c773690f Uploaded
kevyin
parents:
diff changeset
13 <param name="genome_selector" type="select" label="Genome version">
2103c773690f Uploaded
kevyin
parents:
diff changeset
14 <option value="hg19" selected="true">hg19</option>
2103c773690f Uploaded
kevyin
parents:
diff changeset
15 </param>
2103c773690f Uploaded
kevyin
parents:
diff changeset
16 </inputs>
2103c773690f Uploaded
kevyin
parents:
diff changeset
17 <outputs>
2103c773690f Uploaded
kevyin
parents:
diff changeset
18 <!--<data format="html" name="html_outfile" label="index" />-->
2103c773690f Uploaded
kevyin
parents:
diff changeset
19 <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />-->
2103c773690f Uploaded
kevyin
parents:
diff changeset
20 <data format="csv" name="out_annotated" label="${tool.name} on #echo os.path.splitext(str($input_bed.name))[0]#_genome_${genome_selector}" />
2103c773690f Uploaded
kevyin
parents:
diff changeset
21 <data format="txt" name="out_log" label="${tool.name} on #echo os.path.splitext(str($input_bed.name))[0]#_genome_${genome_selector}.log" />
2103c773690f Uploaded
kevyin
parents:
diff changeset
22 </outputs>
2103c773690f Uploaded
kevyin
parents:
diff changeset
23 <tests>
2103c773690f Uploaded
kevyin
parents:
diff changeset
24 <test>
2103c773690f Uploaded
kevyin
parents:
diff changeset
25 <!--<param name="input_file" value="extract_genomic_dna.fa" />-->
2103c773690f Uploaded
kevyin
parents:
diff changeset
26 <!--<output name="html_file" file="sample_output.html" ftype="html" />-->
2103c773690f Uploaded
kevyin
parents:
diff changeset
27 </test>
2103c773690f Uploaded
kevyin
parents:
diff changeset
28 </tests>
2103c773690f Uploaded
kevyin
parents:
diff changeset
29
2103c773690f Uploaded
kevyin
parents:
diff changeset
30 <help>
2103c773690f Uploaded
kevyin
parents:
diff changeset
31
2103c773690f Uploaded
kevyin
parents:
diff changeset
32 .. class:: infomark
2103c773690f Uploaded
kevyin
parents:
diff changeset
33
2103c773690f Uploaded
kevyin
parents:
diff changeset
34 **Homer annoatePeaks**
2103c773690f Uploaded
kevyin
parents:
diff changeset
35 More information on accepted formats
2103c773690f Uploaded
kevyin
parents:
diff changeset
36 http://biowhat.ucsd.edu/homer/ngs/annotation.html
2103c773690f Uploaded
kevyin
parents:
diff changeset
37
2103c773690f Uploaded
kevyin
parents:
diff changeset
38
2103c773690f Uploaded
kevyin
parents:
diff changeset
39 </help>
2103c773690f Uploaded
kevyin
parents:
diff changeset
40 </tool>
2103c773690f Uploaded
kevyin
parents:
diff changeset
41