annotate bed2pos.xml @ 24:b3b65304ee72 draft

Uploaded
author kevyin
date Thu, 20 Dec 2012 17:52:56 -0500
parents 4356089c8e7f
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
12
4356089c8e7f Uploaded
kevyin
parents:
diff changeset
1 <tool id="homer_bed2pos" name="homer_bed2pos" version="0.0.3">
4356089c8e7f Uploaded
kevyin
parents:
diff changeset
2 <requirements>
4356089c8e7f Uploaded
kevyin
parents:
diff changeset
3 <requirement type="package" version="4.1">homer</requirement>
4356089c8e7f Uploaded
kevyin
parents:
diff changeset
4 </requirements>
4356089c8e7f Uploaded
kevyin
parents:
diff changeset
5 <description></description>
4356089c8e7f Uploaded
kevyin
parents:
diff changeset
6 <!--<version_command></version_command>-->
4356089c8e7f Uploaded
kevyin
parents:
diff changeset
7 <command>
4356089c8e7f Uploaded
kevyin
parents:
diff changeset
8 bed2pos.pl $input_bed 1&gt; $out_pos
4356089c8e7f Uploaded
kevyin
parents:
diff changeset
9 2&gt; $out_log || echo "Error running bed2pos." >&amp;2
4356089c8e7f Uploaded
kevyin
parents:
diff changeset
10 </command>
4356089c8e7f Uploaded
kevyin
parents:
diff changeset
11 <inputs>
4356089c8e7f Uploaded
kevyin
parents:
diff changeset
12 <param format="tabular,bed" name="input_bed" type="data" label="BED file" />
4356089c8e7f Uploaded
kevyin
parents:
diff changeset
13 </inputs>
4356089c8e7f Uploaded
kevyin
parents:
diff changeset
14 <outputs>
4356089c8e7f Uploaded
kevyin
parents:
diff changeset
15 <!--<data format="html" name="html_outfile" label="index" />-->
4356089c8e7f Uploaded
kevyin
parents:
diff changeset
16 <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />-->
4356089c8e7f Uploaded
kevyin
parents:
diff changeset
17 <data format="tabular" name="out_pos" label="${tool.name} on #echo os.path.splitext(str($input_bed.name))[0]#" />
4356089c8e7f Uploaded
kevyin
parents:
diff changeset
18 <data format="txt" name="out_log" label="${tool.name} on #echo os.path.splitext(str($input_bed.name))[0]#.log" />
4356089c8e7f Uploaded
kevyin
parents:
diff changeset
19 </outputs>
4356089c8e7f Uploaded
kevyin
parents:
diff changeset
20 <tests>
4356089c8e7f Uploaded
kevyin
parents:
diff changeset
21 <test>
4356089c8e7f Uploaded
kevyin
parents:
diff changeset
22 <!--<param name="input_file" value="extract_genomic_dna.fa" />-->
4356089c8e7f Uploaded
kevyin
parents:
diff changeset
23 <!--<output name="html_file" file="sample_output.html" ftype="html" />-->
4356089c8e7f Uploaded
kevyin
parents:
diff changeset
24 </test>
4356089c8e7f Uploaded
kevyin
parents:
diff changeset
25 </tests>
4356089c8e7f Uploaded
kevyin
parents:
diff changeset
26
4356089c8e7f Uploaded
kevyin
parents:
diff changeset
27 <help>
4356089c8e7f Uploaded
kevyin
parents:
diff changeset
28 .. class:: infomark
4356089c8e7f Uploaded
kevyin
parents:
diff changeset
29
4356089c8e7f Uploaded
kevyin
parents:
diff changeset
30 Converts: BED -(to)-> homer peak positions
4356089c8e7f Uploaded
kevyin
parents:
diff changeset
31
4356089c8e7f Uploaded
kevyin
parents:
diff changeset
32 **Homer bed2pos.pl**
4356089c8e7f Uploaded
kevyin
parents:
diff changeset
33
4356089c8e7f Uploaded
kevyin
parents:
diff changeset
34 http://biowhat.ucsd.edu/homer/ngs/miscellaneous.html
4356089c8e7f Uploaded
kevyin
parents:
diff changeset
35 </help>
4356089c8e7f Uploaded
kevyin
parents:
diff changeset
36 </tool>
4356089c8e7f Uploaded
kevyin
parents:
diff changeset
37