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comparison pos2bed.xml @ 2:7268cbc535e5 draft

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findpeaks and maketagdirectory
author kevyin
date Fri, 23 Nov 2012 00:30:27 -0500
parents 2103c773690f
children
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1:59d58008c40d 2:7268cbc535e5
1 <tool id="homer_pos2bed" name="homer_pos2bed" 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 pos2bed.pl $input_peak 1&gt; $out_bed
9 2&gt; $out_log || echo "Error running pos2bed." >&amp;2
10 </command>
11 <inputs>
12 <param format="tabular" name="input_peak" type="data" label="Homer peak positions" />
13 </inputs>
14 <outputs>
15 <!--<data format="html" name="html_outfile" label="index" />-->
16 <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />-->
17 <data format="bed" name="out_bed" label="${tool.name} on #echo os.path.splitext(str($input_peak.name))[0]#.bed" />
18 <data format="txt" name="out_log" label="${tool.name} on #echo os.path.splitext(str($input_peak.name))[0]#.log" />
19 </outputs>
20 <tests>
21 <test>
22 <!--<param name="input_file" value="extract_genomic_dna.fa" />-->
23 <!--<output name="html_file" file="sample_output.html" ftype="html" />-->
24 </test>
25 </tests>
26
27 <help>
28 .. class:: infomark
29
30 **Homer pos2bed.pl**
31 http://biowhat.ucsd.edu/homer/ngs/miscellaneous.html
32 </help>
33 </tool>
34