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comparison sra_tools-04cc8176e86f/sra_pileup.xml @ 0:c386fe82db82

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Initial commit, moving from test tool shed.
author matt-shirley
date Wed, 25 Sep 2013 21:00:05 -0400
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1 <tool id="sra_pileup" name="Generate pileup format" version="1.1.1">
2 <description> from NCBI sra.</description>
3 <command>sra-pileup --log-level fatal
4 #if str( $region ) != "":
5 --aligned-region $region
6 #end if
7 #if str( $minMapq ) != "":
8 --minmapq $minMapq
9 #end if
10 #if $input.input_select == "file":
11 $input.file
12 #elif $input.input_select == "accession_number":
13 $input.accession
14 #elif $input.input_select == "text":
15 `cat $input.text`
16 #end if
17 > $output</command>
18 <version_string>sra-pileup --version</version_string>
19 <inputs>
20 <conditional name="input">
21 <param name="input_select" type="select" label="select input type">
22 <option value="accession_number">SRR accession</option>
23 <option value="file">SRA archive in current history</option>
24 <option value="text">text file containing SRR accession</option>
25 </param>
26 <when value="file">
27 <param format="sra" name="file" type="data" label="sra archive"/>
28 </when>
29 <when value="accession_number">
30 <param format="text" name="accession" type="text" label="accession"/>
31 </when>
32 <when value="text">
33 <param format="txt" name="text" type="data" label="text file"/>
34 </when>
35 </conditional>
36 <param format="text" name="region" type="text" label="aligned region"/>
37 <param format="text" name="minMapq" type="text" label="minimum mapping quality"/>
38 </inputs>
39 <outputs>
40 <data format="pileup" name="output"/>
41 </outputs>
42 <requirements>
43 <requirement type="package" version="2.3.3-3">sra_toolkit</requirement>
44 </requirements>
45 <help>
46 This tool produces pileup format from sra archives using sra-pileup.
47 Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies.
48 The sra-pileup program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software.
49 Contact Matt Shirley at mdshw5@gmail.com for support and bug reports.
50 </help>
51 </tool>