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author matt-shirley
date Tue, 27 Nov 2012 13:38:25 -0500
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2:39dab3a4578b 3:0031b2d2e80b
1 <tool id="sam_dump" name="Extract SAM" version="1.0.0">
2 <description> format reads from NCBI SRA.</description>
3 <command>sam-dump $header $aligned $primary '$input' > $output</command>
4 <version_string>sam-dump --version</version_string>
5 <inputs>
6 <param format="sra" name="input" type="data" label="sra archive"/>
7 <param format="text" name="header" type="select" value="">
8 <label>Output SAM header</label>
9 <option value="--header">Yes</option>
10 <option value="--no-header">No</option>
11 </param>
12 <param format="text" name="aligned" type="select" value="">
13 <label>Output unaligned reads</label>
14 <option value="">No</option>
15 <option value="--unaligned">Yes</option>
16 </param>
17 <param format="text" name="primary" type="select" value="">
18 <label>Output only primary aligments</label>
19 <option value="">No</option>
20 <option value="--primary">Yes</option>
21 </param>
22 </inputs>
23 <outputs>
24 <data format="sam" name="output"/>
25 </outputs>
26 <requirements>
27 <requirement type="binary">sam-dump</requirement>
28 </requirements>
29 <help>
30 This tool extracts SAM format reads from SRA archives using sam-dump. The sam-dump program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software.
31 Contact Matt Shirley at mdshw5@gmail.com for support and bug reports.
32 </help>
33 </tool>