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First version of sam-dump wrapper. Implemented options for filtering output by alignment status and options for output of sam header.
author mdshw5@gmail.com
date Tue, 13 Nov 2012 14:36:38 -0500
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children d1dc85d3e490
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-1:000000000000 0:c2995e659548
1 <tool id="sam_dump" name="Extract SAM from SRA" version="1.0.0">
2 <description>Extract SAM format reads from SRA data archive.</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 <help>
27 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.
28 Contact Matt Shirley at mdshw5@gmail.com for support and bug reports.
29 </help>
30 </tool>