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comparison sam_dump.xml @ 1:d1dc85d3e490 draft

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Edited description and requirements.
author Matthew Shirley <mdshw5@gmail.com>
date Tue, 13 Nov 2012 16:31:44 -0500
parents c2995e659548
children 39dab3a4578b
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0:c2995e659548 1:d1dc85d3e490
1 <tool id="sam_dump" name="Extract SAM from SRA" version="1.0.0"> 1 <tool id="sam_dump" name="Extract SAM" version="1.0.0">
2 <description>Extract SAM format reads from SRA data archive.</description> 2 <description> format reads from NCBI SRA.</description>
3 <command>sam-dump $header $aligned $primary $input > $output</command> 3 <command>sam-dump $header $aligned $primary $input > $output</command>
4 <version_string>sam-dump --version</version_string> 4 <version_string>sam-dump --version</version_string>
5 <inputs> 5 <inputs>
6 <param format="sra" name="input" type="data" label="sra archive"/> 6 <param format="sra" name="input" type="data" label="sra archive"/>
7 <param format="text" name="header" type="select" value=""> 7 <param format="text" name="header" type="select" value="">
21 </param> 21 </param>
22 </inputs> 22 </inputs>
23 <outputs> 23 <outputs>
24 <data format="sam" name="output"/> 24 <data format="sam" name="output"/>
25 </outputs> 25 </outputs>
26 <requirements>
27 <requirement type="binary">sam-dump</requirement>
28 </requirements>
26 <help> 29 <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. 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.
28 Contact Matt Shirley at mdshw5@gmail.com for support and bug reports. 31 Contact Matt Shirley at mdshw5@gmail.com for support and bug reports.
29 </help> 32 </help>
30 </tool> 33 </tool>