Mercurial > repos > matt-shirley > sra_tools
view sam_dump.xml @ 13:45031bbf6b27 draft
better sra_fetch code, compliant (?) datatype, updated dependencies in tool wrappers
author | Matt Shirley <mdshw5@gmail.com> |
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date | Mon, 17 Jun 2013 16:17:33 -0400 |
parents | cdba74ec9eca |
children | d850324e82cf |
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<tool id="sam_dump" name="Extract SAM" version="1.0.1"> <description> format reads from NCBI SRA.</description> <command>sam-dump $header $aligned $primary '$input' > $output</command> <version_string>sam-dump --version</version_string> <inputs> <param format="sra" name="input" type="data" label="sra archive"/> <param format="text" name="header" type="select" value=""> <label>Output SAM header</label> <option value="--header">Yes</option> <option value="--no-header">No</option> </param> <param format="text" name="aligned" type="select" value=""> <label>Output unaligned reads as well as aligned reads</label> <option value="">No</option> <option value="--unaligned">Yes</option> </param> <param format="text" name="primary" type="select" value=""> <label>Output only primary aligments</label> <option value="">No</option> <option value="--primary">Yes</option> </param> </inputs> <outputs> <data format="sam" name="output"/> </outputs> <requirements> <requirement type="package" version="2.3.2-4">sra_toolkit</requirement> </requirements> <help> 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. Contact Matt Shirley at mdshw5@gmail.com for support and bug reports. </help> </tool>