Mercurial > repos > matt-shirley > sam_dump
changeset 0:c2995e659548 draft
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 |
| parents | |
| children | d1dc85d3e490 |
| files | sam_dump.xml |
| diffstat | 1 files changed, 30 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sam_dump.xml Tue Nov 13 14:36:38 2012 -0500 @@ -0,0 +1,30 @@ +<tool id="sam_dump" name="Extract SAM from SRA" version="1.0.0"> + <description>Extract SAM format reads from SRA data archive.</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</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> + <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>