Mercurial > repos > matt-shirley > sra_tools
view fastq_dump.xml @ 22:423f3eb06428 draft
more fixes for sra datatype, added sra_pileup
author | Matt Shirley <mdshw5@gmail.com> |
---|---|
date | Wed, 19 Jun 2013 14:11:37 -0400 |
parents | d850324e82cf |
children | 5f57967aac3e |
line wrap: on
line source
<tool id="fastq_dump" name="Extract fastq" version="1.0.2"> <description> format reads from NCBI sra.</description> <command>fastq-dump --log-level fatal --accession '${input.name}' --stdout $split $aligned '$input' > $output </command> <version_string>fastq-dump --version</version_string> <inputs> <param format="sra" name="input" type="data" label="sra archive"/> <param format="text" name="split" type="select" value=""> <label>Split read pairs</label> <option value="">No</option> <option value="--split-spot">Yes</option> </param> <param format="text" name="aligned" type="select" value=""> <label>Specify alignment</label> <option value="">All</option> <option value="--aligned">Only aligned</option> <option value="--unaligned">Only unaligned</option> </param> </inputs> <outputs> <data format="fastqsanger" name="output"/> </outputs> <stdio> <exit_code range="127" level="fatal" description="Cannot find fastq-dump binary"/> </stdio> <requirements> <requirement type="package" version="2.3.2-4">sra_toolkit</requirement> </requirements> <help> This tool extracts fastq format reads from sra archives using fastq-dump. The fastq-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>