Mercurial > repos > matt-shirley > sra_tools
view fastq_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 | a1255154fa3f |
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<tool id="fastq_dump" name="Extract fastq" version="1.0.1"> <description> format reads from NCBI SRA.</description> <command>fastq-dump --log-level fatal --report never --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 fastqsanger 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. </help> </tool>