Mercurial > repos > matt-shirley > fastq_dump
comparison fastq_dump.xml @ 0:ba892201bdad draft
Wrote a wrapper for NCBI fastq-dump. Initial version.
| author | Matthew Shirley <mdshw5@gmail.com> |
|---|---|
| date | Mon, 12 Nov 2012 16:50:47 -0500 |
| parents | |
| children | 4c06e5b58662 |
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| -1:000000000000 | 0:ba892201bdad |
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| 1 <tool id="fastq_dump" name="Extract fastq from SRA" version="1.0.0"> | |
| 2 <description>Extract fastq format reads from SRA data archive.</description> | |
| 3 <command>fastq-dump --stdout $split $aligned $input > $output </command> | |
| 4 <version_string>fastq-dump --version</version_string> | |
| 5 <inputs> | |
| 6 <param format="sra" name="input" type="data" label="sra archive"/> | |
| 7 <param format="text" name="split" type="select" value=""> | |
| 8 <label>Split read pairs</label> | |
| 9 <option value="">No</option> | |
| 10 <option value="--split-spot">Yes</option> | |
| 11 </param> | |
| 12 <param format="text" name="split" type="select" value=""> | |
| 13 <label>Specify alignment</label> | |
| 14 <option value="">All</option> | |
| 15 <option value="--aligned">Only aligned</option> | |
| 16 <option value="--unaligned">Only unaligned</option> | |
| 17 </param> | |
| 18 </inputs> | |
| 19 <outputs> | |
| 20 <data format="fastqsanger" name="output"/> | |
| 21 </outputs> | |
| 22 <help> | |
| 23 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. | |
| 24 </help> | |
| 25 </tool> |