Mercurial > repos > matt-shirley > sra_tools
comparison fastq_dump.xml @ 0:cdcc400dcafc draft
Migrated separate tools fastq_dump, sam_dump, and sra_fetch to this repository for further development.
| author | matt-shirley <mdshw5@gmail.com> |
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| date | Tue, 27 Nov 2012 13:31:09 -0500 |
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| -1:000000000000 | 0:cdcc400dcafc |
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| 1 <tool id="fastq_dump" name="Extract fastq" version="1.0.0"> | |
| 2 <description> format reads from NCBI SRA.</description> | |
| 3 <command>./fastq-dump --log-level fatal --report never --accession '${input.name}' --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="aligned" 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 <stdio> | |
| 23 <exit_code range="127" level="fatal" description="Cannot find fastq-dump binary"/> | |
| 24 </stdio> | |
| 25 <requirements> | |
| 26 <requirement type="binary">fastq-dump</requirement> | |
| 27 </requirements> | |
| 28 <help> | |
| 29 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. | |
| 30 </help> | |
| 31 </tool> |