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comparison fastq_dump.xml @ 3:f6bc4bdbd528 draft

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Edited description and requirements.
author Matthew Shirley <mdshw5@gmail.com>
date Tue, 13 Nov 2012 16:29:47 -0500
parents 5b83155a24f4
children 6baa258e80f0
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2:5b83155a24f4 3:f6bc4bdbd528
1 <tool id="fastq_dump" name="Extract fastq from SRA" version="1.0.0"> 1 <tool id="fastq_dump" name="Extract fastq" version="1.0.0">
2 <description>Extract fastq format reads from SRA data archive.</description> 2 <description> format reads from NCBI SRA.</description>
3 <command>fastq-dump --accession ${input.name} --stdout $split $aligned $input > $output </command> 3 <command>fastq-dump --accession ${input.name} --stdout $split $aligned $input > $output </command>
4 <version_string>fastq-dump --version</version_string> 4 <version_string>fastq-dump --version</version_string>
5 <inputs> 5 <inputs>
6 <param format="sra" name="input" type="data" label="sra archive"/> 6 <param format="sra" name="input" type="data" label="sra archive"/>
7 <param format="text" name="split" type="select" value=""> 7 <param format="text" name="split" type="select" value="">
17 </param> 17 </param>
18 </inputs> 18 </inputs>
19 <outputs> 19 <outputs>
20 <data format="fastqsanger" name="output"/> 20 <data format="fastqsanger" name="output"/>
21 </outputs> 21 </outputs>
22 <requirements>
23 <requirement type="binary">fastq-dump</requirement>
24 </requirements>
22 <help> 25 <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. 26 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> 27 </help>
25 </tool> 28 </tool>