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comparison fastq_dump.xml @ 2:5b83155a24f4 draft

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Using proper accession string for read deflines.
author Matthew Shirley <mdshw5@gmail.com>
date Tue, 13 Nov 2012 12:02:29 -0500
parents 4c06e5b58662
children f6bc4bdbd528
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1:4c06e5b58662 2:5b83155a24f4
1 <tool id="fastq_dump" name="Extract fastq from SRA" version="1.0.0"> 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> 2 <description>Extract fastq format reads from SRA data archive.</description>
3 <command>fastq-dump --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="">
8 <label>Split read pairs</label> 8 <label>Split read pairs</label>