Mercurial > repos > matt-shirley > fastq_dump

changeset 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
files fastq_dump.xml
diffstat 1 files changed, 1 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/fastq_dump.xml	Mon Nov 12 19:55:41 2012 -0500
+++ b/fastq_dump.xml	Tue Nov 13 12:02:29 2012 -0500
@@ -1,6 +1,6 @@
 <tool id="fastq_dump" name="Extract fastq from SRA" version="1.0.0">
   <description>Extract fastq format reads from SRA data archive.</description>
-  <command>fastq-dump --stdout $split $aligned $input > $output </command>
+  <command>fastq-dump --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"/>