# HG changeset patch
# User Matthew Shirley <mdshw5@gmail.com>
# Date 1352826149 18000
# Node ID 5b83155a24f4839e654cdcf897d2248c419a2b64
# Parent  4c06e5b586626f7a76d7422b7ff7ed2ebb9bbfac
Using proper accession string for read deflines.

diff -r 4c06e5b58662 -r 5b83155a24f4 fastq_dump.xml
--- 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"/>