# HG changeset patch
# User matt-shirley <mdshw5@gmail.com.
# Date 1352994603 18000
# Node ID 73656a524d45c7af4103e61f77b849ce8dc1e4f4
# Parent  6baa258e80f02dd92af89287a169cc39d80bd0b4
Bug fix for error handling.

diff -r 6baa258e80f0 -r 73656a524d45 fastq_dump.xml
--- a/fastq_dump.xml	Wed Nov 14 16:55:17 2012 -0500
+++ b/fastq_dump.xml	Thu Nov 15 10:50:03 2012 -0500
@@ -1,6 +1,6 @@
 <tool id="fastq_dump" name="Extract fastq" version="1.0.0">
   <description> format reads from NCBI SRA.</description>
-  <command>fastq-dump --log-level fatal --report never --accession '${input.name}' --stdout $split $aligned '$input' > $output </command>
+  <command>./fastq-dump --log-level fatal --report never --accession '${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"/>
@@ -20,7 +20,7 @@
     <data format="fastqsanger" name="output"/>
   </outputs>
   <stdio>
-    <exit_code range="2:" level="fatal" description="Check input dataset"/>
+    <exit_code range="127" level="fatal" description="Cannot find fastq-dump binary"/>
   </stdio>
   <requirements>
     <requirement type="binary">fastq-dump</requirement>