Mercurial > repos > matt-shirley > fastq_dump

changeset 4:6baa258e80f0 draft

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Bug fixes
author Matthew Shirley <mdshw5@gmail.com>
date Wed, 14 Nov 2012 16:55:17 -0500
parents f6bc4bdbd528
children 73656a524d45
files fastq_dump.xml
diffstat 1 files changed, 4 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/fastq_dump.xml	Tue Nov 13 16:29:47 2012 -0500
+++ b/fastq_dump.xml	Wed Nov 14 16:55:17 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 --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"/>
@@ -19,6 +19,9 @@
   <outputs>
     <data format="fastqsanger" name="output"/>
   </outputs>
+  <stdio>
+    <exit_code range="2:" level="fatal" description="Check input dataset"/>
+  </stdio>
   <requirements>
     <requirement type="binary">fastq-dump</requirement>
   </requirements>