Mercurial > repos > matt-shirley > fastq_dump
changeset 5:73656a524d45 draft
Bug fix for error handling.
| author | matt-shirley <mdshw5@gmail.com. |
|---|---|
| date | Thu, 15 Nov 2012 10:50:03 -0500 |
| parents | 6baa258e80f0 |
| children | 7a9ddfd55d71 |
| files | fastq_dump.xml |
| diffstat | 1 files changed, 2 insertions(+), 2 deletions(-) [+] |
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--- 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>