Two things - if you really want to just hide standard output - you can use the XML CDATA idiom to eliminate the need for escaping < and >.
<command><![CDATA[ comand > /dev/null ]]></command
If you want to allow the standard error to just be printed and use the exit code of the tool to determine whether the job has failed - you can add the following block to your tool XML:
<stdio> <exit_code range="1:" /> </stdio>
I think this is a saner default and I would just add this block to all new tools.
You may want to check out the planemo tool builder - it will bootstrap new tool definitions that do both of these (use CDATA for the command and set a default stdio).
http://planemo.readthedocs.org/en/latest/writing_standalone.html
Hope this helps.
-John
On Thu, Apr 16, 2015 at 6:55 AM, Roberto Alonso CIPF ralonso@cipf.es wrote:
Hello,
I am defining some tools for my own galaxy installation and I would like to know if there is a more elegant solution for redirecting error output than the one in the next config file:
<tool id="gatk_mio" name="calling with gatk"> <description>calling with gatk</description> <command> ln -s "${input}" input.bam ; samtools index input.bam; java -jar /home/ralonso/software/GenomeAnalysisTK-3.3-0/GenomeAnalysisTK.jar -T UnifiedGenotyper -R /home/ralonso/BiB/Galaxy/data/Cclementina_v1.0_scaffolds.fa -I input.bam -o $output 2>/dev/null; </command>
<inputs> <param format="bam" name="input" type="data" label="bam"/> </inputs> <outputs> <data format="vcf" name="output" /> </outputs>
<help> bwa </help>
</tool>
Best regards
many thanks
-- Roberto Alonso Functional Genomics Unit Bioinformatics and Genomics Department Prince Felipe Research Center (CIPF) C./Eduardo Primo Yúfera (Científic), nº 3 (junto Oceanografico) 46012 Valencia, Spain Tel: +34 963289680 Ext. 1021 Fax: +34 963289574 E-Mail: ralonso@cipf.es
Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/