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 <ralo...@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&gt;/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: ralo...@cipf.es
>
> ___________________________________________________________
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