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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