Hello,

I would like to add a very simple GATK wrapper to galaxy, but I am facing
one problem. When you want to use UnifiedGenotyper tool, the extension of
the bam file must be .bam, and when you upload something to galaxy it
changes its extension,is there any way to change this extension? or is it
anyway of solving this issue? This is my conf file.

<tool id="gatk_mio" name="calling with gatk">
  <description>calling with gatk</description>


  <command>
      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 -o
$output
  </command>
  <inputs>
    <param format="bam" name="input" type="data" label="bam"/>
  </inputs>
  <outputs>
      <data format="vcf" name="output" />
  </outputs>

  <help>
gatk
  </help>

</tool>

Best regards


-- 
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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