gatk tool config file

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gatk tool config file

Roberto Alonso CIPF
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: [hidden email]

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Re: gatk tool config file

Peter Cock
On Mon, Mar 2, 2015 at 4:08 PM, Roberto Alonso CIPF <[hidden email]> wrote:
> 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?

The most common solution to inflexible tools which insist on a specific
file extension on inputs is to create a symlink with the right extension.
e.g.

https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/samtools/samtools_idxstats/samtools_idxstats.xml

Similarly where a tool does not give you full control of the output
filenames, you must often move/copy the file to the filename which
Galaxy has assigned.

Peter
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