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