gatk tool config file
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: ralonso@cipf.es
On Mon, Mar 2, 2015 at 4:08 PM, Roberto Alonso CIPF <ralonso@cipf.es> 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/... 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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Peter Cock -
Roberto Alonso CIPF