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>/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