<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&gt;/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