<tool id="frags2align" name="Frags to align">
  <description>Extract alignments from a binary Frags file</description>
  <inputs>
    <param name="fragsFile" type="data" format="frags" label="Frags file" help="Binary Frags file" />
    <param name="fastaX" type="data" format="fasta" label="x Genome" help="Single genome file in fasta format"/>    
    <param name="fastaY" type="data" value="fasta" label="y Genome" help="Single genome file in fasta format" />
  </inputs>
  <command>/home/galaxy-bitlab/galaxy/tools/gecko/bin/frags2align.sh $fragsFile $fastaX $fastaY $alignments </command>
  <outputs>
    <data name="alignments" format="txt" label="Frags to align for genomes  ${fastaX.name}_${fastaY.name}"/>
  </outputs>
</tool>