/lib/galaxy/datatypes/converters/fasta_to_bowtie_base_index_converter.xml

<tool id="CONVERTER_fasta_to_bowtie_base_index" name="Convert FASTA to Bowtie base space Index" version="1.0.0">
  <requirements><requirement type='package'>bowtie</requirement></requirements>
  <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
  <!-- Used on the metadata edit page. -->
  <requirements>
      <requirement type="package">bowtie</requirement>
  </requirements>
  <command>
  mkdir ${output.files_path}
  &amp;&amp; bowtie-build --quiet
  -f 
  $input  ${output.files_path}/${output.metadata.base_name}
  </command>
  <inputs>
    <param name="input" type="data" format="fasta" label="Fasta file"/>
  </inputs>
  <outputs>
    <data name="output" format="bowtie_base_index"/>
  </outputs>
  <help>
  </help>
</tool>