<tool id="phytab_hmmsearch" name="PHYTAB HMMSEARCH" version="3.0">
  <description>hmmsearch :: search profile(s) against a sequence database. Produces a phytab output.</description>
  <requirements>
    <requirement type="package">hmmsearch</requirement>
  </requirements>
  <command interpreter="python">
    hmmsearch.py -i $hmm -d $database > $hmmsearch_stdout 2>&amp;1
  </command>
  <inputs>
    <param format="txt" name="hmm" type="data" label="HMM profiles" help="This should be a set of HMM models from hmmbuild"/>
    <param format="txt" name="database" type="data" label="Sequence data" help="This should be a sequence database"/>
  </inputs>
  <outputs>
    <data format="txt" name="hmmsearch_stdout" label="${tool.name} on ${on_string}: stdout" />
    <data format="txt" name="hmmsearch_results" label="${tool.name} on ${on_string}: results" from_work_dir="data/results.data" />
  </outputs>
  <tests>
  </tests>
  <help>
  **hmmsearch v3.0**
  
  Runs hmmsearch on HMM model data.

  See hmmsearch help: ftp://selab.janelia.org/pub/software/hmmer3/3.0/Userguide.pdf
  </help>
</tool>