<?xml version="1.0"?>
<tool id="hmmer_hmmfetch" name="hmmfetch" version="@TOOL_VERSION@">
    <description>retrieve profile HMM(s) from a file</description>
    <expand macro="bio_tools"/>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <command><![CDATA[
hmmfetch -f '$hmmfile' '$keyfile' > '$output'
  ]]></command>
  <inputs>
    <!-- TODO: implement auto-indexing -->
    <expand macro="input_hmm" />
    <param name="keyfile" type="data" format="tabular,txt" label="List of HMM names to extract"/>
  </inputs>
  <outputs>
    <data name="output" format="hmm3" label="Selected HMM Models from $hmmfile.name">
    </data>
  </outputs>
  <tests>
    <test>
      <param name="hmmfile" value="fn3.hmm"/>
      <param name="keyfile" value="fn3.keys"/>
      <output name="output" file="fn3.hmm" lines_diff="4"/>
    </test>
  </tests>
  <help><![CDATA[
@HELP_PRE@

Quickly retrieves one or more profile HMMs from an <hmmfile> (a large Pfam
database, for example). The profile names should be listed in a text file,
separated by newlines

By default, fetched HMMs are printed to standard output in HMMER3 format.

@ATTRIBUTION@
  ]]></help>
  <expand macro="citation"/>
</tool>