<?xml version="1.0"?>
<tool id="hmmer_hmmconvert" name="hmmconvert" version="@TOOL_VERSION@">
    <description>convert profile file to a HMMER format</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <command><![CDATA[
hmmconvert
$format
'$hmmfile'
> '$output'
  ]]></command>
  <inputs>
    <expand macro="input_hmm" />
    <param name="format" type="select" label="Output Format">
      <option value="-a" selected="true">output models in HMMER3 ASCII format</option>
      <!--<option value="-b">output models in HMMER3 binary format</option>-->
      <option value="-2">backward compatible HMMER2 ASCII format</option>
    </param>
  </inputs>
  <outputs>
    <data name="output" format="hmm3" label="$hmmfile.name">
      <change_format>
        <when input="format" value="-2" format="hmm2"/>
      </change_format>
    </data>
  </outputs>
  <tests>
    <test>
      <param name="hmmfile" value="globins4.hmm"/>
      <param name="format" value="-2" ftype="hmm2"/>
      <output name="output" file="globins4.hmm2" compare="sim_size">
          <assert_contents>
              <has_line_matching expression="HMMER2.*"/>
              <has_line_matching expression="ALPH  Amino"/>
              <has_line_matching expression="NSEQ  4"/>
              <has_line_matching expression="//"/>
          </assert_contents>
      </output>
    </test>
  </tests>
  <help><![CDATA[
@HELP_PRE@

The hmmconvert utility converts an input profile file to different HMMER formats.

By default, the input profile can be in any HMMER format, including
old/obsolete formats from HMMER2, ASCII or binary; the output profile is a
current HMMER3 ASCII format.

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