annotate hmmconvert.xml @ 0:62479bdcc059 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569

<?xml version="1.0"?>
<tool id="hmmer_hmmconvert" name="hmmconvert" version="@WRAPPER_VERSION@.0">
  <description>convert profile file to a HMMER format</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <command><![CDATA[
hmmconvert
$format
$hmmfile > $output
      ]]></command>
  <inputs>
    <expand macro="input_hmm" />
    <param type="select" label="Output Format" name="format">
      <option value="-a" selected="true">output models in HMMER3 ASCII format</option>
      <!--<option value="-b">output models in HMMER3 binary format</option>-->
      <option value="-2">backward compatible HMMER2 ASCII format</option>
    </param>
  </inputs>
  <outputs>
    <data format="hmmer3" name="output" label="$msafile.name">
      <change_format>
        <when input="format" value="-a" format="hmmer3"/>
        <when input="format" value="-2" format="hmmer2"/>
      </change_format>
    </data>
  </outputs>
  <tests>
    <test>
      <param name="msafile" value="globins4.hmm"/>
      <param name="format" value="-2"/>
      <output name="output" file="globins4.hmm2"/>
    </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>