<?xml version="1.0"?>
<tool id="hmmer_hmmalign" name="hmmalign" version="@TOOL_VERSION@">
  <description>align sequences to a profile HMM</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <command><![CDATA[
hmmalign

$trim
@FORMAT_SELECTOR@
--outformat stockholm

'$hmmfile'
'$seq'
> '$output'
  ]]></command>
  <inputs>
    <param name="seq" type="data" format="fasta" label="Sequence to align against model" help="Sequence should be in FASTA format"/>
    <expand macro="input_hmm" />
    <!-- TODO: mapali -->
    <param argument="--trim" type="boolean" truevalue="--trim" falsevalue="" label="trim terminal tails of nonaligned residues from alignment" />
    <expand macro="format_selector"/>
  </inputs>
  <outputs>
    <data name="output" format="stockholm" label="Alignment of $seq.name to $hmmfile.name" />
  </outputs>
  <tests>
    <test>
      <param name="hmmfile" value="globins4.hmm"/>
      <param name="seq" value="globins45.fa"/>
      <output name="output" file="globins-45-align.sto" lines_diff="20"/>
    </test>
  </tests>
  <help><![CDATA[
@HELP_PRE@

Perform a multiple sequence alignment of all the sequences in <seqfile> by
aligning them individually to the profile HMM in <hmmfile>. The new alignment
is output to stdout in Stockholm format.  The <hmmfile> should contain only a
single profile. If it contains more, only the first profile in the file will be
used.

Either <hmmfile> or <seqfile> (but not both) may be ’-’ (dash), which means
reading this input from stdin rather than a file.

The sequences in <seqfile> are aligned in unihit local alignment mode.
Therefore they should already be known to contain only a single domain (or a
fragment of one). The optimal alignment may assign some residues as
nonhomologous (N and C states), in which case these residues are still included
in the resulting alignment, but shoved to the outer edges. To trim these
unaligned nonhomologous residues from the result, see the --trim option.


@HELP_PRE_OTH@

@FORMAT_SELECTOR_HELP@

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