<?xml version="1.0"?>
<tool id="hmmer_hmmbuild" name="hmmbuild" version="@TOOL_VERSION@">
  <description>Build a profile HMM from an input multiple alignment</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <command><![CDATA[
hmmbuild

#if $hmmname:
    -n '$hmmname'
#end if

@FORMAT_SELECTOR@
@MCSS@
@ARSWS@
@AEEWS@
@PRIOR@
@HSSI@
@EVAL_CALIB@

@CPU@
@SEED@

@LENGTHS@
#if str($maxinsertlen):
    --maxinsertlen $maxinsertlen
#end if

'$hmmout'
'$msafile'
  ]]></command>
  <inputs>
    <expand macro="input_msa" />
    <param name="hmmname" argument="-n" type="text" optional="true" label="Name for the HMM" />
    <expand macro="format_selector"/>
    <expand macro="mcss"/>
    <expand macro="arsws"/>
    <expand macro="aeews"/>
    <expand macro="prior"/>
    <expand macro="hssi"/>
    <expand macro="eval_calib_xml"/>
    <expand macro="seed"/>

    <expand macro="lengths" />
    <param argument="--maxinsertlen" type="integer" optional="true" label="Pretend all inserts are length &lt;= n" />
  </inputs>
  <outputs>
    <data name="hmmout" format="hmm3" label="HMM profile from $msafile.name"/>
  </outputs>
  <tests>
    <test>
      <param name="msafile" value="globins4.sto"/>
      <expand macro="seed_test" />
      <output name="hmmout" file="globins4.hmm" compare="sim_size">
          <assert_contents>
              <has_line_matching expression="HMMER3/f.*"/>
              <has_line_matching expression="ALPH  amino"/>
              <has_line_matching expression="NSEQ  4"/>
              <has_line_matching expression="//"/>
          </assert_contents>
      </output>
    </test>
    <test>
      <param name="msafile" value="MADE1.sto"/>
      <param name="input_format_select" value="--dna"/>
      <expand macro="seed_test" />
      <output name="hmmout" file="MADE1.hmm" compare="sim_size">
          <assert_contents>
              <has_line_matching expression="HMMER3/f.*"/>
              <has_line_matching expression="ALPH  DNA"/>
              <has_line_matching expression="NSEQ  1997"/>
              <has_line_matching expression="//"/>
          </assert_contents>
      </output>
    </test>
  </tests>
  <help><![CDATA[
@HELP_PRE@

For each multiple sequence alignment in <msafile> build a profile HMM and save
it to a new file <hmmfile out>.

@HELP_PRE_OTH@

@FORMAT_SELECTOR_HELP@
@MCSS_HELP@
@ARSWS_HELP@
@AEEWS_HELP@
@PRIOR_HELP@
@HSSI_HELP@
@EVAL_CALIB_HELP@
@SEED_HELP@
@LENGTHS_HELP@

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