<?xml version="1.0"?>
<tool id="hmmer_hmmsearch" name="hmmsearch" version="@TOOL_VERSION@">
  <description>search profile(s) against a sequence database</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <command><![CDATA[
hmmsearch

@OFORMAT_WITH_OPTS@
@THRESHOLDS@
@CUT@
@ACCEL_HEUR@
@ADV_OPTS@
@CPU@
@SEED@

'$hmmfile'
'$seqdb'
> '$output'
  ]]></command>
  <inputs>
    <expand macro="input_hmm" />
    <!-- todo use Galaxy features like data libraries/data tables/??? -->
    <param name="seqdb" type="data" format="fasta" label="Sequence database to search against"/>
    <expand macro="oformat_with_opts"/>
    <expand macro="thresholds_xml"/>
    <expand macro="cut"/>
    <expand macro="accel_heur_xml"/>
    <expand macro="adv_opts"/>
    <expand macro="seed"/>
  </inputs>
  <outputs>
    <data name="output" format="txt" label="HMM matches of $hmmfile.name in $seqdb.name"/>
    <data name="tblout" format="txt" label="Table of per-sequence hits from HMM matches of $hmmfile.name in $seqdb.name">
      <filter>oformat and 'tblout' in oformat</filter>
    </data>
    <data name="domtblout" format="txt" label="Table of per-domain hits from HMM matches of $hmmfile.name in $seqdb.name">
      <filter>oformat and 'domtblout' in oformat</filter>
    </data>
    <data name="pfamtblout" format="txt" label="Table of per-sequence/per-domain hits from HMM matches of $hmmfile.name in $seqdb.name">
      <filter>oformat and 'pfamtblout' in oformat</filter>
    </data>
  </outputs>
  <tests>
    <test>
      <param name="hmmfile" value="globins4.hmm"/>
      <param name="seqdb" value="uniprot_matches.fasta"/>
      <expand macro="oformat_test" />
      <expand macro="seed_test" />
      <output name="output" file="uniprot_globins_match.out" lines_diff="20"/>
      <output name="domtblout" file="globins.domtblout" lines_diff="10"/>
      <output name="pfamtblout" file="globins.pfamtblout" lines_diff="10"/>
      <output name="tblout" file="globins.tblout" lines_diff="10"/>
    </test>
  </tests>
  <help><![CDATA[
@HELP_PRE@

hmmsearch is used to search one or more profiles against a sequence database.
For each profile in <hmmfile>, use that query profile to search the target
database of sequences in <seqdb>, and output ranked lists of the sequences with
the most significant matches to the profile. To build profiles from multiple
alignments, see hmmbuild.

@HELP_PRE_OTH@

@OFORMAT_WITH_OPTS_HELP@
@THRESHOLDS_HELP@
@CUT_HELP@
@ACCEL_HEUR_HELP@
@ADV_OPTS_HELP@
@SEED_HELP@

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