<?xml version="1.0"?>
<tool id="hmmer_hmmsearch" name="hmmsearch" version="@TOOL_VERSION@+galaxy1">
  <description>search profile(s) against a sequence database</description>
    <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="bio_tools"/>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <command><![CDATA[
@ADDTHREADS@
hmmsearch

@OFORMAT_WITH_OPTS@
@THRESHOLDS@
@THRESHOLDS_DOM@
@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_dom_pfam"/>
    <expand macro="thresholds_cut_dom_xml"/>
    <expand macro="accel_heur_xml"/>
    <expand macro="adv_opts"/>
    <expand macro="seed"/>
  </inputs>
  <outputs>
    <expand macro="output_dom_pfam" tool="PHMMER"/>
  </outputs>
  <tests>
    <test expect_num_outputs="4">
      <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">
          <expand macro="assert_out" tool="hmmsearch"/>
      </output>
      <output name="domtblout" file="globins.domtblout" lines_diff="16">
          <expand macro="assert_tblout" tool="hmmsearch"/>
      </output>
      <output name="pfamtblout" file="globins.pfamtblout" lines_diff="12">
          <expand macro="assert_tblout" tool="hmmsearch"/>
      </output>
      <output name="tblout" file="globins.tblout" lines_diff="16">
          <expand macro="assert_tblout" tool="hmmsearch"/>
      </output>
    </test>
    <test expect_num_outputs="1">
      <param name="hmmfile" value="globins4.hmm"/>
      <param name="seqdb" value="uniprot_matches.fasta"/>
      <expand macro="oformat_test" />
      <param name="oformat" value=""/>
      <expand macro="seed_test" />
      <output name="output" file="uniprot_globins_match.out" lines_diff="20">
          <expand macro="assert_out" tool="hmmsearch"/>
      </output>
    </test>
    <test expect_num_outputs="1"><!-- test with additional evalue threshold options  set -->
      <param name="hmmfile" value="fn3.hmm"/>
      <param name="seqdb" value="uniprot_matches.fasta"/>
      <conditional name="repopt">
        <param name="incE" value="0.00001"/>
        <param name="incdomE" value="0.0001"/>
      </conditional>
      <expand macro="oformat_test" />
      <param name="oformat" value=""/>
      <expand macro="seed_test" />
      <output name="output">
          <expand macro="assert_out" tool="hmmsearch"/>
      </output>
      <assert_command>
        <has_text text="-E 10"/>
        <has_text text="--incE 1e-05"/>
        <has_text text="--domE 10"/>
        <has_text text="--incdomE 0.0001"/>
      </assert_command>
    </test>
    <test expect_num_outputs="1"><!-- test with cut_ga set -->
      <param name="hmmfile" value="fn3.hmm"/>
      <param name="seqdb" value="uniprot_matches.fasta"/>
      <conditional name="repopt">
        <param name="repopt_sel" value="--cut_ga"/>
      </conditional>
      <expand macro="oformat_test" />
      <param name="oformat" value=""/>
      <expand macro="seed_test" />
      <output name="output" file="cut_ga_test.out" lines_diff="10">
          <expand macro="assert_out" tool="hmmsearch"/>
      </output>
    </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>