<?xml version="1.0"?>
<tool id="hmmer_nhmmer" name="nhmmer" version="@TOOL_VERSION@+galaxy1">
  <description>search a DNA model or alignment against a DNA database (BLASTN-like)</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <command><![CDATA[
@ADDTHREADS@
nhmmer

@OFORMAT_WITH_OPTS@
@HSSI@
@THRESHOLDS_NODOM@
@CUT@
@ACCEL_HEUR@
@FORMAT_SELECTOR@
@ADV_OPTS@
@LENGTHS@
@CPU@
@SEED@

'$hmmfile'
'$seqfile'
> '$output'
  ]]></command>
  <inputs>
    <expand macro="input_hmm" />
    <param name="seqfile" type="data" format="fasta" label="Target sequence file"/>
    <expand macro="oformat_with_opts_dfam_alisc"/>
    <expand macro="hssi"/>
    <expand macro="thresholds_nodom"/>
    <expand macro="cut" />
    <expand macro="accel_heur_xml"/>
    <expand macro="format_selector_noprot"/>
    <expand macro="adv_opts"/>
    <expand macro="lengths"/>
    <!-- TODO: block_length toponly bottomonly -->
    <expand macro="seed"/>
  </inputs>
  <outputs>
    <expand macro="output_dfam_alisc" tool="NHMMER"/>
  </outputs>
  <tests>
    <test expect_num_outputs="4">
      <param name="hmmfile" value="MADE1.hmm"/>
      <param name="seqfile" value="dna_target.fa"/>
      <expand macro="oformat_test" />
      <param name="oformat" value="tblout,dfamtblout,aliscoresout"/>
      <expand macro="seed_test" />
      <output name="output" file="nhmmer.out" lines_diff="16">
        <expand macro="assert_out" tool="nhmmer"/>
      </output>
      <output name="tblout" file="nhmmer.out.tblout" lines_diff="12">
        <expand macro="assert_tblout" tool="nhmmer"/>
      </output>
      <output name="aliscoresout" file="nhmmer.out.aliscoresout" lines_diff="10"/>
      <output name="dfamtblout" file="nhmmer.out.dfamtblout" lines_diff="10">
        <assert_contents>
          <has_line_matching expression="# hit scores"/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="1">
      <param name="hmmfile" value="MADE1.hmm"/>
      <param name="seqfile" value="dna_target.fa"/>
      <expand macro="oformat_test" />
      <param name="oformat" value=""/>
      <expand macro="seed_test" />
      <output name="output" file="nhmmer.out" lines_diff="16">
        <expand macro="assert_out" tool="nhmmer"/>
      </output>
    </test>
  </tests>
  <help><![CDATA[
@HELP_PRE@

nhmmer is used to search one or more nucleotide queries against a nucleotide
sequence database. For each query in <queryfile>, use that query to search the
target database of sequences in <seqdb>, and output a ranked list of the hits
with the most significant matches to the query. A query may be either a profile
model built using hmmbuild, a sequence alignment, or a single sequence.
Sequence based queries can be in a number of formats (see --qformat), and can
typically be autodetected. Note that only Stockholm format supports the use of
multiple sequence-based queries.

@HELP_PRE_OTH@

@OFORMAT_WITH_OPTS_N_HELP@
@HSSI_HELP@
@THRESHOLDS_NODOM_HELP@
@CUT_HELP@
@ACCEL_HEUR_HELP@
@FORMAT_SELECTOR_HELP@
@ADV_OPTS_HELP@
@LENGTHS_HELP@
@SEED_HELP@

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