<?xml version="1.0"?>
<tool id="hmmer_nhmmer" name="nhmmer" version="@WRAPPER_VERSION@.0">
  <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[
nhmmer

@OFORMAT_WITH_OPTS_N@
@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_n"/>
    <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>
    <data format="txt" name="output" label="NHMMER search of $seqfile.name in $hmmfile.name"/>

    <data format="txt" name="tblout" label="Table of per-sequence hits from HMM matches of $seqfile.name in $hmmfile.name">
      <filter>'tblout' in str(oformat)</filter>
    </data>
    <data format="txt" name="dfamtblout" label="Table of per-sequence/per-domain hits from HMM matches of $seqfile.name in $hmmfile.name">
      <filter>'pfamtblout' in str(oformat)</filter>
    </data>
    <data format="txt" name="aliscoresout" label="Scores for positional matches of $seqfile.name in $hmmfile.name">
      <filter>'aliscoresout' in str(oformat)</filter>
    </data>
  </outputs>
  <tests>
    <test>
      <param name="hmmfile" value="MADE1.hmm"/>
      <param name="seqfile" value="dna_target.fa"/>
      <expand macro="oformat_test" />
      <expand macro="seed_test" />
      <output name="output" file="nhmmer.out" lines_diff="32"/>
    </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>