<?xml version="1.0"?>
<tool id="hmmer_hmmscan" name="hmmscan" version="@WRAPPER_VERSION@.0">
  <description>search sequence(s) against a profile database</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <command><![CDATA[
## "Press" database
hmmpress $hmmfile;
## Scan
hmmscan

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

$hmmfile
$seqfile
> $output;
## Remove pressed database. Eventually will be replaced with a dedicated tool/datatype
rm ${hmmfile}.h3m ${hmmfile}.h3i ${hmmfile}.h3f ${hmmfile}.h3p;
      ]]></command>
  <inputs>
    <expand macro="input_hmm" />
    <!-- todo use Galaxy features like data libraries/data tables/??? -->
    <param name="seqfile" type="data" format="fasta" label="Sequence file"/>
    <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 format="txt" name="output" label="HMM matches 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 oformat</filter>
    </data>
    <data format="txt" name="domtblout" label="Table of per-domain hits from HMM matches of $seqfile.name in $hmmfile.name">
      <filter>'domtblout' in oformat</filter>
    </data>
    <data format="txt" name="pfamtblout" label="Table of per-sequence/per-domain hits from HMM matches of $seqfile.name in $hmmfile.name">
      <filter>'pfamtblout' in 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="MADE1.out" lines_diff="24"/>
      <output name="tblout" file="MADE1.out.tblout" lines_diff="20"/>
      <output name="domtblout" file="MADE1.out.domtblout" lines_diff="20"/>
      <output name="pfamtblout" file="MADE1.out.pfamtblout" lines_diff="20"/>
    </test>
  </tests>
  <help><![CDATA[
@HELP_PRE@

hmmscan is used to search protein sequences against collections of protein
profiles. For each sequence in <seqfile>, use that query sequence to search the
target database of profiles in <hmmfile>, and output ranked lists of the profiles
with the most significant matches to the sequence.

@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>