<?xml version="1.0"?>
<tool id="hmmer_jackhmmer" name="jackhmmer" version="@WRAPPER_VERSION@.0">
  <description>iteratively search a protein sequence against a protein database (PSIBLAST-like)</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <command><![CDATA[
jackhmmer
-N $N
@OFORMAT_WITH_OPTS_NOPFAM@
@HSSI@
@THRESHOLDS@
@ACCEL_HEUR@
@MCSS@
@ARSWS@
@AEEWS@
@PRIOR@

@EVAL_CALIB@
@ADV_OPTS@
@CPU@
@SEED@

$seqfile
$seqdb
> $output
      ]]></command>
  <inputs>
    <param name="seqfile" type="data" format="fasta" label="Protein sequence to search with"/>
    <!-- todo use Galaxy features like data libraries/data tables/??? -->
    <param name="N" type="integer" value="5" min="1" label="Maximum number of iterations" help="(-N)"/>
    <param name="seqdb" type="data" format="fasta" label="Sequence Database"/>
    <expand macro="oformat_with_opts_nopfam"/>
    <expand macro="hssi"/>
    <expand macro="thresholds_xml"/>
    <expand macro="accel_heur_xml"/>
    <expand macro="mcss"/>
    <expand macro="arsws"/>
    <expand macro="aeews"/>
    <expand macro="prior"/>
    <expand macro="eval_calib_xml"/>
    <expand macro="adv_opts"/>
    <expand macro="seed"/>
  </inputs>
  <outputs>
    <data format="txt" name="output" label="PHMMER search of $seqfile.name in $seqdb.name"/>
    <data format="txt" name="tblout" label="Table of per-sequence hits from HMM matches of $seqfile.name in $seqdb.name">
      <filter>'tblout' in str(oformat)</filter>
    </data>
    <data format="txt" name="domtblout" label="Table of per-domain hits from HMM matches of $seqfile.name in $seqdb.name">
      <filter>'domtblout' in str(oformat)</filter>
    </data>
  </outputs>
  <tests>
    <test>
      <param name="seqfile" value="uniprot_matches.fasta"/>
      <param name="seqdb" value="globins45.fa"/>
      <expand macro="oformat_test" />
      <expand macro="seed_test" />
      <output name="output" file="jackhmmer.out" lines_diff="180"/>
      <output name="domtblout" file="jackhmmer.domtblout" lines_diff="10"/>
      <output name="tblout" file="jackhmmer.tblout" lines_diff="10"/>
    </test>
  </tests>
  <help><![CDATA[
@HELP_PRE@

jackhmmer iteratively searches each query sequence in <seqfile> against the
target sequence(s) in <seqdb>. The first iteration is identical to a phmmer
search. For the next iteration, a multiple alignment of the query together
with all target sequences satisfying inclusion thresholds is assembled, a
profile is constructed from this alignment (identical to using hmmbuild on the
alignment), and profile search of the <seqdb> is done (identical to an
hmmsearch with the profile).


@HELP_PRE_OTH@

@OFORMAT_WITH_OPTS_HELP_NOPFAM@
@HSSI_HELP@
@THRESHOLDS_HELP@
@ACCEL_HEUR_HELP@
@MCSS_HELP@
@ARSWS_HELP@
@AEEWS_HELP@
@PRIOR_HELP@
@EVAL_CALIB_HELP@
@ADV_OPTS_HELP@
@SEED_HELP@

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