<?xml version="1.0"?>
<tool id="hmmer_phmmer" name="phmmer" version="@TOOL_VERSION@">
  <description>search a protein sequence against a protein database (BLASTP-like)</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <command><![CDATA[
phmmer

@OFORMAT_WITH_OPTS@
@HSSI@
@THRESHOLDS@
@ACCEL_HEUR@
@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="seqdb" type="data" format="fasta" label="Sequence Database"/>
    <expand macro="oformat_with_opts"/>
    <expand macro="hssi"/>
    <expand macro="thresholds_xml"/>
    <expand macro="accel_heur_xml"/>
    <expand macro="eval_calib_xml"/>
    <expand macro="adv_opts"/>
    <expand macro="seed"/>
  </inputs>
  <outputs>
    <data name="output" format="txt" label="PHMMER search of $seqfile.name in $seqdb.name"/>
    <data name="tblout" format="txt" label="Table of per-sequence hits from HMM matches of $seqfile.name in $seqdb.name">
      <filter>oformat and 'tblout' in oformat</filter>
    </data>
    <data name="domtblout" format="txt" label="Table of per-domain hits from HMM matches of $seqfile.name in $seqdb.name">
      <filter>oformat and 'domtblout' in oformat</filter>
    </data>
    <data name="pfamtblout" format="txt" label="Table of per-sequence/per-domain hits from HMM matches of $seqfile.name in $seqdb.name">
      <filter>oformat and 'pfamtblout' in oformat</filter>
    </data>
  </outputs>
  <tests>
    <test>
      <param name="seqfile" value="globins45.fa"/>
      <param name="seqdb" value="uniprot_matches.fasta"/>
      <expand macro="oformat_test" />
      <expand macro="seed_test" />
      <output name="output" file="phmmer.out" lines_diff="200"/>
      <!-- Lines diff is high due to a line of cpu/timing information for EACH sequence -->
      <output name="domtblout" file="phmmer.domtblout" lines_diff="10"/>
      <output name="pfamtblout" file="phmmer.pfamtblout" lines_diff="10"/>
      <output name="tblout" file="phmmer.tblout" lines_diff="10"/>
    </test>
  </tests>
  <help><![CDATA[
@HELP_PRE@

phmmer is used to search one or more query protein sequences against a protein
sequence database.  For each query sequence in <seqfile>, use that sequence to
search the target database of sequences in <seqdb>, and output ranked lists of
the sequences with the most significant matches to the query.


@HELP_PRE_OTH@

@OFORMAT_WITH_OPTS_HELP@
@HSSI_HELP@
@THRESHOLDS_HELP@
@ACCEL_HEUR_HELP@
@EVAL_CALIB_HELP@
@ADV_OPTS_HELP@
@SEED_HELP@

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