<?xml version="1.0"?>
<tool id="bioext_bealign" name="Align sequences" version="@VERSION@.0">
  <description>to a reference using a codon alignment
  algorithm</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <version_command>bealign --version</version_command>
  <command detect_errors="exit_code"><![CDATA[
    bealign --reference '$select_reference.reference' --alphabet $advanced.alphabet
        #if $advanced.expected_identity:
            --expected-identity $advanced.expected_identity
        #end if
        --score-matrix $advanced.score_matrix $advanced.reverse_complement $advanced.keep_reference
        #if $advanced.discard:
            --discard '$discarded_reads'
        #end if
        '$input' '$output'
    ]]></command>
  <inputs>
    <param name="input" type="data" format="fasta" label="Input reads"/>
    <conditional name="select_reference">
      <param name="reference_type" type="select">
        <option value="preset">Select preset</option>
        <option value="dataset">Use a history dataset</option>
      </param>
      <when value="preset">
        <param argument="--reference" type="select">
          <option value="HXB2_tat">HXB2 tat</option>
          <option value="HXB2_gag">HXB2 gag</option>
          <option value="HXB2_pol">HXB2 polymerase</option>
          <option value="HXB2_int">HXB2 integrase</option>
          <option value="HXB2_vif">HXB2 vif</option>
          <option value="HXB2_pr">HXB2 protease</option>
          <option value="HXB2_vpr">HXB2 vpr</option>
          <option value="NL4-3_prrt">NL4-3 protease and reverse
          transcriptase</option>
          <option value="HXB2_nef">HXB2 nef</option>
          <option value="HXB2_env">HXB2 envelope</option>
          <option value="HXB2_rt">HXB2 reverse
          transcriptase</option>
          <option value="HXB2_prrt">HXB2 protease and reverse
          transcriptase</option>
          <option value="HXB2_rev">HXB2 rev</option>
          <option value="HXB2_vpu">HXB2 vpu</option>
        </param>
      </when>
      <when value="dataset">
        <param argument="--reference" type="data" format="fasta" label="Reference sequences"/>
      </when>
    </conditional>
    <section name="advanced" title="Advanced options" expanded="False">
      <param name="expected_identity" argument="--expected-identity" type="float" min="0" max="1" optional="True" label="Discard sequences that are insufficiently identical to the reference"/>
      <param argument="--alphabet" type="select" label="Alphabet to use for alignment">
        <option value="codon" selected="True">Codon</option>
        <option value="dna">DNA</option>
        <option value="amino">Amino acids</option>
      </param>
      <param name="score_matrix" argument="--score-matrix" type="select" label="Parametrize using score matrix">
        <option value="BLOSUM62" selected="True">Blocks
        substitution</option>
        <option value="DNA65">DNA, 65% expected identity</option>
        <option value="DNA70">DNA, 70% expected identity</option>
        <option value="DNA88">DNA, 88% expected identity</option>
        <option value="DNA80">DNA, 80% expected identity</option>
        <option value="DNA95">DNA, 95% expected identity</option>
        <option value="PAM200">PAM 200 substitution</option>
        <option value="PAM250">PAM 250 substitution</option>
        <option value="HIV_BETWEEN_F">HIV between+F</option>
      </param>
      <param name="discard" argument="--discard" type="boolean" checked="False" truevalue="True" falsevalue="False" label="Output discarded sequences to a separate dataset"/>
      <param name="reverse_complement" argument="--reverse-complement" type="boolean" checked="False" truevalue="--reverse-complement" falsevalue="" label="Also try to align against reverse complement of reference"/>
      <param name="keep_reference" argument="--keep-reference" type="boolean" checked="False" truevalue="--keep-reference" falsevalue="" label="Include reference as first sequence in aligned BAM"/>
    </section>
  </inputs>
  <outputs>
    <data name="output" format="bam"/>
    <data name="discarded_reads" format="fasta">
      <filter>advanced['discard']</filter>
    </data>
  </outputs>
  <tests>
    <test>
      <param name="input" ftype="fasta" value="bealign-in1.fa"/>
      <param name="reference_type" value="dataset"/>
      <param name="score_matrix" value="HIV_BETWEEN_F"/>
      <param name="reference" ftype="fasta" value="bealign-in-ref-1.fa"/>
      <output name="output" file="bealign-out1.bam"/>
    </test>
    <test>
      <param name="input" ftype="fasta" value="bealign-in2.fa"/>
      <param name="reference_type" value="dataset"/>
      <param name="score_matrix" value="BLOSUM62"/>
      <param name="reference" ftype="fasta" value="bealign-in-ref-2.fa"/>
      <output name="output" file="bealign-out2.bam"/>
    </test>
    <test>
      <param name="input" ftype="fasta" value="bealign-in2.fa"/>
      <param name="reference_type" value="dataset"/>
      <param name="expected_identity" value="0.9"/>
      <param name="score_matrix" value="BLOSUM62"/>
      <param name="reference" ftype="fasta" value="bealign-in-ref-2.fa"/>
      <output name="output" file="bealign-out3.bam"/>
    </test>
  </tests>
  <help><![CDATA[
bealign
-------

Align sequences to a reference using a codon alignment algorithm.

NOTES
-----

Reference can be one of the presets or a custom history reference.
    ]]></help>
  <expand macro="citations"/>
</tool>