<tool id="positions2snv_alignment" name="Positions to SNV alignment" version ="1.8.2">
  <description>Create a SNV-only alignment from the SNVPhyl positions table.</description>
  <requirements>
    <requirement type="package" version="1.8.2">snvphyl-tools</requirement>
  </requirements>
  <command detect_errors="exit_code"><![CDATA[
	positions2snv_alignment.pl -i $snv_table -o $output -f $out_format $keep_all 
        #if $reference_name:
          --reference-name $reference_name
        #end if
  ]]></command>
  <inputs>
    <param name="snv_table" type="data" label="SNV table" format="tabular"/>
    <param name="out_format" type="select" label="Output alignment format">
      <option value="phylip">Phylip alignment format</option>
      <option value="fasta">FASTA alignment format</option>
    </param>
    <param name="keep_all" type="boolean" checked="false" label="Keep all positions"
      help="Keep all positions with status 'filtered' in the SNV alignment" truevalue="--keep-all" falsevalue="" />
    <param name="reference_name" type="text" label="Reference genome name" value="Reference"
      help="Name of reference genome in produced alignment" />
  </inputs>
  <outputs>
    <data format="phylip" name="output">
      <change_format>
        <when input="out_format" value="phylip" format="phylip"/>
        <when input="out_format" value="fasta" format="fasta"/>
      </change_format>
    </data>
  </outputs>
  <tests>
    <test>
      <param name="snv_table" value="positions.tsv"/>
      <param name="out_format" value="phylip"/>

      <output name="output" file="expected.phy"/>
    </test>
    <test>
      <param name="snv_table" value="positions.tsv"/>
      <param name="out_format" value="fasta"/>

      <output name="output" file="expected.fasta"/>
    </test>
    <test>
      <param name="snv_table" value="positions.tsv"/>
      <param name="out_format" value="fasta"/>
      <param name="keep_all" value="true" />

      <output name="output" file="expected-all.fasta"/>
    </test>
    <test>
      <param name="snv_table" value="positions.tsv"/>
      <param name="out_format" value="fasta"/>

      <output name="output" file="expected.fasta"/>
    </test>
    <test>
      <param name="snv_table" value="positions.tsv"/>
      <param name="out_format" value="fasta"/>
      <param name="reference_name" value="ChangedRefName" />

      <output name="output" file="expected-changed-ref-name.fasta"/>
    </test>
  </tests>

  <help>
What it does
============

Creates a SNV-only alignment from the SNVPhyl SNV positions table.

  </help>

  <citations>
  </citations>
</tool>