<tool id="positions2snv_invariant_alignment" name="Positions to SNV invariant alignment" version ="@VERSION@+galaxy1">
  <description>Create a SNV and non-variant alignment from the SNVPhyl positions table and a reference genome.</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <command detect_errors="exit_code"><![CDATA[
	positions2snv_invariant_alignment.pl -i $snv_table --reference-file $reference_genome -o outputs -f $out_format $keep_all $merge_alignment
  ]]></command>
  <inputs>
    <param name="snv_table" type="data" label="SNV table" format="tabular"/>
    <param name="reference_genome" type="data" label="Reference genome" format="fasta"/>
    <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="merge_alignment" type="boolean" checked="false" label="Merge alignment to single file" 
      help="Merge individual sequences in reference file to single sequence in final alignment" truevalue="--merge-alignment" falsevalue="" />
    <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="" />
  </inputs>
  <outputs>
    <collection name="alignments" type="list" label="Alignment files">
      <discover_datasets pattern="__name_and_ext__" directory="outputs" />
    </collection>
  </outputs>
  <tests>
    <test>
      <param name="snv_table" value="positions.tsv"/>
      <param name="reference_genome" value="reference.fasta"/>
      <param name="out_format" value="fasta"/>
      <param name="merge_alignment" value="true" />

      <output_collection name="alignments" type="list">
        <element name="alignment_merged" file="expected-merged.fasta"/>
      </output_collection>
    </test>
    <test>
      <param name="snv_table" value="positions.tsv"/>
      <param name="reference_genome" value="reference.fasta"/>
      <param name="out_format" value="phylip"/>
      <param name="merge_alignment" value="true" />

      <output_collection name="alignments" type="list">
        <element name="alignment_merged" file="expected-merged.phy"/>
      </output_collection>
    </test>
    <test>
      <param name="snv_table" value="positions.tsv"/>
      <param name="reference_genome" value="reference.fasta"/>
      <param name="out_format" value="fasta"/>
      <param name="merge_alignment" value="true" />
      <param name="keep_all" value="true" />

      <output_collection name="alignments" type="list">
        <element name="alignment_merged" file="expected-merged-all.fasta"/>
      </output_collection>
    </test>
    <test>
      <param name="snv_table" value="positions.tsv"/>
      <param name="reference_genome" value="reference.fasta"/>
      <param name="out_format" value="fasta"/>

      <output_collection name="alignments" type="list">
        <element name="ref1" file="ref1.fasta"/>
        <element name="ref2" file="ref2.fasta"/>
      </output_collection>
    </test>
    <test>
      <param name="snv_table" value="positions.tsv"/>
      <param name="reference_genome" value="reference.fasta"/>
      <param name="out_format" value="fasta"/>
      <param name="keep_all" value="true" />

      <output_collection name="alignments" type="list">
        <element name="ref1" file="ref1-all.fasta"/>
        <element name="ref2" file="ref2-all.fasta"/>
      </output_collection>
    </test>
  </tests>

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

Creates a SNV and non-variant alignment from the SNVPhyl SNV positions table and a reference genome.

  </help>
  <expand macro="citations"/>
</tool>