<tool id="vcftools_consensus" name="Consensus" version="0.1.11">
    <description>Apply VCF variants to a fasta file to create consensus sequence</description>

    <requirements>
        <requirement type="package" version="0.1.19">samtools</requirement>
        <requirement type="package" version="1.3.2">htslib</requirement>
        <requirement type="package" version="0.1.11">vcftools</requirement>
    </requirements>

    <stdio>
        <!--<regex match=".*" source="both" level="log" description="tool progress"/>-->
        <exit_code range="1:" level="fatal" />
    </stdio>

    <command>
    <![CDATA[
        ln -s '${variants}' variants.vcf &&
        vcf-sort variants.vcf | bgzip -c > variants.sorted.vcf.gz &&

        tabix -p vcf variants.sorted.vcf.gz  &&

        #if $ref_genome_source.index_source == 'history':
          ln -s '${ref_genome_source.ref_file}' reference.fasta &&
          samtools faidx reference.fasta &&
        #end if

        cat
        #if $ref_genome_source.index_source == 'builtin'
          '${ ref_genome_source.reference_genome.fields.path }'
        #else
          reference.fasta
        #end if
        | vcf-consensus variants.sorted.vcf.gz > '${output}'
    ]]>
    </command>
    <inputs>
      <conditional name="ref_genome_source">
        <param name="index_source" type="select" label="Reference genome source">
          <option value="builtin">Built-in genome</option>
          <option value="history">History</option>
        </param>
        <when value="builtin">
          <param name="reference_genome" type="select">
            <options from_data_table="fasta_indexes">
              <filter column="2" type="sort_by" />
              <validator message="No suitable reference genomes found" type="no_options" />
            </options>
          </param>
        </when>
        <when value="history">
          <param name="ref_file" type="data" format="fasta" label="Reference genome" />
        </when>
      </conditional>
      <param name="variants" label="Datasets containing Variants" type="data" format="vcf" />
    </inputs>

    <outputs>
        <data name="output" format="fasta"/>
    </outputs>

    <tests>
      <test>
        <param name="index_source" value="history" />
        <param ftype="fasta" name="ref_file" value="reference.fasta" />
        <param ftype="vcf" name="variants" value="sample1.vcf" />
        <output name="output" ftype="fasta" file="output1.fasta" />
      </test>
    </tests>

    <help>
        Please see the VCFtools `documentation`__ for help and further information.

        .. __: http://vcftools.sourceforge.net/docs.html
    </help>
    <citations>
      <citation type="doi">10.1093/bioinformatics/btr330</citation>
    </citations>
</tool>