<tool id="affr2vcf" name="Convert Affymetrix" version="1.9">
    <description>genotype calls and intensities to VCF</description>
    <requirements>
        <requirement type="package" version="1.9">bcftools-gtc2vcf-plugin</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
#set text_outputs_dir = 'text_outputs'
export BCFTOOLS_PLUGINS=\$(dirname `which bcftools`)/../libexec/bcftools &&
mkdir $text_outputs_dir &&
bcftools +\$BCFTOOLS_PLUGINS/affy2vcf.so
#if str($reference_genome_source_cond.reference_genome_source) == "history":
    --fasta-ref '$reference_genome_source_cond.history_item'
#else:
    --fasta-ref '$reference_genome_source_cond.locally_cached_item'
#end if
--annot '$annot'
--snp-posteriors '$text_outputs_dir/snp_posteriors.txt'
--summary '$text_outputs_dir/summary.txt'
--report '$text_outputs_dir/report.txt'
--calls '$text_outputs_dir/calls.txt'
--confidences '$text_outputs_dir/confidences.txt'
#if str($output_gender_estimate) == "yes"
    --sex '$text_outputs_dir/gender_estimate.txt'
#end if
#if str($append_version) == "no":
    --no-version
#end if
--output '$output'
--output_type $output_type
--threads \${GALAXY_SLOTS:-4}
    ]]></command>
    <inputs>
        <param name="annot" type="data" format="csv" label="Probeset annotation file" />
        <conditional name="reference_genome_source_cond">
            <param name="reference_genome_source" type="select" label="Will you select a reference reference genome from your history or use a locally cached genome index?">
                <option value="history" selected="true">Use a reference genome from my history</option>
                <option value="cached">Use a locally cached genome index</option>
            </param>
            <when value="history">
                <param name="history_item" type="data" format="fasta" label="Select reference genome" />
            </when>
            <when value="cached">
                <param name="locally_cached_item" type="select" format="fasta" label="Fasta reference sequence">
                    <options from_data_table="all_fasta">
                        <column name="name" index="1"/>
                        <column name="value" index="2"/>
                        <column name="path" index="2"/>
                        <filter type="sort_by" column="1"/>
                        <validator type="no_options" message="No cached Fasta genome references are available." />
                    </options>
                </param>
            </when>
        </conditional>
        <param name="output_gender_estimate" type="select" force_select="true" label="Output apt-probeset-genotype gender estimate?">
            <option value="no" selected="true">No</option>
            <option value="yes">Yes</option>
        </param>
        <param name="append_version" type="select" force_select="true" label="Append version and command line to the header?">
            <option value="no" selected="true">No</option>
            <option value="yes">Yes</option>
        </param>
        <param name="output_type" type="select" force_select="true" label="Select format for output?">
            <option value="v" selected="true">Uncompressed VCF</option>
            <option value="z">Compressed VCF</option>
            <option value="u" selected="true">Uncompressed BCF</option>
            <option value="b">Compressed BCF</option>
        </param>
    </inputs>
    <outputs>
        <collection name="txt_outputs" type="list" label="${tool.name} (reports) on ${on_string}">
            <discover_datasets pattern="__name__" directory="output" format="txt" />
        </collection>
        <data name="output" format="vcf" />
    </outputs>
    <tests>
        <test>
        </test>
    </tests>
    <help>
This tool converts Affymetrix genotype calls and intensity files to VCF format.

-----

**Required options**

**Other options**
    </help>
    <citations>
        <citation type="bibtex">
            @misc{None,
            journal = {None},
            author = {Genovese, Giulio},
            title = {None},
            year = {None},
            url = {https://github.com/freeseek/gtc2vcf},}
        </citation>
    </citations>
</tool>