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<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'
mkdir $text_outputs_dir &&
bcftools +affy2vcf.so
-- fasta_ref '$fasta_ref'
--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($output_gender_estimate_cond.output_gender_estimate) == "yes"
    --sex '$text_outputs_dir/gender_estimate.txt'
#end if
#if str($append_version) == "no":
    --no-version
#end if
--output '$output'
--output_type $output_type
--threads \${GALAXY_SLOTS:-4}
    ]]></command>
    <inputs>
        <param name="annot" type="data" format="csv" label="Probeset annotation file" />
        <param name="fasta_ref" type="select" format="fasta" label="Fasta reference sequence">
            <options from_data_table="all_fasta">
                <column name="name" index="1"/>
                <column name="value" index="2"/>
                <column name="path" index="2"/>
                <filter type="sort_by" column="1"/>
                <validator type="no_options" message="No Fasta genome references are available.  Use the Fetch Genome DBKeys All Fasta Data Manager tool in Galaxy to install and populate the all_fasta data table."/>
            </options>
        </param>
        <conditional name="output_gender_estimate_cond">
            <param name="output_gender_estimate" type="select" force_select="true" label="Output apt-probeset-genotype gender estimate?">
                <option value="no" selected="true">No</option>
                <option value="yes">Yes</option>
            </param>
            <when value="no" />
            <when value="yes"/>
        </conditional>
        <conditional name="append_version_cond">
            <param name="append_version" type="select" force_select="true" label="Append version and command line to the header?">
                <option value="no" selected="true">No</option>
                <option value="yes">Yes</option>
            </param>
            <when value="no" />
            <when value="yes"/>
        </conditional>
    </inputs>
    <outputs>
        <collection name="txt_outputs" type="list" label="${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>