<tool id="affr2vcf" name="Convert Affymetrix" version="@WRAPPER_VERSION@">
    <description>genotype calls and intensities to VCF</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="1.9">bcftools-gtc2vcf-plugin</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
@PREPARE_ENV@
#set text_outputs_dir = 'text_outputs'
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.fields.path'
#end if
--annot '$annot'
--snp-posteriors '$snp_posteriors'
--summary '$summary'
--report '$report'
--calls '$calls'
--confidences '$confidences'
#if str($output_gender_estimate_cond.output_gender_estimate) == "yes"
    --sex '$output_gender_estimate'
#end if
#if str($append_version) == "no":
    --no-version
#end if
--output '$output'
--output-type $output_type
@THREADS@
    ]]></command>
    <inputs>
        <param name="annot" type="data" format="csv" label="Probeset annotation file" />
        <param name="summary" type="data" format="txt" label="Apt-probeset genotype summary file" />
        <param name="snp_posteriors" type="data" format="txt" label="Apt-probeset genotype snp-posteriors file" />
        <param name="report" type="data" format="txt" label="Apt-probeset genotype report file" />
        <param name="confidences" type="data" format="txt" label="Apt-probeset genotype confidences file" />
        <param name="calls" type="data" format="txt" label="Apt-probeset genotype calls file" />
        <conditional name="reference_genome_source_cond">
            <param name="reference_genome_source" type="select" label="Choose the source for the reference genome">
                <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="2"/>
                        <column name="value" index="0"/>
                        <column name="path" index="3"/>
                        <filter type="sort_by" column="1"/>
                        <validator type="no_options" message="No cached Fasta genome references are available for the build associated with the selected probeset annotation file." />
                    </options>
                </param>
            </when>
        </conditional>
        <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>
        <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>
        <expand macro="vcf_output"/>
        <data name="output_gender_estimate" format="txt" label="${tool.name} (gender estimate) on ${on_string}">
            <filter>output_gender_estimate_cond['output_gender_estimate'] == "yes"</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="reference_genome_source" value="history"/>
            <param name="history_item" value="sub50_adig_genome.fasta" ftype="fasta"/>
            <param name="annot" value="axiom_acropsnp_coral_annotation.r1.csv" ftype="csv"/>
            <param name="summary" value="sub50_axiomgt1.summary.txt" ftype="txt"/>
            <param name="snp_posteriors" value="sub50_axiomgt1.snp_posteriors.txt" ftype="txt"/>
            <param name="report" value="axiomgt1.report.txt" ftype="txt"/>
            <param name="confidences" value="sub50_axiomgt1.confidences.txt" ftype="txt"/>
            <param name="calls" value="sub50_axiomgt1.calls.txt" ftype="txt"/>
            <output name="output" value="output.vcf" ftype="vcf"/>
        </test>
    </tests>
    <help>
This tool converts Affymetrix genotype calls and intensity files to VCF format.

-----

**Required options**

 * **Probeset annotation file** - probeset annotation file produced by the sequencing run.
 * **Apt-probeset genotype summary file** - apt-probeset genotype summary file produced by the sequencing run.
 * **Apt-probeset genotype snp-posteriors file** - apt-probeset genotype snp-posteriors file produced by the sequencing run.
 * **Apt-probeset genotype report file** - apt-probeset genotype report file produced by the sequencing run.
 * **Apt-probeset genotype confidences file** - apt-probeset genotype confidences file produced by the sequencing run.
 * **Apt-probeset genotype calls file** - apt-probeset genotype calls file produced by the sequencing run.
 * **Choose the source for the reference genome** - select a reference genome from your history or one installed into your local Galaxy environment by a data manager tool.

**Other options**

 * **Output apt-probeset-genotype gender estimate** - output apt-probeset-genotype gender estimate into an additional dataset.
 * **Append version and command line to the header** - append version and command line to the header of the output VCF dataset.
 * **Select format for output** - select one of uncompressed/compressed VCF/BCF.
    </help>
    <citations>
        <expand macro="citation1"/>
        <citation type="bibtex">
            @misc{None,
            journal = {None},
            author = {Genovese, Giulio},
            title = {None},
            year = {None},
            url = {https://github.com/freeseek/gtc2vcf},}
        </citation>
    </citations>
</tool>