<tool id="vcfcheck" name="VCFcheck:" version="@WRAPPER_VERSION@+galaxy0">
    <description>Verify that the reference allele matches the reference genome</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"></expand>
    <stdio>
        <regex match="index file" source="stderr" level="warning"/>
    </stdio>
    <command><![CDATA[
        #set $reference_fasta_filename = "localref.fa"
        #if str( $reference_source.reference_source_selector ) == "history":
            ln -s '${reference_source.ref_file}' '${reference_fasta_filename}' &&
        #else:
            #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
        #end if
        vcfcheck $failure_selector -f '${reference_fasta_filename}' '${input_vcf}' > '${out_file1}'
    ]]></command>
    <inputs>
        <conditional name="reference_source">
            <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
                <option value="cached">Locally cached</option>
                <option value="history">History</option>
            </param>
            <when value="cached">
                <param name="ref_file" type="select" label="Select reference genome">
                    <options from_data_table="fasta_indexes">
                    <!--<filter type="data_meta" key="dbkey" ref="input_bam" column="value"/>-->
                    </options>
                    <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
                </param>
                <param name="input_vcf" type="data" format="vcf" label="Select VCF dataset">
                <!-- Validators are commented to allow users apply too to any build. May need to be revised in the future
                <validator type="unspecified_build" />
                <validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." />
                -->
                </param>
            </when>
            <when value="history"> <!-- FIX ME!!!! -->
                <param name="ref_file" type="data" format="fasta" label="Using reference file" />
                <param name="input_vcf" type="data" format="vcf" label="Select VCF dataset" />
            </when>
        </conditional>
        <param name="failure_selector" type="select" display="radio" label="Exclude or include failed sites">
            <option value="-x">Exculde failures (-x option)</option>
            <option value="-k">Keep failures (-k option)</option>
        </param>
    </inputs>
    <outputs>
        <data format="vcf" name="out_file1" />
    </outputs>
    <tests>
        <test>
            <param name="reference_source_selector" value="history" />
            <param name="failure_selection" value="-x" />
            <param name="input_vcf" value="vcflib-phix.vcf"/>
            <param name="ref_file" value="vcflib-test-genome-phix.fa" />
            <output name="out_file1" file="vcfcheck-test1.vcf"/>
        </test>
    </tests>
    <help>

Verifies that the VCF REF field matches the reference as described.  

The options are::

    -x, --exclude-failures If a record fails, don't print it.  Otherwise do.
    -k, --keep-failures    Print if the record fails, otherwise not.

----

Vcfcheck @IS_PART_OF_VCFLIB@
    </help>
    <expand macro="citations" />
</tool>