<tool id="merquryfk_hapmaker" name="MerquryFK HAPmaker" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2">
    <description>Generates hap-mer tables from FastK k-mer data of maternal, paternal, and child sequences</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        mkdir -p input_files
        && mkdir -p hapmaker_ktabs
        && ln -s '$maternal_ktab_tar' maternal.tar
        && tar -xf maternal.tar
        && mv ktabfiles ktabfiles_maternal
        && mv ktabfiles_maternal/output.ktab input_files/maternal.ktab
        && mv "\$(find ktabfiles_maternal -type f -name '*.ktab.1')" "input_files/.maternal.ktab.1"
        && ln -s '$paternal_ktab_tar' paternal.tar
        && tar -xf paternal.tar
        && mv ktabfiles ktabfiles_paternal
        && mv ktabfiles_paternal/output.ktab input_files/paternal.ktab
        && mv "\$(find ktabfiles_paternal -type f -name '*.ktab.1')" "input_files/.paternal.ktab.1"
        && ln -s '$child_ktab_tar' child.tar
        && tar -xf child.tar
        && mv ktabfiles ktabfiles_child
        && mv ktabfiles_child/output.ktab input_files/child.ktab
        && mv "\$(find ktabfiles_child -type f -name '*.ktab.1')" "input_files/.child.ktab.1"
        && HAPmaker -v 
        -T\${GALAXY_SLOTS:-4}
        input_files/maternal.ktab
        input_files/paternal.ktab
        input_files/child.ktab
        && mv input_files/.*.hap* hapmaker_ktabs
        && tar -czvf HapK_ktab_files.tar.gz hapmaker_ktabs
    ]]></command>
    <inputs>
        <param name="maternal_ktab_tar" type="data" format="fastk_ktab_tar" label="Select the TAR file consisting of maternal ktab file from FastK"/>
        <param name="paternal_ktab_tar" type="data" format="fastk_ktab_tar" label="Select the TAR file consisting of paternal ktab file from FastK"/>
        <param name="child_ktab_tar" type="data" format="fastk_ktab_tar" label="Select the TAR file consisting of child ktab file from FastK"/>
    </inputs>
    <outputs>
        <data name="paternal_out" format="fastk_ktab" from_work_dir="paternal.hap.ktab" label="${tool.name} on ${on_string}: paternal hap-mers"/>
        <data name="maternal_out" format="fastk_ktab" from_work_dir="maternal.hap.ktab" label="${tool.name} on ${on_string}: maternal hap-mers"/>
        <data name="intermediate_ktab" format="fastk_ktab_tar" from_work_dir="HapK_ktab_files.tar.gz" label="${tool.name} on ${on_string}: HapMaker Intermediate Ktab files"/>
    </outputs>
    <tests>
        <test expect_num_outputs="3">
            <param name="maternal_ktab_tar" ftype="fastk_ktab_tar" value="maternal.tar"/>
            <param name="paternal_ktab_tar" ftype="fastk_ktab_tar" value="paternal.tar"/>
            <param name="child_ktab_tar" ftype="fastk_ktab_tar" value="child.tar"/>
            <output name="paternal_out" value="paternal.hap.ktab"/>
            <output name="maternal_out" value="maternal.hap.ktab"/>
            <output name="intermediate_ktab" ftype="fastk_ktab_tar">
                <assert_contents>
                    <has_archive_member path="hapmaker_ktabs/.maternal.hap.ktab.1"/>
                    <has_archive_member path="hapmaker_ktabs/.paternal.hap.ktab.1"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
        HAPmaker generates hap-mer tables for parental datasets for merquryfk pipeline. Before running HAPplot or MerquryFK in trio mode, it is necessary to generate a table of hap-mers 
        for both the mother and father, using FastK k-mer tables from the maternal, paternal, and child sequence data sets. 
        The output of this process produces two k-mer tables: <mat>.hap.ktab for the maternal hap-mers and <pat>.hap.ktab for the paternal hap-mers.
    ]]></help>
    <expand macro="citation"/>
</tool>