<tool id="cooc_tabmut" name="Cojac: tabmut" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"
      profile="@PROFILE@">
    <description>
        exports co-occurrence results from mutbamscan as a table
    </description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="biotools"/>
    <expand macro="requirements"/>
    <expand macro="version"/>
    <command detect_errors="exit_code"><![CDATA[
cojac cooc-tabmut
    #if $cooc_data.ext == 'json'
        -j '$cooc_data'
    #else
        -y '$cooc_data'
    #end if
    #if $table_orientation.choice == 'lines'
        -l
    #else if $table_orientation.choice == 'multiindex'
        -m
    #end if
    #if $out_format == 'tsv':
        -o cooc-table.tsv
    #else:
        -o cooc-table.csv
    #end if
    -q
    ]]></command>
    <inputs>
        <param name="cooc_data" type="data" format="json,yaml" label="Results generated by mutbamscan"/>
        <conditional name="table_orientation">
            <param name="choice" type="select" label="Output table orientation">
                <option value="columns">Column-oriented table (default)</option>
                <option value="lines">Line-oriented table</option>
                <option value="multiindex">Multi-level indexing (amplicons and counts
                    categories)
                </option>
            </param>
            <when value="columns"/>
            <when value="lines"/>
            <when value="multiindex"/>
        </conditional>
        <param name="out_format" type="select" label="Type of output to produce">
            <option value="tsv">Tab-separated (TSV)</option>
            <option value="csv">Comma-separated (CSV)</option>
        </param>
    </inputs>
    <outputs>
        <data name="table_tsv" format="tsv" label="${tool.name} on ${on_string}: Mutation co-occurrence (TSV table)" from_work_dir="cooc-table.tsv">
            <filter>out_format == 'tsv'</filter>
        </data>
        <data name="table_csv" format="csv" label="${tool.name} on ${on_string}: Mutation co-occurrence (CSV table)" from_work_dir="cooc-table.csv">
            <filter>out_format == 'csv'</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="cooc_data" value="cooc-test111.json"/>
            <conditional name="table_orientation">
                <param name="choice" value="columns"/>
            </conditional>
            <output name="table_tsv" ftype="tsv">
                <assert_contents>
                    <has_text text="A76"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <param name="cooc_data" value="cooc-test111.json"/>
            <conditional name="table_orientation">
                <param name="choice" value="columns"/>
            </conditional>
            <param name="out_format" value="csv"/>
            <output name="table_csv" ftype="csv">
                <assert_contents>
                    <has_text text="A76"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
@HELP_HEADER@

Information about **cojac cooc_tabmut** method
==============================================

The method exports a JSON or YAML file as a CSV/TSV table for downstream analysis (e.g.: RStudio).

    ]]></help>
    <expand macro="citations"/>
</tool>