<tool id="meryl_arithmetic_kmers" name="Meryl" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@@SUFFIX_VERSION@" profile="@PROFILE@">
    <description>apply arithmetic operations to k-mer counts</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="edam_ontology"/>
    <xrefs>
        <xref type="bio.tools">meryl</xref>
    </xrefs>
    <expand macro="requirements"/>
    <version_command>meryl --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
    export GALAXY_MEMORY_GB=\$((\${GALAXY_MEMORY_MB:-8192}/1024)) &&
    mkdir  -p ./temp_db/ &&
    tar -xmf $input_meryldb_02 --use-compress-program="pigz -p \${GALAXY_SLOTS:-1}" -C ./temp_db/ &&
    mv ./temp_db/* tmp.meryl &&
    meryl
    $arithmetic_operations
    $X
    tmp.meryl
    output read-db.meryl &&
    tar -cf read-db.meryldb --use-compress-program="pigz -p \${GALAXY_SLOTS:-1}" read-db.meryl
    ]]></command>
    <inputs>
        <param name="arithmetic_operations" type="select" label="Arithmetic operations" help="Select an operation to be executed">
            <option value="increase">Increase: add x to the count of each k-mer</option>
            <option value="decrease">Decrease: subtract x from the count of each k-mer</option>
            <option value="multiply">Multiply: multiply the count of each k-mer by x</option>
            <option value="divide">Divide: divide the count of each k-mer by x</option>
            <option value="divide-round">Divide-round: divide the count of each k-mer by x and round the results</option>
            <option value="modulo">Modulo: set the count of each k-mer to the remainder of the count divided by x</option>
        </param>
        <param name="input_meryldb_02" type="data" format="meryldb" label="Input meryldb" help="Select a meryldb dataset"/>
        <param name="X" type="integer" min="1" max="1000000" value="" optional="true" label="Operand"/>
    </inputs>
    <outputs>
        <data name="read_db" format="meryldb" from_work_dir="read-db.meryldb"/>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="X" value="100000"/>
            <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb"/>
            <param name="arithmetic_operations" value="increase"/>
            <output name="read_db" ftype="meryldb">
                <assert_contents>
                    <has_size value="58946" delta="3000"/>
                    <expand macro="meryldb_archive_assumptions"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <param name="X" value="100"/>
            <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb"/>
            <param name="arithmetic_operations" value="decrease"/>
            <output name="read_db" ftype="meryldb">
                <assert_contents>
                    <has_size value="45595" delta="3000"/>
                    <expand macro="meryldb_archive_assumptions"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <param name="X" value="3"/>
            <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb"/>
            <param name="arithmetic_operations" value="multiply"/>
            <output name="read_db" ftype="meryldb">
                <assert_contents>
                    <has_size value="60645" delta="3000"/>
                    <expand macro="meryldb_archive_assumptions"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <param name="X" value="2"/>
            <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb"/>
            <param name="arithmetic_operations" value="divide"/>
            <output name="read_db" ftype="meryldb">
                <assert_contents>
                    <has_size value="58481" delta="3000"/>
                    <expand macro="meryldb_archive_assumptions"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <param name="X" value="2"/>
            <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb"/>
            <param name="arithmetic_operations" value="divide-round"/>
            <output name="read_db" ftype="meryldb">
                <assert_contents>
                    <has_size value="58236" delta="3000"/>
                    <expand macro="meryldb_archive_assumptions"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <param name="X" value="3"/>
            <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb"/>
            <param name="arithmetic_operations" value="modulo"/>
            <output name="read_db" ftype="meryldb">
                <assert_contents>
                    <has_size value="36971" delta="3000"/>
                    <expand macro="meryldb_archive_assumptions"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>

.. class:: infomark

**Purpose**

Meryl is the k-mer counter. This tool applies arithmetic operations on k-mer counts: 

- Increase: add x to the count of each k-mer
- Decrease: subsctract x from the count of each k-mer
- Multiply: multiply the count of each k-mer by x
- Divide: divide the count of each k-mer by x
- Divide-round: divide the count of each k-mer by x and round th results
- Modulo: set the count of each k-mer to the remainder of the count divided by x
        </help>
    <expand macro="citations"/>
</tool>