view histogram-kmers.xml @ 1:9a0227fa7521 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312

<tool id="meryl_histogram_kmers" name="Meryl" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@@SUFFIX_VERSION@" profile="@PROFILE@">
    <description>get k-mer frequency histogram</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 histogram tmp.meryl > read-db.hist
    ]]></command>
    <inputs>
        <param name="input_meryldb_02" type="data" format="meryldb" label="Input meryldb"/>
    </inputs>
    <outputs>
        <data name="read_db_hist" format="tabular" from_work_dir="read-db.hist"/>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb"/>
            <output name="read_db_hist" file="output_24.read-db.hist"/>
        </test>
    </tests>
    <help>

.. class:: infomark

**Purpose**

Meryl is the k-mer counter. This tool determines a k-mer frequency histogram.
        </help>
    <expand macro="citations"/>
</tool>