view centrifuge_kreport.xml @ 0:d4372c7fa79d draft

planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/centrifuge

<tool id="centrifuge_kreport" name="centrifuge_kreport" version="0.1.0">
    <description>Centrifuge-kreport creates Kraken-style reports from centrifuge out files</description>
    <requirements>
        <requirement type="package" version="1.0.3">centrifuge</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        centrifuge-kreport
          -x '${db.fields.path}'
          $input > output.txt
    ]]></command>
    <inputs>
        <param type="data" name="input" format="tabular" />
        <param name="db" type="select" label="Select a reference database">
            <options from_data_table="centrifuge_indices">
                <filter type="sort_by" column="2"/>
                <validator type="no_options" message="No indexes are available for the selected input dataset"/>
            </options>
        </param>
    </inputs>
    <outputs>
        <data format="tsv" name="output" from_work_dir="output.txt" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="test-data_centrifuge-kreport/defaults.tsv"/>
            <output name="output" file="defaults.tsv.kreport"/>
        </test>
    </tests>
    <help><![CDATA[
Usage: centrifuge-kreport -x <index name> OPTIONS <centrifuge output file(s)>

centrifuge-kreport creates Kraken-style reports from centrifuge out files.

Options:
    -x INDEX            (REQUIRED) Centrifuge index

    --only-unique        Only count reads that were uniquely assigned to one taxon
    --show-zeros         Show clades that have zero reads, too
    --is-count-table     The format of the file is 'TAXID<tab>COUNT' instead of the standard
                         Centrifuge output format

    --min-score SCORE    Require a minimum score for reads to be counted
    --min-length LENGTH  Require a minimum alignment length to the read
    ]]></help>
    <citations>
        <citation type="doi">10.1101/gr.210641.116</citation>
    </citations>
</tool>