annotate kaiju-mergeOutputs.xml @ 1:01585d091036 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/kaiju commit ace4e37c66a95ee5f648b95a92911e1fdf212967

<tool id="kaiju_mergeoutputs" name="kaiju-mergeOutputs" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="xrefs"/>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        sort -k2,2 '$kaiju_table'  > kaiju.out.sort &&
        sort -k2,2 '$kraken_table' > kraken.out.sort &&
        kaiju-mergeOutputs
            -i kaiju.out.sort
            -j kraken.out.sort
            -o '$combined_out'
            -c $optional.conflict.mode
            #if $optional.conflict.mode in ["lca", "lowest"]
                -t '$reference.fields.path'/nodes.dmp
            #end if
            $optional.s
            -v
    ]]></command>
    <inputs>
        <param name="kaiju_table" type="data" format="tabular" label="kaiju output table"/>
        <param name="kraken_table" type="data" format="tabular" label="Another output table" help="e.g. from kraken"/>
        <section name="optional" title="Optional arguments" expanded="false">
            <conditional name="conflict">
                <param argument="-c" name="mode" type="select" label="Conflict resolution mode">
                    <option value="1">use taxid from 1st input</option>
                    <option value="2">use taxid from 2nd input</option>
                    <option value="lca" selected="true">least common ancestor (LCA) of the two taxon IDs</option>
                    <option value="lowest">lower rank of the two taxa is used if they are within the same lineage and LCA otherwise</option>
                </param>
                <when value="1"/>
                <when value="2"/>
                <when value="lca">
                    <expand macro="reference"/>
                </when>
                <when value="lowest">
                    <expand macro="reference"/>
                </when>
            </conditional>
            <param argument="-s" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Use score" help="Use 4th column with classification score to give precedence to taxon with better score" />
        </section>
    </inputs>
    <outputs>
        <data name="combined_out" format="tabular"/>
    </outputs>
    <tests>
        <test>
            <param name="kaiju_table" value="kaiju.out"/>
            <param name="kraken_table" value="kaiju.out"/>
            <output name="combined_out" value="kaiju.out"/>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

**What it does**

Merge two tab-separated output files in the column format (see above) used by Kaiju and Kraken. Only the first three columns are used.


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