annotate ete_init_taxdb.xml @ 5:817031b8486d draft

planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0

<tool id="ete_init_taxdb" name="ETE taxa DB generator" version="@VERSION@">
    <description>generates the ETE sqlite DB from the NCBI taxdump.tar.gz</description>
    <macros>
        <import>ete_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
python '$__tool_directory__/ete_init_taxdb.py'
#if $latestcond.latest == "local"
    -t '$latestcond.taxdump'
#end if
-d '$database'
    ]]></command>
    <inputs>
        <conditional name="latestcond">
            <param name="latest" type="select" label="Get latest version" help="Get the latest version of the taxdump from the NCBI website">
                <option value="local" selected="true">Use a local taxdump</option>
                <option value="latest">Get latest taxdump online</option>
            </param>
            <when value="local">
                <param name="taxdump" type="data" format="tar" label="NCBI taxdump" help="NCBI taxonomy database dump in tar.gz format" />
            </when>
            <when value="latest" />
        </conditional>
    </inputs>
    <outputs>
        <data name="database" format="sqlite" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="latest" value="local" />
            <param name="taxdump" ftype="tar" value="taxdump.tar.gz" />
            <output name="database" file="taxdump.sqlite" compare="sim_size" />
        </test>
    </tests>
    <help><![CDATA[
Generates the ETE sqlite data base from the NCBI taxdump.tar.gz using the `ETE Toolkit`_.

.. _ETE Toolkit: http://etetoolkit.org/

**Input**

- NCBI taxdump: NCBI taxdump in tar.gz format. If not given the latest is downloaded from ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz

**Output**

- *(ETE3) Taxonomy Database* a sqlite database that has been created by ETE from the NCBI taxonomy dump
    ]]></help>
    <expand macro="citations" />
</tool>