annotate organism_sync.xml @ 0:98e917aa6819 draft

planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268

<?xml version="1.0"?>
<tool id="organism_sync" profile="16.04" name="Synchronize an organism" version="@WRAPPER_VERSION@.0">
    <description>from Chado to Tripal</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <code file="tripal.py"/>
    <expand macro="stdio"/>
    <command><![CDATA[

        @AUTH@

        tripaille organism sync

            --organism_id '${organism_id}'

        &&

        echo "Data loaded" > $results
    ]]></command>
    <inputs>
        <param argument="--organism_id"
               type="select"
               dynamic_options="list_organisms()"
               label="Organism" />
    </inputs>
    <outputs>
        <data format="txt" name="results" label="Synchronize Organism into Tripal" />
    </outputs>
    <tests>
        <test expect_failure="true">
            <param name="organism_id" value="Testus testus" />

            <expand macro="test_result" />
        </test>
    </tests>
    <help><![CDATA[
        @HELP_OVERVIEW@

        **Synchronize Organism**

        With this tool, you can synchronize an organism from the Chado database into the Tripal instance.
        A corresponding Drupal node will be created.

        @HELP@
    ]]></help>
    <expand macro="citation"/>
</tool>