annotate feature_sync.xml @ 2:e621d1187d73 draft

planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 81a83f06b49db32928ba0cd44e5b6d0431868d27

<?xml version="1.0"?>
<tool id="feature_sync" profile="16.04" name="Synchronize features" version="@WRAPPER_VERSION@.1">
    <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 feature sync

            #for $rep in $repeat_types:
                --types '${rep.types}'
            #end for

            #for $rep in $repeat_ids:
                --ids '${rep.ids}'
            #end for

            --organism_id '${organism_id}'

        &&

        echo "Data loaded" > $results
    ]]></command>
    <inputs>
        <param argument="--organism_id"
               type="select"
               dynamic_options="list_organisms()"
               label="Organism" />

        <repeat name="repeat_types" title="Feature types">
            <param name="types"
                   argument="--types"
                   type="text"
                   optional="true"
                   label="Feature type to synchronize"
                   help="Type of records to be synced (e.g. 'gene' or 'mRNA')" />
        </repeat>

        <repeat name="repeat_ids" title="Feature ids">
            <param name="ids"
                   argument="--ids"
                   type="text"
                   optional="true"
                   label="Feature to synchronize"
                   help="Name of a feature to be synced (e.g. 'gene0001')" />
        </repeat>
        <expand macro="wait_for"/>
    </inputs>
    <outputs>
        <data format="txt" name="results" label="Synchronize features into Tripal" />
    </outputs>
    <tests>
        <test expect_failure="true">
            <param name="organism" value="Testus testus" />
            <param name="types" value="gene mRNA" />
            <param name="types" value="gene0001 gene0002" />

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

        **Synchronize Features**

        With this tool, you can synchronize some features from the Chado database into the Tripal instance.
        A corresponding Drupal node will be created for each feature.

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