annotate analysis_load_go.xml @ 6:8332cd93e77a draft default tip

"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit ea279e5b47cf3d5767328d17b0e40e57b0238ea1"

<?xml version="1.0"?>
<tool id="analysis_load_go" profile="16.04" name="Load Blast2GO results" version="@WRAPPER_VERSION@.0">
    <description>into Tripal</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <code file="tripal.py"/>
    <expand macro="stdio"/>
    <command><![CDATA[
        tmp_dir=`mktemp -d -p "@DATA_DIR@"` && chmod a+rx "\${tmp_dir}"

        &&

        cp '${input}' "\${tmp_dir}/blast2go.gaf"

        &&

        @AUTH@

        tripaille analysis load_go

            --organism_id '${organism}'

            @ANALYSIS@

            #if str($matching.query_re):
                --re_name '${matching.query_re}'
            #end if

            #if $matching.query_uniquename:
                --query_matching 'uniquename'
            #else
                --query_matching 'uniquename'
            #end if

            --query_type '$matching.query_type'

            "\${tmp_dir}/blast2go.gaf"

        &&

        echo "Data loaded" > '$results'
    ]]></command>
    <inputs>
        <param name="input"
               type="data"
               format="txt"
               label="Blast2Go results (GAF file)" />

        <param argument="--organism"
               type="select"
               dynamic_options="list_organisms()"
               label="Organism" />

        <expand macro="matching"/>
        <expand macro="analysis" />
        <expand macro="wait_for"/>
    </inputs>
    <outputs>
        <data format="txt" name="results" label="Load Blast2GO results into Tripal" />
    </outputs>
    <tests>
        <test expect_failure="true" expect_exit_code="1">
            <param name="input" value="blast2go.gaf" />
            <param name="query_type" value="polypeptide" />
            <param name="query_uniquename" value="true" />
            <section name="analysis">
                <param name="name" value="Some analysis" />
                <param name="program" value="interproscan" />
                <param name="program_version" value="58.2" />
                <param name="algorithm" value="blast2go" />
                <param name="source" value="NCBI" />
                <param name="source_version" value="1.0" />
                <param name="source_uri" value="http://ncbi.com/somewhere" />
                <param name="description" value="My cool new test analysis" />
                <param name="date" value="2016-12-12" />
            </section>

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

        **Load Blast2Go results**

        With this tool, you can load Blast2go results into the Tripal/Chado database.

        A corresponding analysis will be created, keep in mind that you cannot add multiple analysis with the same program, program version and source.

        The `tripal_analysis_go <http://github.com/tripal/tripal_analysis_go>`_ module must be installed and configured on the Tripal instance.

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