annotate analysis_load_interpro.xml @ 5:9a4b816d8a86 draft

planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 35c5eff77b573a66f3611b4906417df9a440c857

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

        &&

        cp '${input}' "\${tmp_dir}/interpro.xml"

        &&

        @AUTH@

        tripaille analysis load_interpro

            @ANALYSIS@

            --interpro_parameters '${params}'

            ${parse_go}

            @MATCHING@

            "\${tmp_dir}/interpro.xml"

        &&

        echo "Data loaded" > '$results'
    ]]></command>
    <inputs>
        <param name="input"
               type="data"
               format="xml"
               label="InterProScan results" />

        <param name="parse_go"
               type="boolean"
               checked="true"
               truevalue="--parse_go"
               falsevalue=""
               label="Load GO annotation to the database" />

        <param name="params"
               type="text"
               label="InterProScan parameters used to produce the results" />

        <expand macro="matching"/>
        <expand macro="analysis" />
        <expand macro="wait_for"/>
    </inputs>
    <outputs>
        <data format="txt" name="results" label="Load InterProScan results into Tripal" />
    </outputs>
    <tests>
        <test expect_failure="true" expect_exit_code="1">
            <param name="input" value="interpro.xml" />
            <param name="parse_go" value="true" />
            <param name="params" value="--some --param" />
            <param name="query_type" value="mRNA" />
            <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="interproscan" />
                <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 InterProScan results**

        With this tool, you can load InterProScan 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_interpro <http://github.com/tripal/tripal_analysis_interpro>`_ module must be installed and configured on the Tripal instance.

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