<?xml version="1.0"?>
<tool id="analysis_load_blast" profile="16.04" name="Load Blast 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 '${blast_output}' "\${tmp_dir}/blast_input.xml"

        &&

        @AUTH@

        tripaille analysis load_blast

            --is_concat

            --blastdb_id '${blastdb}'

            --blast_parameters '${params}'

            @MATCHING@

            @ANALYSIS@

            "\${tmp_dir}/blast_input.xml"

        &&

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

        <param argument="--blastdb"
               type="select"
               dynamic_options="list_blastdbs()"
               label="Blast databank used" />

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

        <expand macro="matching"/>

        <expand macro="analysis" />
    </inputs>
    <outputs>
        <data format="txt" name="results" label="Load Blast results into Tripal" />
    </outputs>
    <tests>
        <test expect_failure="true" expect_exit_code="1">
            <param name="blast_output" value="blast.xml" />
            <param name="blastdb" value="genbank:protein" />
            <param name="params" value="-e 0.001" />
            <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="blastp" />
                <param name="program_version" value="2.5.0" />
                <param name="algorithm" value="blast" />
                <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 Blast results**

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

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