annotate macros.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"?>
<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="3.2.1">python-tripal</requirement>
            <yield/>
        </requirements>
    </xml>

    <xml name="stdio">
        <stdio>
            <regex level="fatal" match="Exception:" source="stderr" />
            <regex level="fatal" match="error" source="stderr" />
            <exit_code range="1:" />
        </stdio>
    </xml>

    <token name="@WRAPPER_VERSION@">3.2.1</token>

    <xml name="citation">
        <citations>
            <citation type="doi">10.1093/database/bat075</citation>
        </citations>
    </xml>

    <token name="@HELP_OVERVIEW@"><![CDATA[
        **Python-tripal Overview**

        Python-tripal provides several tools allowing to load data into a remote Chado-based Tripal database.
        The tripal_rest_api Tripal module must be installed on the remote server to use these tools.
    ]]></token>

    <token name="@HELP@"><![CDATA[
        **Useful Links**

        `Tripal project website <http://tripal.info/>`_

        `Tripal REST API module <http://github.com/abretaud/tripal_rest_api>`_: a Tripal module required to use these galaxy tools
    ]]></token>

    <token name="@DATA_DIR@">\$GALAXY_TRIPAL_SHARED_DIR</token>

    <token name="@AUTH@"><![CDATA[
        echo "__default: local" > '.auth.yml' &&
        echo "local:" >> '.auth.yml' &&
        echo "    tripal_url: \"\$GALAXY_TRIPAL_URL\"" >> '.auth.yml' &&
        echo "    username: \"\$GALAXY_TRIPAL_USER\"" >> '.auth.yml' &&
        echo "    password: \"\$GALAXY_TRIPAL_PASSWORD\"" >> '.auth.yml' &&

        TRIPAILLE_GLOBAL_CONFIG_PATH='.auth.yml'
    ]]></token>

    <xml name="wait_for">
        <param name="wait_for"
               type="data"
               format="data"
               optional="true"
               label="Run this only after the following dataset is ready"
               help="Use this if you want to delay the job execution until some data is already loaded. The selected dataset will not be used for anything else."/>
    </xml>

    <xml name="test_result">
        <assert_stderr>
            <has_text text="MissingSchema" />
        </assert_stderr>
    </xml>

    <xml name="analysis">
        <section name="analysis" title="Analysis" expanded="True">
            <param name="name"
                   type="text"
                   label="The analysis name [mandatory]">
                <expand macro="sanitized"/>
            </param>

            <param name="program"
                   type="text"
                   label="Program name [mandatory]"
                   help="Name of the program that was used to perform this analysis">
                <expand macro="sanitized"/>
            </param>
            <param name="program_version"
                   type="text"
                   label="Program version [mandatory]"
                   help="Version of the program that was used to perform this analysis"/>
            <param name="source"
                   type="text"
                   label="Source name [mandatory]"
                   help="Where this analysis comes from">
                <expand macro="sanitized"/>
            </param>

            <param name="source_version"
                   argument="--sourceversion"
                   type="text"
                   optional="True"
                   label="Source version" />
            <param name="source_uri"
                   argument="--sourceuri"
                   type="text"
                   optional="True"
                   label="Source URI"
                   help="URI where source data was retrieved" />
            <param name="algorithm"
                   argument="--algorithm"
                   type="text"
                   label="Algorithm"
                   optional="True"
                   help="Algorithm of the program that was used to perform this analysis" />
            <param name="description"
                   argument="--description"
                   type="text"
                   optional="True"
                   label="Analysis description">
                <expand macro="sanitized"/>
            </param>
            <param name="date"
                   argument="--date_executed"
                   type="text"
                   optional="True"
                   label="Execution date"
                   help="Format: yyyy-mm-dd  Default: Today">
                <validator type="regex" message="Date in YYYY-MM-DD format">^[0-9]{4}-[0-9]{2}-[0-9]{2}$</validator>
            </param>
        </section>
    </xml>

    <xml name="feature_rel">
        <param name="rel_subject_re"
               argument="--rel-subject-re"
               type="text"
               label="Regular expression to extract the unique name of the parent feature"
               help="this regex will be applied on the fasta definition line to generate the unique name of the parent feature">
            <expand macro="sanitized"/>
        </param>

        <param name="rel_subject_type"
               argument="--rel-subject-type"
               type="text"
               label="Sequence type of the parent"
               help="this should be a Sequence Ontology term" />
    </xml>

    <xml name="match_type">
        <param name="match_type"
               argument="--match-type"
               type="select"
               label="Match type for already loaded features">
            <option value="uniquename" selected="true">Unique name</option>
            <option value="name">Name</option>
        </param>
    </xml>

    <xml name="matching">
        <section name="matching" title="Feature matching" expanded="True">
            <param name="query_type"
                   type="text"
                   label="The feature type of the blast query"
                   help="It must be a valid Sequence Ontology term. e.g. 'contig', 'gene', 'mRNA', 'polypeptide'" />

            <param name="query_uniquename"
                   type="boolean"
                   checked="false"
                   truevalue="--query_uniquename"
                   falsevalue=""
                   label="Find blast query features using their Unique name"
                   help="Feature name will be used otherwise" />

            <param name="query_re"
                   type="text"
                   optional="true"
                   label="Regular expression to extract the feature name from the blast query name"
                   help="leave empty if the first word in query name is sufficient">
                <expand macro="sanitized"/>
            </param>
        </section>
    </xml>

    <xml name="sanitized">
        <sanitizer>
            <valid initial="string.printable">
                <remove value="&apos;"/>
            </valid>
            <mapping initial="none">
                <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;"/>
                <add source="(" target="\("/>
                <add source=")" target="\)"/>
            </mapping>
        </sanitizer>
    </xml>

    <token name="@MATCHING@"><![CDATA[
        #if str($matching.query_re):
            --query_re '${matching.query_re}'
        #end if

        $matching.query_uniquename

        --query_type '$matching.query_type'
    ]]></token>

    <token name="@ANALYSIS@"><![CDATA[
        #if $analysis.algorithm:
            --algorithm '$analysis.algorithm'
        #end if
        #if $analysis.source_version:
            --sourceversion '$analysis.source_version'
        #end if
        #if $analysis.source_uri:
            --sourceuri '$analysis.source_uri'
        #end if
        #if $analysis.description:
            --description '$analysis.description'
        #end if
        #if $analysis.date:
            --date_executed '$analysis.date'
        #end if

        '$analysis.name'
        '$analysis.program'
        '$analysis.program_version'
        '$analysis.source'
    ]]></token>
</macros>