annotate db_index.xml @ 5:1d109af32d7c draft

planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 869e5fd8535deca8325777efcd31c70a514b582a

<?xml version="1.0"?>
<tool id="db_index" profile="16.04" name="Index Tripal data" version="@WRAPPER_VERSION@.1">
    <description>using Elasticsearch</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <command><![CDATA[

        @AUTH@

        tripaille db index

            --mode '${table.mode}'

            #if $table.mode == "table":
              --index_name "${table.index_name}"
            #end if

            #if $queues:
              --queues "$queues"
            #end if

            #if $tokenizer:
              --tokenizer "$tokenizer"
            #end if

            #if $table.mode == "table":
                --table '${table.table}'

                #for $rep in $table.repeat_fields:
                  --fields "${rep.field_name}|${rep.field_type}"
                #end for

                #for $rep in $table.repeat_links:
                  --links "${rep.column}|${rep.url}"
                #end for
            #end if

            #if $expose.do_expose == "yes":
                --exposed
                --index_url '${expose.index_url}'
            #end if

        &&

        echo "Data loaded" > $results
    ]]></command>
    <inputs>
        <conditional name="table">
            <param name="mode"
                   type="select"
                   label="Data to index">
                <option value="website" selected="true">Index all the Tripal content</option>
                <option value="table">Index a specific table</option>
                <option value="nodes">Index all website nodes</option>
                <option value="entities">Index all website entities (Tripal 3 only)</option>
            </param>
            <when value="website"/>
            <when value="table">
                <param name="table"
                       argument="--table"
                       type="text"
                       label="Table to index"
                       help="The name of a Chado (or custom) table to index" />
                <param name="index_name" label="Index Name" argument="--index_name" type="text" help="Index name" />
                <repeat name="repeat_fields" title="Fields">
                    <param name="field_name"
                           label="Field name"
                           argument="--fields"
                           type="text"
                           help="Field to index" />
                    <param name="field_type"
                           label="Field
                           type" type="select"
                           help="Field type">
                        <option value="string" selected="true">string</option>
                        <option value="keyword">keyword</option>
                        <option value="date">date</option>
                        <option value="long">long</option>
                        <option value="double">double</option>
                        <option value="boolean">boolean</option>
                        <option value="ip">ip</option>
                        <option value="object">object</option>
                        <option value="nested">nested</option>
                        <option value="geo_point">geo_point</option>
                        <option value="geo_shape">geo_shape</option>
                        <option value="completion">completion</option>
                    </param>
                </repeat>
                <repeat name="repeat_links" title="Links">
                    <param name="column"
                           label="Table column where to display links"
                           type="text"
                           help="Should be in the list of indexed column" />
                    <param name="url"
                           label="Links url"
                           type="text"
                           help="e.g.: /your/url/[any-column-name]"/>
                </repeat>
            </when>
            <when value="nodes"/>
            <when value="entities"/>
        </conditional>
        <param name="tokenizer"
               type="select"
               label="Tokenizer to use">
            <option value="standard" selected="true">standard</option>
            <option value="letter">letter</option>
            <option value="lowercase">lowercase</option>
            <option value="whitespace">whitespace</option>
            <option value="uax_url_email">uax_url_email</option>
            <option value="classic">classic</option>
            <option value="ngram">ngram</option>
            <option value="edge_ngram">edge_ngram</option>
            <option value="keyword">keyword</option>
            <option value="pattern">pattern</option>
            <option value="path_hierarchy">path_hierarchy</option>
        </param>
        <param name="queues" label="Queues" argument="queues" type="integer" value="10" help="Number of indexing task queues" />
        <conditional name="expose">
            <param name="do_expose" type="select" label="Expose the index to other websites (read-only)">
                <option value="yes" selected="true">No</option>
                <option value="no">No</option>
            </param>
            <when value="no"/>
            <when value="yes">
                <param name="index_url" label="Index Url" argument="--index_url" type="text" help="In order for other sites to link back to your results page, you must specify a path where the form for this index can be reached" />
            </when>
            <when value="nodes"/>
            <when value="entities"/>
        </conditional>
        <expand macro="wait_for"/>
    </inputs>
    <outputs>
        <data format="txt" name="results" label="Index Tripal data" />
    </outputs>
    <tests>
        <test expect_failure="true" expect_exit_code="1">
            <conditional name="table">
                <param name="mode" value="all" />
            </conditional>

            <expand macro="test_result" />
        </test>
        <test expect_failure="true" expect_exit_code="1">
            <conditional name="table">
                <param name="mode" value="singles" />
                <param name="table" value="organism" />
                <param name="fields" value="genus species description" />
            </conditional>

            <expand macro="test_result" />
        </test>
        <test expect_failure="true" expect_exit_code="1">
            <conditional name="table">
                <param name="mode" value="singles" />
                <param name="table" value="organism" />
                <param name="fields" value="genus species description" />
            </conditional>
            <conditional name="expose">
                <param name="expose" value="yes" />
                <param name="index_url" value="http://google.com" />
            </conditional>

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

        **Index using Elasticsearch**

        With this tool, you can trigger indexing of a Tripal instance content using Elasticsearch.

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

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