view macros.xml @ 31:9c5d82d3c87e draft

planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit cd459f55fcb828e250986412fb779234ad89b3b2

<macros>
    <xml name="verify_hub_structure" token_genome="Dbia3" token_test="common">
        <!--genomes.txt -->
        <extra_files type="file" name="myHub/genomes.txt" value="@TEST@/myHub/genomes.txt" />

        <extra_files type="file" name="myHub/@GENOME@.html" value="@TEST@/myHub/@GENOME@.html"/>
        <!-- hub.txt -->
        <extra_files type="file" name="myHub/hub.txt" value="@TEST@/myHub/hub.txt" lines_diff="2">
            <assert_contents>
                <has_text text="email"/>
            </assert_contents>
        </extra_files>
        <!-- 2bit file -->
        <extra_files type="file" name="myHub/@GENOME@/@GENOME@.2bit" value="common/@GENOME@.2bit" />
        <!-- groups.txt -->
        <extra_files type="file" name="myHub/@GENOME@/groups.txt" value="@TEST@/myHub/@GENOME@/groups.txt" />
        <!-- description.html -->
        <extra_files type="file" name="myHub/@GENOME@/description.html" value="@TEST@/myHub/@GENOME@/description.html"/>
        <!-- trackDb.txt -->
        <extra_files type="file" name="myHub/@GENOME@/trackDb.txt">
            <assert_contents>
                <has_text text="track"/>
                <has_text text="longLabel"/>
                <has_text text="shortLabel"/>
                <has_text text="bigDataUrl"/>
                <has_text text="type"/>
                <has_text text="visibility"/>
                <has_text text="thickDrawItem"/>
                <has_text text="priority"/>
                <has_text text="color"/>
                <has_text text="group"/>
                <yield />
            </assert_contents>
        </extra_files>
    </xml>

    <xml name="verify_hub_structure_no_track" token_genome="Dbia3" token_test="common">
        <!--genomes.txt -->
        <extra_files type="file" name="myHub/genomes.txt" value="@TEST@/myHub/genomes.txt" />

        <extra_files type="file" name="myHub/@GENOME@.html" value="@TEST@/myHub/@GENOME@.html"/>
        <!-- hub.txt -->
        <extra_files type="file" name="myHub/hub.txt" value="@TEST@/myHub/hub.txt" lines_diff="2">
            <assert_contents>
                <has_text text="email"/>
            </assert_contents>
        </extra_files>
        <!-- 2bit file -->
        <extra_files type="file" name="myHub/@GENOME@/@GENOME@.2bit" value="common/@GENOME@.2bit" />
        <!-- description.html -->
        <extra_files type="file" name="myHub/@GENOME@/description.html" value="@TEST@/myHub/@GENOME@/description.html"/>
    </xml>


    <xml name="add_trix_file">
        <conditional name="add_trix_index">
            <param name="add_trix_index_selector" type="select" label="Add Trix index that allow for fast look-up of free text associated with a list of identifiers." help="More about Trix index: https://genome.ucsc.edu/goldenpath/help/trix.html">
                <option value="no" selected="true">No</option>
                <option value="yes">Yes</option>
            </param>
            <when value="yes">
                <param name="trix_index" 
                    type="data"
                    format="txt"
                    multiple="true"
                    min="2"
                    max="2"
                    label="Specify Trix index" 
                    help="Dataset collection containing ix and ixx files generated by UCSC Trix Index Generator"
                />
                <yield />
            </when>
            <when value="no">
            </when>
        </conditional>
    </xml>


</macros>