comparison macros.xml @ 85:3b2ff9864995 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty

84:5c295cc220ed

            <option value="compact">compact</option>
            <option value="reducedRepresentation">reducedRepresentation</option>
            <option value="collapse">collapse</option>
        </param>
        <param label="Max height" name="max_height" type="integer" value="600" help="Maximum height that the track is permitted to reach in pixels."/>
    </xml>

    <xml name="track_styling_feature">
        <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false">
        <conditional name="track_style">

                    help="Multiple references can be used for mashmap PAF. A URI source requires all the associated tabix index files to be in place.">
                    <option value="history" selected="true">PAF reference comparison genome from a history file</option>
                    <option value="uri">PAF reference comparison genome tabix .gz URI with index files at the corresponding URIs</option>
                </param>
                <when value="history">
                    <repeat name="refgenomes" title="PAF reference comparison genome used to make the PAF" min="1">
                       <param label="@LABEL@" format="@FORMAT@" name="annotation" multiple="True" optional="true" type="data" />
                       <param label="Please provide a short name for track display" name="annoname" type="text"
                       help="Short names take less track space. No spaces allowed here">
                             <sanitizer invalid_char="_">
                                <valid initial="string.printable" >
                                    <remove value=" " />
                                </valid>
                              </sanitizer>
                        </param>
                    </repeat>
                </when>
                <when value="uri">
                    <repeat name="refgenomes" title="PAF reference comparison genome URI" min="1">
                       <param label="@LABEL@" name="annotation"  type="text" />
                       <param label="Short name for this reference" name="annoname" type="text" help="Short names take less track space">
                             <sanitizer invalid_char="_">
                                <valid initial="string.printable" >
                                    <remove value="'" />

85:3b2ff9864995

            <option value="compact">compact</option>
            <option value="reducedRepresentation">reducedRepresentation</option>
            <option value="collapse">collapse</option>
        </param>
        <param label="Max height" name="max_height" type="integer" value="600" help="Maximum height that the track is permitted to reach in pixels."/>
    </xml>

    <xml name="track_styling_vgp">
         <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false">
        <param label="Show labels" name="show_labels" type="boolean" checked="false" truevalue="true" falsevalue="false" />
        <param label="Show descriptions" name="show_descriptions" type="boolean" checked="false" truevalue="true" falsevalue="false" />
        <param name="display" type="select" label="Display style" help="How the track will be displayed by default">
            <option value="LinearBasicDisplay" selected="true">LinearBasicDisplay</option>
            <option value="LinearPileupDisplay">LinearPileupDisplay - good for dense tracks at scale</option>
            <option value="LinearArcDisplay">LinearArcDisplay</option>
        </param>
        </section>
    </xml>

    <xml name="track_styling_feature">
        <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false">
        <conditional name="track_style">

                    help="Multiple references can be used for mashmap PAF. A URI source requires all the associated tabix index files to be in place.">
                    <option value="history" selected="true">PAF reference comparison genome from a history file</option>
                    <option value="uri">PAF reference comparison genome tabix .gz URI with index files at the corresponding URIs</option>
                </param>
                <when value="history">
                       <param label="@LABEL@" format="@FORMAT@" name="annotation"  type="data"
                          help="Add all PAF reference comparison genomes used to make the PAF" multiple="true" />
                </when>
                <when value="uri">
                    <repeat name="refuri" title="PAF reference comparison genome URI" min="1">
                       <param label="@LABEL@" name="annotation"  type="text" />
                       <param label="Short name for this reference" name="annoname" type="text" help="Short names take less track space">
                             <sanitizer invalid_char="_">
                                <valid initial="string.printable" >
                                    <remove value="'" />