comparison macros.xml @ 62:ab0d6782a95f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty

61:e7a6f7a7148d

            <option value="RdYlBu">RdYlBu: Red - Yellow - Blue</option>
            <option value="RdYlGn">RdYlBu: Red - Yellow - Green</option>
            <option value="Spectral">Spectral</option>
        </param>
    </xml>

    <xml name="general_options">
        <section name="jbgen" title="General JBrowse Options [Advanced]" expanded="false">
            <conditional name="ucol">
                <param name="formcoll" type="select" label="Convert a collection of track files rather than filling in the tool form"

            <conditional name="track_style">
                <param name="display" type="select" label="Display style" help="How the track will be displayed by default">
                    <option value="LinearAlignmentsDisplay" selected="true">LinearAlignmentsDisplay</option>
                    <option value="LinearPileupDisplay">LinearPileupDisplay</option>
                    <option value="LinearSNPCoverageDisplay">LinearSNPCoverageDisplay</option>
                </param>
                <when value="LinearAlignmentsDisplay"/>
                <when value="LinearPileupDisplay"/>
                <when value="LinearSNPCoverageDisplay">
                    <param name="displayCrossHatches" label="Draw cross hatches" type="boolean" checked="true" truevalue="true" falsevalue="false" />
                    <param name="minScore" label="Min score" type="integer" value="" optional="true"/>
                    <param name="maxScore" label="Max score" type="integer" value="" optional="true"/>
                </when>
            </conditional>
        </section>
    </xml>

    <xml name="track_styling_vcf">
        <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false">
            <conditional name="track_style">
                <param name="display" type="select" label="Display style" help="How the track will be displayed by default">
                    <option value="LinearVariantDisplay" selected="true">LinearVariantDisplay</option>
                </param>
                <when value="LinearVariantDisplay">
                    <expand macro="track_styling_linear"/>
                </when>
            </conditional>
        </section>
    </xml>

    <xml name="track_styling_bigwig">

                </when>
            </conditional>
        </section>
    </xml>

    <xml name="track_menu">
        <section name="jbmenu" title="JBrowse Contextual Menu options [Advanced]" expanded="false">
            <repeat name="track_menu" title="Track Menu">
                <param label="Menu action"
                        type="select"

62:ab0d6782a95f

            <option value="RdYlBu">RdYlBu: Red - Yellow - Blue</option>
            <option value="RdYlGn">RdYlBu: Red - Yellow - Green</option>
            <option value="Spectral">Spectral</option>
        </param>
    </xml>


    <xml name="general_options">
        <section name="jbgen" title="General JBrowse Options [Advanced]" expanded="false">
            <conditional name="ucol">
                <param name="formcoll" type="select" label="Convert a collection of track files rather than filling in the tool form"

            <conditional name="track_style">
                <param name="display" type="select" label="Display style" help="How the track will be displayed by default">
                    <option value="LinearAlignmentsDisplay" selected="true">LinearAlignmentsDisplay</option>
                    <option value="LinearPileupDisplay">LinearPileupDisplay</option>
                    <option value="LinearSNPCoverageDisplay">LinearSNPCoverageDisplay</option>
                    <option value="LinearReadArcsDisplay">LinearReadArcsDisplay</option>
                    <option value="LinearReadCloudDisplay">LinearReadCloudDisplay</option>
                </param>
                <!-- TODO check if possible to handle more options than just the display style-->
                <when value="LinearAlignmentsDisplay"/>
                <when value="LinearPileupDisplay"/>
                <when value="LinearSNPCoverageDisplay">
                    <param name="displayCrossHatches" label="Draw cross hatches" type="boolean" checked="true" truevalue="true" falsevalue="false" />
                    <param name="minScore" label="Min score" type="integer" value="" optional="true"/>
                    <param name="maxScore" label="Max score" type="integer" value="" optional="true"/>
                </when>
                <when value="LinearReadArcsDisplay"/>
                <when value="LinearReadCloudDisplay"/>
            </conditional>
        </section>
    </xml>

    <xml name="track_styling_vcf">
        <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false">
            <conditional name="track_style">
                <param name="display" type="select" label="Display style" help="How the track will be displayed by default">
                    <option value="LinearVariantDisplay" selected="true">LinearVariantDisplay</option>
                    <option value="LinearPairedArcDisplay">LinearPairedArcDisplay</option>
                </param>
                <when value="LinearVariantDisplay">
                    <expand macro="track_styling_linear"/>
                </when>
                <when value="LinearPairedArcDisplay"/>
            </conditional>
        </section>
    </xml>

    <xml name="track_styling_bigwig">

                </when>
            </conditional>
        </section>
    </xml>

    <!-- TODO use this -->
    <xml name="track_menu">
        <section name="jbmenu" title="JBrowse Contextual Menu options [Advanced]" expanded="false">
            <repeat name="track_menu" title="Track Menu">
                <param label="Menu action"
                        type="select"