annotate macros.xml @ 71:e26a8a6d2d2e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cf208cecf0140ff43d145a44713ab7108057fb8b

<?xml version="1.0"?>
<macros>
    <token name="@TOOL_VERSION@">2.10.1</token>
    <xml name = "edamInc">
        <edam_topics>
            <edam_topic>topic_3307</edam_topic>
            <edam_topic>topic_0092</edam_topic>
        </edam_topics>
        <edam_operations>
            <edam_operation>operation_0573</edam_operation>
            <edam_operation>operation_0564</edam_operation>
        </edam_operations>
    </xml>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">jbrowse2</requirement>
            <requirement type="package" version="1.81">biopython</requirement>
            <requirement type="package" version="0.7.1">bcbio-gff</requirement>
            <requirement type="package" version="1.19">samtools</requirement>
            <requirement type="package" version="6.0.1">pyyaml</requirement>
            <requirement type="package" version="1.11">tabix</requirement>
            <requirement type="package" version="4.6.0">findutils</requirement>
            <requirement type="package" version="0.0.8">hictk</requirement>
            <yield/>
        </requirements>
    </xml>
    <token name="@DATA_DIR@">\$GALAXY_JBROWSE_SHARED_DIR</token>
    <token name="@WRAPPER_VERSION@">galaxy2</token>
    <token name="@ATTRIBUTION@"><![CDATA[
**Attribution**
This Galaxy tool relies on the JBrowse2, maintained by the GMOD Community. The Galaxy wrapper is maintained by Ross Lazarus
until the IUC complete their own.
]]>
    </token>
    <xml name="genome_selector"
        token_help=""
        token_label="Fasta sequences"
        token_optional="False" >
        <conditional name="reference_genome">
            <param help="Built-in references" label="Reference genome to display" name="genome_type_select" type="select">
                <option selected="True" value="indexed">Use a built-in genome</option>
                <option value="history">Use a genome from history</option>
            </param>
            <when value="indexed">
                <param
                help="@HELP@"
                label="@LABEL@"
                name="genomes"
                type="select"
                optional="@OPTIONAL@"
                >
                    <options from_data_table="all_fasta">
                        <filter column="2" type="sort_by" />
                        <validator message="No genomes are available for the selected input dataset" type="no_options" />
                    </options>
                </param>
            </when>
            <when value="history">
                <param
                format="fasta"
                label="@LABEL@"
                help="@HELP@"
                name="genomes"
                type="data"
                optional="@OPTIONAL@"
                multiple="True" />
            </when>
        </conditional>
    </xml>

    <xml name="auto_manual_tk"
        token_cond_label="Color"
        token_cond_name="color"
        token_select_label="Color Specification"
        token_select_name="color_select"
        token_automatic_label="Automatically selected"
        token_manual_label="Manual Color Selection">
        <conditional name="@COND_NAME@" label="@COND_LABEL@">
            <param type="select" label="@SELECT_LABEL@" name="@SELECT_NAME@">
                <option value="automatic" selected="true">@AUTOMATIC_LABEL@</option>
                <option value="manual">@MANUAL_LABEL@</option>
            </param>
            <when value="automatic">
            </when>
            <when value="manual">
                <yield />
            </when>
        </conditional>
    </xml>

    <xml name="jb_color"
        token_label="JBrowse style.color"
        token_name="style_color"
        token_value="goldenrod"
        token_help="Basic color of features. Most glyphs interpret this as the fill color of the rectangle they draw. Color syntax is the same as that used for CSS"
        >
        <param label="@LABEL@" type="color" name="@NAME@" value="@VALUE@" help="@HELP@">
            <sanitizer>
                <valid initial="string.letters,string.digits">
                    <add value="#" />
                </valid>
            </sanitizer>
        </param>
    </xml>

    <xml name="auto_color"
        token_cond_label="Color"
        token_cond_name="color"
        token_select_label="Color Selection"
        token_select_name="color_select"
        token_automatic_label="Automatically selected"
        token_manual_label="Manual Color Selection">
        <expand macro="auto_manual_tk"
                cond_label="@COND_LABEL@"
                cond_name="@COND_NAME@"
                select_label="@SELECT_LABEL@"
                select_name="@SELECT_NAME@"
                automatic_label="@AUTOMATIC_LABEL@"
                manual_label="@MANUAL_LABEL@">
            <expand macro="jb_color" />
            <yield />
        </expand>
    </xml>



    <xml name="brewer_scheme">
        <param type="select" label="Brewer color Scheme" name="brewer_scheme">
            <option value="BrBg">BrBg: Brown - Blue Green</option>
            <option value="PiYg">PiYg: Pink - Yellow Green</option>
            <option value="PRGn">PRGn: Purple Red - Green</option>
            <option value="PuOr">PuOr: Purple - Orange</option>
            <option value="RdBu" selected="true">RdBu: Red - Blue</option>
            <option value="RdGy">RdGy: Red - Gray</option>
            <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"
                    help="A collection of bam/vcf and other track types will be converted into a JBrowse2 automatically">
                    <option value="form" selected="true">Fill in the tool form to specify tracks for the output JBrowse2</option>
                    <option value="collect">Convert a collection of suitable track files</option>
                </param>
                <when value="collect">
                       <param label="Collection of bed, bam and other track files" name="autoCollection" type="data_collection" />
                </when>
                <when value="form">
                </when>
            </conditional>

            <param label="Create a zip archive for downloading rather than viewing " name="zipOut" help="Default is to make an interactive browser appear when the 'eye' icon is activated"
            type="boolean" checked="false" truevalue="true" falsevalue="false" />
            <param label="Subset to display to new users" type="text" name="defaultLocation" value="" help="Initial subset to be shown for users who have never visited the browser before. Example: 'ctgA:1234..5678'"/>
            <param label="Session name" type="text" name="session_name" value="New session" help="Displayed at the top of the window"/>
            <param label="Enable analytics" help="Will send usage data to Google Analytics, see https://github.com/GMOD/jbrowse-components/issues/1166" name="enableAnalytics" type="boolean" checked="false" truevalue="true" falsevalue="false" />

            <param name="primary_color" type="color" label="Primary color" value="#0D233F">
                <sanitizer>
                    <valid initial="string.ascii_letters,string.digits">
                        <add value="#" />
                    </valid>
                </sanitizer>
            </param>
            <param name="secondary_color" type="color" label="Secondary color" value="#721E63">
                <sanitizer>
                <valid initial="string.ascii_letters,string.digits">
                    <add value="#" />
                </valid>
                </sanitizer>
            </param>
            <param name="tertiary_color" type="color" label="Tertiary color" value="#135560">
                <sanitizer>
                    <valid initial="string.ascii_letters,string.digits">
                        <add value="#" />
                    </valid>
                </sanitizer>
            </param>
            <param name="quaternary_color" type="color" label="Quaternary color" value="#FFB11D">
                <sanitizer>
                    <valid initial="string.ascii_letters,string.digits">
                        <add value="#" />
                    </valid>
                </sanitizer>
            </param>

            <param label="Font size" name="font_size" type="integer" value="10" />
        </section>
    </xml>

    <xml name="color_selection_minmax">
        <section name="jbcolor" title="JBrowse Color Options [Advanced]" expanded="false">
        <!-- Abuse auto/manual for bicolor pivot. Means we'll have to handle the
            auto case as well, but may be safe to just say "brewer colors? Pff,
            red/blue" -->
        <expand macro="auto_manual_tk"
                token_cond_label="Color"
                token_cond_name="color"
                token_select_label="Color Selection"
                token_select_name="color_select"
                token_automatic_label="Automatically selected"
                token_manual_label="Manual Color Selection">
            <expand macro="jb_color"
                    label="JBrowse style.pos_color"
                    name="style_pos_color"
                    value="blue"
                    help="CSS color, default 'blue'. When drawing bicolor plots, the fill color to use for values that are above the pivot point." />
            <expand macro="jb_color"
                    label="JBrowse style.neg_color"
                    name="style_neg_color"
                    value="red"
                    help=" CSS color, default 'red'. When drawing bicolor plots, the fill color to use for values that are below the pivot point." />
        </expand>

        <conditional name="bicolor_pivot" label="Bicolor Pivot">
            <param type="select" label="Bicolor Pivot" name="bicolor_pivot_select">
                <option value="zero" selected="true">Zero</option>
                <option value="mean">Mean</option>
                <option value="custom">Custom Value</option>
            </param>
            <when value="zero" />
            <when value="mean" />
            <when value="custom">
                <param label="JBrowse style.bicolor_pivot" type="float" name="pivot_point" value="0.0" help="Where to change from pos_color to neg_color when drawing bicolor plots." />
            </when>
        </conditional>
        </section>
    </xml>

    <xml name="color_selection"
        token_scaling_lin_select="true"
        token_scaling_log_select="false"
        >
        <section name="jbcolor_scale" title="JBrowse Feature Score Scaling &amp; Coloring Options [Advanced]" expanded="false">
        <conditional name="color_score" label="JBrowse style.color &amp; Score relationship">
            <param type="select" label="Color Score Algorithm" name="color_score_select" help="How to color the features. If it is based on score, then features with a score attribute anywhere in their hierachy will have their color affected by the score. If you choose to ignore the score, then you'll be able to select a single solid color for every feature in the track">
                <option value="score">Based on score</option>
                <option value="none" selected="true">Ignore score</option>
            </param>
            <when value="none">
                <!-- When no scaling is done, no scores available, then just let the
                    user choose a base color for the track -->
                <expand macro="auto_color" />
            </when>
            <when value="score">
                <!-- Scaling -->
                <param type="select" label="JBrowse style.color function's score scaling" name="score_scaling"
                    help="How should the colors be distributed across the values? For blast results which distributes scores on the scale of approximately [1e-500, 10], it makes sense to request a logarithmic scaling of the color values. Logarithmic is indeed the default for blast. However other analysis methods may produce scores on ranges such as [0, 100] where a linear scale would be more appropriate for color distribution.">
                    <option value="linear" selected="@SCALING_LIN_SELECT@">Linear scaling</option>
                    <option value="logarithmic" selected="false">Logarithmic scaling</option>
                    <option value="blast" selected="@SCALING_LOG_SELECT@">Blast scaling</option>
                </param>

                <!-- Scaling Bounds -->
                <conditional name="score_scales" label="Minimum/Maximum values for track scores">
                    <param type="select" label="How should minimum and maximum values be determined for the scores of the features" name="scale_select">
                        <option value="automatic" selected="true">Automatically determined</option>
                        <option value="manual">Manually specify minimum and maximum expected scores for the feature track</option>
                    </param>
                    <when value="automatic" />
                    <when value="manual">
                        <param label="Minimum expected score" name="minimum" type="integer" value="0" />
                        <param label="Maximum expected score" name="maximum" type="integer" value="100" />
                    </when>
                </conditional>

                <!-- Scale color -->
                <conditional name="color_scheme" label="Color Scheme for scored features">
                    <param type="select" label="JBrowse style.color function's color scheme for scored values" name="score_scheme">
                        <option value="opacity">Opacity (high scores = 1.0 opacity)</option>
                        <!--<option value="brewer">Brewer Color Schemes</option>-->
                    </param>
                    <when value="opacity">
                        <!-- Single color selection mode -->
                        <expand macro="auto_color" />
                    </when>
                    <!--<when value="brewer">-->
                        <!--[> Brewer continuum selection <]-->
                        <!--<expand macro="brewer_scheme" />-->
                    <!--</when>-->
                </conditional>
            </when>
        </conditional>
        </section>
    </xml>

    <xml name="track_visibility">
        <param type="select" label="Track Visibility" name="track_visibility">
            <option value="default_off">Off when browser opens</option>
            <option value="default_on" selected="true">On when browser opens</option>
        </param>
    </xml>

    <xml name="track_styling_linear">
        <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_mode" type="select" label="Display mode">
            <option value="normal" selected="true">normal</option>
            <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">
            <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>
            <when value="LinearPileupDisplay">
                <expand macro="track_styling_linear"/>
            </when>
            <when value="LinearBasicDisplay">
                <expand macro="track_styling_linear"/>

                <!-- examples: https://github.com/GMOD/jbrowse-components/discussions/2729
                        and https://github.com/GMOD/jbrowse-components/blob/main/plugins/svg/src/SvgFeatureRenderer/configSchema.ts#L41  -->
                <param label="Features label"
                        type="text"
                        name="label"
                        value="jexl:get(feature,'name') || get(feature,'id')"
                        help="See https://jbrowse.org/jb2/docs/config_guide/#configuration-callbacks for syntax">
                    <sanitizer>
                        <valid initial="default">
                            <add value="|" />
                            <add value="{"/>
                            <add value="}"/>
                            <add value="!"/>
                            <add value="?"/>
                            <add value="+"/>
                            <add value="="/>
                            <add value="'"/>
                        </valid>
                    </sanitizer>
                </param>
                <param label="Features description"
                        type="text"
                        name="description"
                        value="jexl:get(feature,'note') || get(feature,'description')"
                        help="See https://jbrowse.org/jb2/docs/config_guide/#configuration-callbacks for syntax">
                    <sanitizer>
                        <valid initial="default">
                            <add value="|" />
                            <add value="{"/>
                            <add value="}"/>
                            <add value="!"/>
                            <add value="?"/>
                            <add value="+"/>
                            <add value="="/>
                            <add value="'"/>
                        </valid>
                    </sanitizer>
                </param>
            </when>
            <when value="LinearArcDisplay"/>
        </conditional>
        </section>
    </xml>

    <xml name="track_styling_xam">
        <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="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">
        <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="LinearWiggleDisplay" selected="true">LinearWiggleDisplay</option>
                </param>
                <when value="LinearWiggleDisplay">
                    <param name="autoscale" type="select" label="Autoscale type">
                        <option value="local" selected="true">Local</option>
                        <option value="global">Global</option>
                        <option value="globalsd">Global ± 3σ</option>
                        <option value="localsd">Local ± 3σ</option>
                    </param>
                    <param name="resolution" label="Resolution" type="integer" value="1"/>
                    <param name="summaryScoreMode" type="select" label="Autoscale type">
                        <option value="max">Max</option>
                        <option value="min">Min</option>
                        <option value="avg">Avg</option>
                        <option value="whiskers" selected="true">Whiskers (combines all three)</option>
                    </param>
                    <param name="filled" label="Fill in histogram" type="boolean" checked="true" truevalue="true" falsevalue="false" />
                    <param name="scaleType" type="select" label="Autoscale type">
                        <option value="linear" selected="true">Linear</option>
                        <option value="log">Log</option>
                    </param>
                    <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_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"
                        name="menu_action"
                        help="Action performed when user clicks on the menu">
                    <option value="iframeDialog" selected="true">iframeDialog: causes the given url to be opened in a popup dialog box within JBrowse, in an iframe element.</option>
                    <option value="newWindow">newWindow: causes the given url to be opened in a new browser window.</option>
                    <option value="navigateTo">navigateTo: opens the given url in the same browser window, navigating the user away from JBrowse.</option>
                </param>
                <param label="Menu label"
                        type="text"
                        name="menu_label"
                        help="Will be displayed in the contextual menu on each feature ({name}, {id}, {type}, {start}, {end}, {strand} variables will be interpreted)">
                    <expand macro="menu_sanitize" />
                </param>
                <param label="Menu title"
                        type="text"
                        name="menu_title"
                        help="Will be displayed in the popup title bar if displayed ({id}, {type}, {start}, {end}, {strand} variables will be interpreted)">
                    <expand macro="menu_sanitize" />
                </param>
                <param label="Menu url"
                        type="text"
                        name="menu_url"
                        help="Destination URL ({name}, {id}, {type}, {start}, {end}, {strand} variables will be interpreted)">
                    <expand macro="menu_sanitize" />
                </param>
                <param label="Menu icon"
                        type="select"
                        name="menu_icon"
                        help="Icon to display next to menu label">
                    <option value="dijitIconBookmark" selected="true">Bookmark</option>
                    <option value="dijitIconSave">Save</option>
                    <option value="dijitIconPrint">Print</option>
                    <option value="dijitIconCut">Cut</option>
                    <option value="dijitIconCopy">Copy</option>
                    <option value="dijitIconClear">Clear</option>
                    <option value="dijitIconDelete">Delete</option>
                    <option value="dijitIconUndo">Undo</option>
                    <option value="dijitIconEdit">Edit</option>
                    <option value="dijitIconNewTask">New Task</option>
                    <option value="dijitIconEditTask">Edit Task</option>
                    <option value="dijitIconEditProperty">Edit Property</option>
                    <option value="dijitIconTask">Task</option>
                    <option value="dijitIconFilter">Filter</option>
                    <option value="dijitIconConfigure">Configure</option>
                    <option value="dijitIconSearch">Search</option>
                    <option value="dijitIconApplication">Application</option>
                    <option value="dijitIconChart">Chart</option>
                    <option value="dijitIconConnector">Connector</option>
                    <option value="dijitIconDatabase">Database</option>
                    <option value="dijitIconDocuments">Documents</option>
                    <option value="dijitIconMail">Mail</option>
                    <option value="dijitLeaf">Leaf</option>
                    <option value="dijitIconFile">File</option>
                    <option value="dijitIconFunction">Function</option>
                    <option value="dijitIconKey">Key</option>
                    <option value="dijitIconPackage">Package</option>
                    <option value="dijitIconSample">Sample</option>
                    <option value="dijitIconTable">Table</option>
                    <option value="dijitIconUsers">Users</option>
                    <option value="dijitIconFolderClosed">Folder Closed</option>
                    <option value="dijitIconFolderOpen">Folder Open</option>
                    <option value="dijitIconError">Error</option>
                </param>
            </repeat>
        </section>
    </xml>

    <xml name="menu_sanitize">
        <sanitizer>
            <valid>
                <add value="{"/>
                <add value="}"/>
                <add value="!"/>
                <add value="?"/>
                <add value="&amp;"/>
                <add value="+"/>
                <add value="="/>
                <add value="'"/>
                <add value='"'/>
            </valid>
        </sanitizer>
    </xml>

    <xml name="input_conditional" token_label="Track Data" token_format="data">
        <conditional name="useuri">
                <param name="insource" type="select" label="Define track data as a history file or an internet URI"
                    help="A public URI implies that all the associated tabix files are also in place. They are created for history files">
                    <option value="history" selected="true">Track data from a history file</option>
                    <option value="uri" >Tabix data URI - index files must be available at corresponding URI</option>
                </param>
                <when value="history">
                       <param label="@LABEL@" format="@FORMAT@" name="annotation" multiple="True" optional="true" type="data" />
                </when>
                <when value="uri">
                       <param label="@LABEL@" name="annouri"  type="text" />
                       <param label="Short name for track display" name="annoname" type="text" >
                             <sanitizer invalid_char="_">
                                <valid initial="string.printable" >
                                    <remove value="'" />
                                </valid>
                              </sanitizer>
                        </param>
                </when>
            </conditional>
     </xml>
    <xml name="pafref_conditional" token_label="Track Data" token_format="data">
        <conditional name="pafuseuri">
                <param name="insource" type="select" label="PAF reference data from a history file or an internet URI?"
                    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="Short name for track display" name="annoname" type="text" help="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="'" />
                                </valid>
                              </sanitizer>
                        </param>
                    </repeat>
                </when>
            </conditional>
     </xml>
    <xml name="citations">
        <citations>
        <citation type="doi">10.1186/s13059-016-0924-1</citation>
        <citation type="doi">10.1101/gr.094607.109</citation>
        </citations>
    </xml>
</macros>