Mercurial > repos > fubar > jbrowse2
diff macros.xml @ 0:d78175596286 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
| author | fubar |
|---|---|
| date | Mon, 08 Jan 2024 09:20:33 +0000 |
| parents | |
| children | 2de9f585505b |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Jan 08 09:20:33 2024 +0000 @@ -0,0 +1,509 @@ +<?xml version="1.0"?> +<macros> + <token name="@TOOL_VERSION@">2.10.0</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="1.82">biopython</requirement> + <requirement type="package" version="0.7.0">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> + <yield/> + </requirements> + </xml> + <token name="@DATA_DIR@">\$GALAXY_JBROWSE_SHARED_DIR</token> + <token name="@WRAPPER_VERSION@">galaxy0</token> + <token name="@ATTRIBUTION@"><![CDATA[ +**Attribution** +This Galaxy tool relies on the JBrowse, maintained by the GMOD Community. The Galaxy wrapper is developed by the IUC +This xml currently fails silently when profile=22.05 is set. +]]> + </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"> + <param label="Default location" type="text" name="defaultLocation" value="" help="Initial location 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 & Coloring Options [Advanced]" expanded="false"> + <conditional name="color_score" label="JBrowse style.color & 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="true" truevalue="true" falsevalue="false" /> + <param label="Show descriptions" name="show_descriptions" type="boolean" checked="true" 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="LinearArcDisplay">LinearArcDisplay</option> + </param> + <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> + </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"> + <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="&"/> + <add value="+"/> + <add value="="/> + <add value="'"/> + <add value='"'/> + </valid> + </sanitizer> + </xml> + + + <xml name="input_conditional" token_label="Track Data" token_format="data"> + <param label="@LABEL@" format="@FORMAT@" name="annotation" type="data" multiple="True"/> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1101/gr.094607.109</citation> + </citations> + </xml> +</macros>