Mercurial > repos > bgruening > jbrowse2
diff macros.xml @ 0:53c2be00bb6f draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
author | bgruening |
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date | Wed, 05 Jun 2024 08:15:49 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Jun 05 08:15:49 2024 +0000 @@ -0,0 +1,481 @@ +<macros> + <token name="@TOOL_VERSION@">2.11.1</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="1.82">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="0.0.12-0">hictk</requirement> + <requirement type="package" version="3.0">zip</requirement> + <yield/> + </requirements> + </xml> + <token name="@DATA_DIR@">\$GALAXY_JBROWSE_SHARED_DIR</token> + <token name="@VERSION_SUFFIX@">0</token> + <xml name="creators"> + <creator> + <person givenName="Helena" familyName="Rasche" url="https://github.com/hexylena"/> + <person givenName="Anthony" familyName="Bretaudeau" url="https://github.com/abretaud"/> + <person givenName="Ross" familyName="Lazarus" url="https://github.com/fubar2/"/> + </creator> + </xml> + <xml name="genome_selector" token_help="" token_label="Fasta sequences" token_optional="False"> + <conditional name="reference_genome"> + <param name="genome_type_select" type="select" label="Reference genome to display" help="Built-in references"> + <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 name="genomes" type="select" optional="@OPTIONAL@" label="@LABEL@" help="@HELP@"> + <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 name="genomes" type="data" format="fasta" optional="@OPTIONAL@" label="@LABEL@" help="@HELP@" 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 name="@SELECT_NAME@" type="select" label="@SELECT_LABEL@"> + <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 name="@NAME@" type="color" value="@VALUE@" label="@LABEL@" 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 name="brewer_scheme" type="select" label="Brewer color 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 name="autoCollection" type="data_collection" label="Collection of bed, bam and other track files"/> + </when> + <when value="form"/> + </conditional> + <param name="zipOut" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Create a zip archive for downloading rather than viewing" help="Default is to make an interactive browser appear when the 'eye' icon is activated"/> + <param name="defaultLocation" type="text" value="" label="Subset to display to new users" help="Initial subset to be shown for users who have never visited the browser before. Example: 'ctgA:1234..5678"/> + <param name="session_name" type="text" value="New JBrowse2 session" label="Session name" help="Displayed at the top of the window"/> + <param name="enableAnalytics" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Enable analytics" help="Will send usage data to Google Analytics, see https://github.com/GMOD/jbrowse-components/issues/1166"/> + <param name="primary_color" type="color" value="#0D233F" label="Primary color"> + <sanitizer> + <valid initial="string.ascii_letters,string.digits"> + <add value="#"/> + </valid> + </sanitizer> + </param> + <param name="secondary_color" type="color" value="#721E63" label="Secondary color"> + <sanitizer> + <valid initial="string.ascii_letters,string.digits"> + <add value="#"/> + </valid> + </sanitizer> + </param> + <param name="tertiary_color" type="color" value="#135560" label="Tertiary color"> + <sanitizer> + <valid initial="string.ascii_letters,string.digits"> + <add value="#"/> + </valid> + </sanitizer> + </param> + <param name="quaternary_color" type="color" value="#FFB11D" label="Quaternary color"> + <sanitizer> + <valid initial="string.ascii_letters,string.digits"> + <add value="#"/> + </valid> + </sanitizer> + </param> + <param name="font_size" type="integer" value="10" label="Font size"/> + </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 name="bicolor_pivot_select" type="select" label="Bicolor Pivot"> + <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 name="pivot_point" type="float" value="0.0" label="JBrowse style.bicolor_pivot" 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 name="color_score_select" type="select" label="Color Score Algorithm" 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 name="score_scaling" type="select" label="JBrowse style.color function's 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 name="scale_select" type="select" label="How should minimum and maximum values be determined for the scores of the features"> + <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 name="minimum" type="integer" value="0" label="Minimum expected score"/> + <param name="maximum" type="integer" value="100" label="Maximum expected score"/> + </when> + </conditional> + <!-- Scale color --> + <conditional name="color_scheme" label="Color Scheme for scored features"> + <param name="score_scheme" type="select" label="JBrowse style.color function's color scheme for scored values"> + <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 name="track_visibility" type="select" label="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 name="show_labels" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show labels"/> + <param name="show_descriptions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show descriptions"/> + <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 name="max_height" type="integer" value="600" label="Max height" 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 name="show_labels" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show labels"/> + <param name="show_descriptions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show descriptions"/> + <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"> + <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 name="label" type="text" value="jexl:get(feature,'name') || get(feature,'id')" label="Features label" 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 name="description" type="text" value="jexl:get(feature,'note') || get(feature,'description')" label="Features 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" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Draw cross hatches"/> + <param name="minScore" type="integer" value="" optional="true" label="Min score"/> + <param name="maxScore" type="integer" value="" optional="true" label="Max score"/> + </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" type="integer" value="1" label="Resolution"/> + <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" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Fill in histogram"/> + <param name="scaleType" type="select" label="Autoscale type"> + <option value="linear" selected="true">Linear</option> + <option value="log">Log</option> + </param> + <param name="displayCrossHatches" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Draw cross hatches"/> + <param name="minScore" type="integer" value="" optional="true" label="Min score"/> + <param name="maxScore" type="integer" value="" optional="true" label="Max score"/> + </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 name="menu_action" type="select" label="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 name="menu_label" type="text" label="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 name="menu_title" type="text" label="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 name="menu_url" type="text" label="Menu url" help="Destination URL ({name}, {id}, {type}, {start}, {end}, {strand} variables will be interpreted)"> + <expand macro="menu_sanitize"/> + </param> + <param name="menu_icon" type="select" label="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"> + <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 name="annotation" type="data" format="@FORMAT@" optional="true" label="@LABEL@" multiple="True"/> + </when> + <when value="uri"> + <param name="annouri" type="text" label="@LABEL@"/> + <param name="annoname" type="text" label="Short name for track display"> + <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"> + <param name="annotation" type="data" format="@FORMAT@" label="@LABEL@" 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 name="annotation" type="text" label="@LABEL@"/> + <param name="annoname" type="text" label="Short name for this reference" 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>