Mercurial > repos > fubar > jbrowse2
view macros.xml @ 116:b55199c56abd draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7b9eed035bb929af8907bb9f810b0c201562cdf2
author | bgruening |
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date | Wed, 28 Aug 2024 07:34:43 +0000 |
parents | 4aec47f872b3 |
children | c4b77883c0a7 |
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<macros> <token name="@TOOL_VERSION@">2.13.1</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@">1</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="Advanced JBrowse Options: collections, locations, colours, font size and default bp per pixel" 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" collection_type="list" 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="bpPerPx" type="integer" min="1" value="50" label="Base pairs per display pixel for default view" help="Make the default window show more or less BP of sequence. For some reason not automatable in JB2, sorry"/> <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> <param name="usebedscore" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use column 5 as a score for the display if bed format" help="The *Bigwig extremes to bed features* tool generates bed files with scores 1 or -1. This option renders them red and blue"/> </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="color" type="color" value="#135560" label="Wiggle colour"> <sanitizer> <valid initial="string.ascii_letters,string.digits"> <add value="#"/> </valid> </sanitizer> </param> <param name="autoscale" type="select" label="Autoscale type"> <option value="global">Global</option> <option value="globalsd" selected="true">Global ± 3σ</option> <option value="local">Local</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: Internet connection required to view. Tabix index files must be available</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@" help="Requires internet. Will show an error if not online. Saves all the tabix file disk storage"/> <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>