Mercurial > repos > eduardo > annotateviz
diff macros.xml @ 0:7537482eed36 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty
| author | eduardo |
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| date | Sat, 17 Jun 2017 13:31:06 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Sat Jun 17 13:31:06 2017 -0400 @@ -0,0 +1,344 @@ +<?xml version="1.0"?> +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="0.8">gffutils</requirement> + <requirement type="package" version="1.12.1">jbrowse</requirement> + <requirement type="package" version="2.7">python</requirement> + <requirement type="package" version="1.66">biopython</requirement> + <requirement type="package" version="0.6.2">bcbiogff</requirement> + <requirement type="package" version="1.2">samtools</requirement> + <requirement type="package" version="3.11">pyyaml</requirement> + <yield/> + </requirements> + </xml> + <token name="@DATA_DIR@">\$GALAXY_JBROWSE_SHARED_DIR</token> + <token name="@WRAPPER_VERSION@">0.5.1</token> + <xml name="stdio"> + <stdio> + <exit_code range="1:"/> + <exit_code range=":-1"/> + <regex match="Error:"/> + <regex match="Exception:"/> + </stdio> + </xml> + <token name="@ATTRIBUTION@"><![CDATA[ +**Attribution** + +This Galaxy tool relies on the JBrowse, maintained by the GMOD Community. The Galaxy wrapper is a fork of Eric Rasche JBrowse wrapper +]]> + </token> + <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="track_display"> + <param type="select" label="Track Visibility" name="track_visibility"> + <option value="default_off">Off for new users</option> + <option value="default_on">On for new users</option> + <option value="force">Force On</option> + <option value="always">Always On (ignores URL parameters)</option> + </param> + </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="Track Padding" type="integer" value="20" name="trackPadding" help="Spacing between tracks in the genome view, in pixels." /> + + <param label="Enable Share Link" name="shareLink" type="boolean" checked="true" truevalue="true" falsevalue="false" /> + <param label="About the Browser" type="text" name="aboutDescription" value="" help="Description of the browser to be used in the 'About' popup" /> + + <param label="Show Track List" name="show_tracklist" type="boolean" checked="true" truevalue="true" falsevalue="false" help="Optionally hide the track list"/> + <param label="Show Navigation" name="show_nav" type="boolean" checked="true" truevalue="true" falsevalue="false" help="Optionally hide the navigation menu"/> + <param label="Show Overview" name="show_overview" type="boolean" checked="true" truevalue="true" falsevalue="false" help="Optionally hide the overview bar"/> + <param label="Show Menu" name="show_menu" type="boolean" checked="true" truevalue="true" falsevalue="false" help="Optionally hide the menu bar"/> + + <param label="Hide Genome Options" name="hideGenomeOptions" type="boolean" truevalue="true" falsevalue="false" help="Hide options for opening a sequence file"/> + </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">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> + <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_styling" + token_classname="feature" + token_label="name,id" + token_description="note,description" + token_height="100px"> + <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false"> + <param label="JBrowse style.className" type="text" + name="style_classname" + value="@CLASSNAME@" + help="Set CSS style.className property"/> + <param label="JBrowse style.label" + type="text" + name="style_label" + value="@LABEL@" + help="Comma-separated list of case-insensitive feature tags to use for showing the feature's label. The first one found will be used. Default 'name,id'" /> + <param label="JBrowse style.description" + type="text" + name="style_description" + value="@DESCRIPTION@" + help="Comma-separated list of case-insensitive feature tags to check for the feature's long description. The first one found will be used."/> + <param label="JBrowse style.height" + type="text" + name="style_height" + value="@HEIGHT@" + help="Height in pixels of glyphs. Default value varies from glyph to glyph. Note that the 'compact' displayMode uses style->height * 0.35 so changing style height can adjust the compact visualization."/> + </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 ({name}, {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>