Mercurial > repos > fubar > jbrowse2
diff macros.xml @ 97:74074746ccd8 draft
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
| author | fubar |
|---|---|
| date | Sat, 01 Jun 2024 05:37:13 +0000 |
| parents | 4c517a0041a8 |
| children | b1260bca5fdc |
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--- a/macros.xml Thu Apr 25 07:25:52 2024 +0000 +++ b/macros.xml Sat Jun 01 05:37:13 2024 +0000 @@ -1,7 +1,6 @@ -<?xml version="1.0"?> <macros> <token name="@TOOL_VERSION@">2.11.0</token> - <xml name = "edamInc"> + <xml name="edamInc"> <edam_topics> <edam_topic>topic_3307</edam_topic> <edam_topic>topic_0092</edam_topic> @@ -33,100 +32,65 @@ maintained by Ross Lazarus and Bjoern Gruening until the IUC complete their own. ]]> </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 help="Built-in references" label="Reference genome to display" name="genome_type_select" type="select"> + <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 - help="@HELP@" - label="@LABEL@" - name="genomes" - type="select" - optional="@OPTIONAL@" - > + <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" /> + <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" /> + <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"> + <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@"> + <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 /> + <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@"> + <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="#" /> + <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 /> + <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"> + <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> @@ -138,247 +102,203 @@ <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"> + <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" /> + <param name="autoCollection" type="data_collection" label="Collection of bed, bam and other track files"/> </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 JB2 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"> + <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 JB2 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="#" /> + <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"> + <param name="secondary_color" type="color" value="#721E63" label="Secondary color"> <sanitizer> <valid initial="string.ascii_letters,string.digits"> - <add value="#" /> + <add value="#"/> </valid> </sanitizer> </param> - <param name="quaternary_color" type="color" label="Quaternary color" value="#FFB11D"> + <param name="tertiary_color" type="color" value="#135560" label="Tertiary color"> <sanitizer> <valid initial="string.ascii_letters,string.digits"> - <add value="#" /> + <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 label="Font size" name="font_size" type="integer" value="10" /> + <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 + <!-- 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> + <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" - > + <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> + <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> - - <!-- 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> + <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> - <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">--> + <!-- 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> + <!--</when>--> + </conditional> + </when> + </conditional> </section> </xml> - <xml name="track_visibility"> - <param type="select" label="Track Visibility" 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 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="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 label="Max height" name="max_height" type="integer" value="600" help="Maximum height that the track is permitted to reach in pixels."/> + <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 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" 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="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> - <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_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"> @@ -393,16 +313,15 @@ <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"/> + <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"> @@ -417,7 +336,6 @@ </conditional> </section> </xml> - <xml name="track_styling_bigwig"> <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false"> <conditional name="track_style"> @@ -431,59 +349,43 @@ <option value="globalsd">Global ± 3σ</option> <option value="localsd">Local ± 3σ</option> </param> - <param name="resolution" label="Resolution" type="integer" value="1"/> + <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" label="Fill in histogram" type="boolean" checked="true" truevalue="true" falsevalue="false" /> + <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" 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"/> + <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 label="Menu action" - type="select" - name="menu_action" - help="Action performed when user clicks on the 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 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 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 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 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 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 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 label="Menu icon" - type="select" - name="menu_icon" - help="Icon to display next to menu label"> + <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> @@ -521,7 +423,6 @@ </repeat> </section> </xml> - <xml name="menu_sanitize"> <sanitizer> <valid> @@ -533,28 +434,26 @@ <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"> + <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> + <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" /> + <param name="annotation" type="data" format="@FORMAT@" optional="true" label="@LABEL@" multiple="True"/> </when> <when value="uri"> - <param label="@LABEL@" name="annouri" type="text" /> - <param label="Short name for track display" name="annoname" type="text" > + <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> + <valid initial="string.printable"> + <remove value="'"/> + </valid> </sanitizer> </param> </when> @@ -562,24 +461,22 @@ </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."> + <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 label="@LABEL@" format="@FORMAT@" name="annotation" type="data" - help="Add all PAF reference comparison genomes used to make the PAF" multiple="true" /> + <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 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 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> @@ -587,8 +484,8 @@ </xml> <xml name="citations"> <citations> - <citation type="doi">10.1186/s13059-016-0924-1</citation> - <citation type="doi">10.1101/gr.094607.109</citation> + <citation type="doi">10.1186/s13059-016-0924-1</citation> + <citation type="doi">10.1101/gr.094607.109</citation> </citations> </xml> </macros>