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comparison macros.xml @ 97:74074746ccd8 draft

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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
comparison
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96:5ef1ba2031f2 97:74074746ccd8
1 <?xml version="1.0"?>
2 <macros> 1 <macros>
3 <token name="@TOOL_VERSION@">2.11.0</token> 2 <token name="@TOOL_VERSION@">2.11.0</token>
4 <xml name = "edamInc"> 3 <xml name="edamInc">
5 <edam_topics> 4 <edam_topics>
6 <edam_topic>topic_3307</edam_topic> 5 <edam_topic>topic_3307</edam_topic>
7 <edam_topic>topic_0092</edam_topic> 6 <edam_topic>topic_0092</edam_topic>
8 </edam_topics> 7 </edam_topics>
9 <edam_operations> 8 <edam_operations>
31 **Attribution** 30 **Attribution**
32 This Galaxy tool relies on the JBrowse2, maintained by the GMOD Community. The Galaxy wrapper is 31 This Galaxy tool relies on the JBrowse2, maintained by the GMOD Community. The Galaxy wrapper is
33 maintained by Ross Lazarus and Bjoern Gruening until the IUC complete their own. 32 maintained by Ross Lazarus and Bjoern Gruening until the IUC complete their own.
34 ]]> 33 ]]>
35 </token> 34 </token>
35 <xml name="creators">
36 <creator>
37 <person givenName="Helena" familyName="Rasche" url="https://github.com/hexylena" />
38 <person givenName="Anthony" familyName="Bretaudeau" url="https://github.com/abretaud" />
39 <person givenName="Ross" familyName="Lazarus" url="https://github.com/fubar2/" />
40 </creator>
41 </xml>
36 <xml name="genome_selector" 42 <xml name="genome_selector"
37 token_help="" 43 token_help=""
38 token_label="Fasta sequences" 44 token_label="Fasta sequences"
39 token_optional="False" > 45 token_optional="False" >
40 <conditional name="reference_genome"> 46 <conditional name="reference_genome">
41 <param help="Built-in references" label="Reference genome to display" name="genome_type_select" type="select"> 47 <param name="genome_type_select" type="select" label="Reference genome to display" help="Built-in references">
42 <option selected="True" value="indexed">Use a built-in genome</option> 48 <option selected="True" value="indexed">Use a built-in genome</option>
43 <option value="history">Use a genome from history</option> 49 <option value="history">Use a genome from history</option>
44 </param> 50 </param>
45 <when value="indexed"> 51 <when value="indexed">
46 <param 52 <param name="genomes" type="select" optional="@OPTIONAL@" label="@LABEL@" help="@HELP@">
47 help="@HELP@"
48 label="@LABEL@"
49 name="genomes"
50 type="select"
51 optional="@OPTIONAL@"
52 >
53 <options from_data_table="all_fasta"> 53 <options from_data_table="all_fasta">
54 <filter column="2" type="sort_by" /> 54 <filter column="2" type="sort_by"/>
55 <validator message="No genomes are available for the selected input dataset" type="no_options" /> 55 <validator message="No genomes are available for the selected input dataset" type="no_options"/>
56 </options> 56 </options>
57 </param> 57 </param>
58 </when> 58 </when>
59 <when value="history"> 59 <when value="history">
60 <param 60 <param name="genomes" type="data" format="fasta" optional="@OPTIONAL@" label="@LABEL@" help="@HELP@" multiple="True"/>
61 format="fasta"
62 label="@LABEL@"
63 help="@HELP@"
64 name="genomes"
65 type="data"
66 optional="@OPTIONAL@"
67 multiple="True" />
68 </when> 61 </when>
69 </conditional> 62 </conditional>
70 </xml> 63 </xml>
71 64 <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">
72 <xml name="auto_manual_tk"
73 token_cond_label="Color"
74 token_cond_name="color"
75 token_select_label="Color Specification"
76 token_select_name="color_select"
77 token_automatic_label="Automatically selected"
78 token_manual_label="Manual Color Selection">
79 <conditional name="@COND_NAME@" label="@COND_LABEL@"> 65 <conditional name="@COND_NAME@" label="@COND_LABEL@">
80 <param type="select" label="@SELECT_LABEL@" name="@SELECT_NAME@"> 66 <param name="@SELECT_NAME@" type="select" label="@SELECT_LABEL@">
81 <option value="automatic" selected="true">@AUTOMATIC_LABEL@</option> 67 <option value="automatic" selected="true">@AUTOMATIC_LABEL@</option>
82 <option value="manual">@MANUAL_LABEL@</option> 68 <option value="manual">@MANUAL_LABEL@</option>
83 </param> 69 </param>
84 <when value="automatic"> 70 <when value="automatic">
85 </when> 71 </when>
86 <when value="manual"> 72 <when value="manual">
87 <yield /> 73 <yield/>
88 </when> 74 </when>
89 </conditional> 75 </conditional>
90 </xml> 76 </xml>
91 77 <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">
92 <xml name="jb_color" 78 <param name="@NAME@" type="color" value="@VALUE@" label="@LABEL@" help="@HELP@">
93 token_label="JBrowse style.color"
94 token_name="style_color"
95 token_value="goldenrod"
96 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"
97 >
98 <param label="@LABEL@" type="color" name="@NAME@" value="@VALUE@" help="@HELP@">
99 <sanitizer> 79 <sanitizer>
100 <valid initial="string.letters,string.digits"> 80 <valid initial="string.letters,string.digits">
101 <add value="#" /> 81 <add value="#"/>
102 </valid> 82 </valid>
103 </sanitizer> 83 </sanitizer>
104 </param> 84 </param>
105 </xml> 85 </xml>
106 86 <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">
107 <xml name="auto_color" 87 <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@">
108 token_cond_label="Color" 88 <expand macro="jb_color"/>
109 token_cond_name="color" 89 <yield/>
110 token_select_label="Color Selection"
111 token_select_name="color_select"
112 token_automatic_label="Automatically selected"
113 token_manual_label="Manual Color Selection">
114 <expand macro="auto_manual_tk"
115 cond_label="@COND_LABEL@"
116 cond_name="@COND_NAME@"
117 select_label="@SELECT_LABEL@"
118 select_name="@SELECT_NAME@"
119 automatic_label="@AUTOMATIC_LABEL@"
120 manual_label="@MANUAL_LABEL@">
121 <expand macro="jb_color" />
122 <yield />
123 </expand> 90 </expand>
124 </xml> 91 </xml>
125
126
127
128 <xml name="brewer_scheme"> 92 <xml name="brewer_scheme">
129 <param type="select" label="Brewer color Scheme" name="brewer_scheme"> 93 <param name="brewer_scheme" type="select" label="Brewer color Scheme">
130 <option value="BrBg">BrBg: Brown - Blue Green</option> 94 <option value="BrBg">BrBg: Brown - Blue Green</option>
131 <option value="PiYg">PiYg: Pink - Yellow Green</option> 95 <option value="PiYg">PiYg: Pink - Yellow Green</option>
132 <option value="PRGn">PRGn: Purple Red - Green</option> 96 <option value="PRGn">PRGn: Purple Red - Green</option>
133 <option value="PuOr">PuOr: Purple - Orange</option> 97 <option value="PuOr">PuOr: Purple - Orange</option>
134 <option value="RdBu" selected="true">RdBu: Red - Blue</option> 98 <option value="RdBu" selected="true">RdBu: Red - Blue</option>
136 <option value="RdYlBu">RdYlBu: Red - Yellow - Blue</option> 100 <option value="RdYlBu">RdYlBu: Red - Yellow - Blue</option>
137 <option value="RdYlGn">RdYlBu: Red - Yellow - Green</option> 101 <option value="RdYlGn">RdYlBu: Red - Yellow - Green</option>
138 <option value="Spectral">Spectral</option> 102 <option value="Spectral">Spectral</option>
139 </param> 103 </param>
140 </xml> 104 </xml>
141
142
143 <xml name="general_options"> 105 <xml name="general_options">
144 <section name="jbgen" title="General JBrowse Options [Advanced]" expanded="false"> 106 <section name="jbgen" title="General JBrowse Options [Advanced]" expanded="false">
145 <conditional name="ucol"> 107 <conditional name="ucol">
146 <param name="formcoll" type="select" label="Convert a collection of track files rather than filling in the tool form" 108 <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">
147 help="A collection of bam/vcf and other track types will be converted into a JBrowse2 automatically">
148 <option value="form" selected="true">Fill in the tool form to specify tracks for the output JBrowse2</option> 109 <option value="form" selected="true">Fill in the tool form to specify tracks for the output JBrowse2</option>
149 <option value="collect">Convert a collection of suitable track files</option> 110 <option value="collect">Convert a collection of suitable track files</option>
150 </param> 111 </param>
151 <when value="collect"> 112 <when value="collect">
152 <param label="Collection of bed, bam and other track files" name="autoCollection" type="data_collection" /> 113 <param name="autoCollection" type="data_collection" label="Collection of bed, bam and other track files"/>
153 </when> 114 </when>
154 <when value="form"> 115 <when value="form">
155 </when> 116 </when>
156 </conditional> 117 </conditional>
157 118 <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"/>
158 <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" 119 <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"/>
159 type="boolean" checked="false" truevalue="true" falsevalue="false" /> 120 <param name="session_name" type="text" value="New JB2 session" label="Session name" help="Displayed at the top of the window"/>
160 <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'"/> 121 <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"/>
161 <param label="Session name" type="text" name="session_name" value="New JB2 session" help="Displayed at the top of the window"/> 122 <param name="primary_color" type="color" value="#0D233F" label="Primary color">
162 <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" />
163
164 <param name="primary_color" type="color" label="Primary color" value="#0D233F">
165 <sanitizer> 123 <sanitizer>
166 <valid initial="string.ascii_letters,string.digits"> 124 <valid initial="string.ascii_letters,string.digits">
167 <add value="#" /> 125 <add value="#"/>
168 </valid> 126 </valid>
169 </sanitizer> 127 </sanitizer>
170 </param> 128 </param>
171 <param name="secondary_color" type="color" label="Secondary color" value="#721E63"> 129 <param name="secondary_color" type="color" value="#721E63" label="Secondary color">
172 <sanitizer>
173 <valid initial="string.ascii_letters,string.digits">
174 <add value="#" />
175 </valid>
176 </sanitizer>
177 </param>
178 <param name="tertiary_color" type="color" label="Tertiary color" value="#135560">
179 <sanitizer> 130 <sanitizer>
180 <valid initial="string.ascii_letters,string.digits"> 131 <valid initial="string.ascii_letters,string.digits">
181 <add value="#" /> 132 <add value="#"/>
182 </valid> 133 </valid>
183 </sanitizer> 134 </sanitizer>
184 </param> 135 </param>
185 <param name="quaternary_color" type="color" label="Quaternary color" value="#FFB11D"> 136 <param name="tertiary_color" type="color" value="#135560" label="Tertiary color">
186 <sanitizer> 137 <sanitizer>
187 <valid initial="string.ascii_letters,string.digits"> 138 <valid initial="string.ascii_letters,string.digits">
188 <add value="#" /> 139 <add value="#"/>
189 </valid> 140 </valid>
190 </sanitizer> 141 </sanitizer>
191 </param> 142 </param>
192 143 <param name="quaternary_color" type="color" value="#FFB11D" label="Quaternary color">
193 <param label="Font size" name="font_size" type="integer" value="10" /> 144 <sanitizer>
194 </section> 145 <valid initial="string.ascii_letters,string.digits">
195 </xml> 146 <add value="#"/>
196 147 </valid>
148 </sanitizer>
149 </param>
150 <param name="font_size" type="integer" value="10" label="Font size"/>
151 </section>
152 </xml>
197 <xml name="color_selection_minmax"> 153 <xml name="color_selection_minmax">
198 <section name="jbcolor" title="JBrowse Color Options [Advanced]" expanded="false"> 154 <section name="jbcolor" title="JBrowse Color Options [Advanced]" expanded="false">
199 <!-- Abuse auto/manual for bicolor pivot. Means we'll have to handle the 155 <!-- Abuse auto/manual for bicolor pivot. Means we'll have to handle the
200 auto case as well, but may be safe to just say "brewer colors? Pff, 156 auto case as well, but may be safe to just say "brewer colors? Pff,
201 red/blue" --> 157 red/blue" -->
202 <expand macro="auto_manual_tk" 158 <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">
203 token_cond_label="Color" 159 <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."/>
204 token_cond_name="color" 160 <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."/>
205 token_select_label="Color Selection" 161 </expand>
206 token_select_name="color_select" 162 <conditional name="bicolor_pivot" label="Bicolor Pivot">
207 token_automatic_label="Automatically selected" 163 <param name="bicolor_pivot_select" type="select" label="Bicolor Pivot">
208 token_manual_label="Manual Color Selection"> 164 <option value="zero" selected="true">Zero</option>
209 <expand macro="jb_color" 165 <option value="mean">Mean</option>
210 label="JBrowse style.pos_color" 166 <option value="custom">Custom Value</option>
211 name="style_pos_color" 167 </param>
212 value="blue" 168 <when value="zero"/>
213 help="CSS color, default 'blue'. When drawing bicolor plots, the fill color to use for values that are above the pivot point." /> 169 <when value="mean"/>
214 <expand macro="jb_color" 170 <when value="custom">
215 label="JBrowse style.neg_color" 171 <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."/>
216 name="style_neg_color" 172 </when>
217 value="red" 173 </conditional>
218 help=" CSS color, default 'red'. When drawing bicolor plots, the fill color to use for values that are below the pivot point." /> 174 </section>
219 </expand> 175 </xml>
220 176 <xml name="color_selection" token_scaling_lin_select="true" token_scaling_log_select="false">
221 <conditional name="bicolor_pivot" label="Bicolor Pivot">
222 <param type="select" label="Bicolor Pivot" name="bicolor_pivot_select">
223 <option value="zero" selected="true">Zero</option>
224 <option value="mean">Mean</option>
225 <option value="custom">Custom Value</option>
226 </param>
227 <when value="zero" />
228 <when value="mean" />
229 <when value="custom">
230 <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." />
231 </when>
232 </conditional>
233 </section>
234 </xml>
235
236 <xml name="color_selection"
237 token_scaling_lin_select="true"
238 token_scaling_log_select="false"
239 >
240 <section name="jbcolor_scale" title="JBrowse Feature Score Scaling &amp; Coloring Options [Advanced]" expanded="false"> 177 <section name="jbcolor_scale" title="JBrowse Feature Score Scaling &amp; Coloring Options [Advanced]" expanded="false">
241 <conditional name="color_score" label="JBrowse style.color &amp; Score relationship"> 178 <conditional name="color_score" label="JBrowse style.color &amp; Score relationship">
242 <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"> 179 <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">
243 <option value="score">Based on score</option> 180 <option value="score">Based on score</option>
244 <option value="none" selected="true">Ignore score</option> 181 <option value="none" selected="true">Ignore score</option>
245 </param> 182 </param>
246 <when value="none"> 183 <when value="none">
247 <!-- When no scaling is done, no scores available, then just let the 184 <!-- When no scaling is done, no scores available, then just let the
248 user choose a base color for the track --> 185 user choose a base color for the track -->
249 <expand macro="auto_color" /> 186 <expand macro="auto_color"/>
250 </when> 187 </when>
251 <when value="score"> 188 <when value="score">
252 <!-- Scaling --> 189 <!-- Scaling -->
253 <param type="select" label="JBrowse style.color function's score scaling" name="score_scaling" 190 <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.">
254 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."> 191 <option value="linear" selected="@SCALING_LIN_SELECT@">Linear scaling</option>
255 <option value="linear" selected="@SCALING_LIN_SELECT@">Linear scaling</option> 192 <option value="logarithmic" selected="false">Logarithmic scaling</option>
256 <option value="logarithmic" selected="false">Logarithmic scaling</option> 193 <option value="blast" selected="@SCALING_LOG_SELECT@">Blast scaling</option>
257 <option value="blast" selected="@SCALING_LOG_SELECT@">Blast scaling</option> 194 </param>
258 </param> 195 <!-- Scaling Bounds -->
259 196 <conditional name="score_scales" label="Minimum/Maximum values for track scores">
260 <!-- Scaling Bounds --> 197 <param name="scale_select" type="select" label="How should minimum and maximum values be determined for the scores of the features">
261 <conditional name="score_scales" label="Minimum/Maximum values for track scores"> 198 <option value="automatic" selected="true">Automatically determined</option>
262 <param type="select" label="How should minimum and maximum values be determined for the scores of the features" name="scale_select"> 199 <option value="manual">Manually specify minimum and maximum expected scores for the feature track</option>
263 <option value="automatic" selected="true">Automatically determined</option> 200 </param>
264 <option value="manual">Manually specify minimum and maximum expected scores for the feature track</option> 201 <when value="automatic"/>
265 </param> 202 <when value="manual">
266 <when value="automatic" /> 203 <param name="minimum" type="integer" value="0" label="Minimum expected score"/>
267 <when value="manual"> 204 <param name="maximum" type="integer" value="100" label="Maximum expected score"/>
268 <param label="Minimum expected score" name="minimum" type="integer" value="0" /> 205 </when>
269 <param label="Maximum expected score" name="maximum" type="integer" value="100" /> 206 </conditional>
270 </when> 207 <!-- Scale color -->
271 </conditional> 208 <conditional name="color_scheme" label="Color Scheme for scored features">
272 209 <param name="score_scheme" type="select" label="JBrowse style.color function's color scheme for scored values">
273 <!-- Scale color --> 210 <option value="opacity">Opacity (high scores = 1.0 opacity)</option>
274 <conditional name="color_scheme" label="Color Scheme for scored features"> 211 <!--<option value="brewer">Brewer Color Schemes</option>-->
275 <param type="select" label="JBrowse style.color function's color scheme for scored values" name="score_scheme"> 212 </param>
276 <option value="opacity">Opacity (high scores = 1.0 opacity)</option> 213 <when value="opacity">
277 <!--<option value="brewer">Brewer Color Schemes</option>--> 214 <!-- Single color selection mode -->
278 </param> 215 <expand macro="auto_color"/>
279 <when value="opacity"> 216 </when>
280 <!-- Single color selection mode --> 217 <!--<when value="brewer">-->
281 <expand macro="auto_color" />
282 </when>
283 <!--<when value="brewer">-->
284 <!--[> Brewer continuum selection <]--> 218 <!--[> Brewer continuum selection <]-->
285 <!--<expand macro="brewer_scheme" />--> 219 <!--<expand macro="brewer_scheme" />-->
286 <!--</when>--> 220 <!--</when>-->
287 </conditional> 221 </conditional>
288 </when> 222 </when>
289 </conditional> 223 </conditional>
290 </section> 224 </section>
291 </xml> 225 </xml>
292
293 <xml name="track_visibility"> 226 <xml name="track_visibility">
294 <param type="select" label="Track Visibility" name="track_visibility"> 227 <param name="track_visibility" type="select" label="Track Visibility">
295 <option value="default_off">Off when browser opens</option> 228 <option value="default_off">Off when browser opens</option>
296 <option value="default_on" selected="true">On when browser opens</option> 229 <option value="default_on" selected="true">On when browser opens</option>
297 </param> 230 </param>
298 </xml> 231 </xml>
299
300 <xml name="track_styling_linear"> 232 <xml name="track_styling_linear">
301 <param label="Show labels" name="show_labels" type="boolean" checked="false" truevalue="true" falsevalue="false" /> 233 <param name="show_labels" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show labels"/>
302 <param label="Show descriptions" name="show_descriptions" type="boolean" checked="false" truevalue="true" falsevalue="false" /> 234 <param name="show_descriptions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show descriptions"/>
303 <param name="display_mode" type="select" label="Display mode"> 235 <param name="display_mode" type="select" label="Display mode">
304 <option value="normal" selected="true">normal</option> 236 <option value="normal" selected="true">normal</option>
305 <option value="compact">compact</option> 237 <option value="compact">compact</option>
306 <option value="reducedRepresentation">reducedRepresentation</option> 238 <option value="reducedRepresentation">reducedRepresentation</option>
307 <option value="collapse">collapse</option> 239 <option value="collapse">collapse</option>
308 </param> 240 </param>
309 <param label="Max height" name="max_height" type="integer" value="600" help="Maximum height that the track is permitted to reach in pixels."/> 241 <param name="max_height" type="integer" value="600" label="Max height" help="Maximum height that the track is permitted to reach in pixels."/>
310 </xml> 242 </xml>
311
312 <xml name="track_styling_vgp"> 243 <xml name="track_styling_vgp">
313 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false">
314 <param label="Show labels" name="show_labels" type="boolean" checked="false" truevalue="true" falsevalue="false" />
315 <param label="Show descriptions" name="show_descriptions" type="boolean" checked="false" truevalue="true" falsevalue="false" />
316 <param name="display" type="select" label="Display style" help="How the track will be displayed by default">
317 <option value="LinearBasicDisplay" selected="true">LinearBasicDisplay</option>
318 <option value="LinearPileupDisplay">LinearPileupDisplay - good for dense tracks at scale</option>
319 <option value="LinearArcDisplay">LinearArcDisplay</option>
320 </param>
321 </section>
322 </xml>
323
324 <xml name="track_styling_feature">
325 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false"> 244 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false">
326 <conditional name="track_style"> 245 <param name="show_labels" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show labels"/>
246 <param name="show_descriptions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show descriptions"/>
327 <param name="display" type="select" label="Display style" help="How the track will be displayed by default"> 247 <param name="display" type="select" label="Display style" help="How the track will be displayed by default">
328 <option value="LinearBasicDisplay" selected="true">LinearBasicDisplay</option> 248 <option value="LinearBasicDisplay" selected="true">LinearBasicDisplay</option>
329 <option value="LinearPileupDisplay">LinearPileupDisplay - good for dense tracks at scale</option> 249 <option value="LinearPileupDisplay">LinearPileupDisplay - good for dense tracks at scale</option>
330 <option value="LinearArcDisplay">LinearArcDisplay</option> 250 <option value="LinearArcDisplay">LinearArcDisplay</option>
331 </param> 251 </param>
332 <when value="LinearPileupDisplay"> 252 </section>
333 <expand macro="track_styling_linear"/> 253 </xml>
334 </when> 254 <xml name="track_styling_feature">
335 <when value="LinearBasicDisplay"> 255 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false">
336 <expand macro="track_styling_linear"/> 256 <conditional name="track_style">
337 257 <param name="display" type="select" label="Display style" help="How the track will be displayed by default">
338 <!-- examples: https://github.com/GMOD/jbrowse-components/discussions/2729 258 <option value="LinearBasicDisplay" selected="true">LinearBasicDisplay</option>
259 <option value="LinearPileupDisplay">LinearPileupDisplay - good for dense tracks at scale</option>
260 <option value="LinearArcDisplay">LinearArcDisplay</option>
261 </param>
262 <when value="LinearPileupDisplay">
263 <expand macro="track_styling_linear"/>
264 </when>
265 <when value="LinearBasicDisplay">
266 <expand macro="track_styling_linear"/>
267 <!-- examples: https://github.com/GMOD/jbrowse-components/discussions/2729
339 and https://github.com/GMOD/jbrowse-components/blob/main/plugins/svg/src/SvgFeatureRenderer/configSchema.ts#L41 --> 268 and https://github.com/GMOD/jbrowse-components/blob/main/plugins/svg/src/SvgFeatureRenderer/configSchema.ts#L41 -->
340 <param label="Features label" 269 <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">
341 type="text" 270 <sanitizer>
342 name="label" 271 <valid initial="default">
343 value="jexl:get(feature,'name') || get(feature,'id')" 272 <add value="|"/>
344 help="See https://jbrowse.org/jb2/docs/config_guide/#configuration-callbacks for syntax"> 273 <add value="{"/>
345 <sanitizer> 274 <add value="}"/>
346 <valid initial="default"> 275 <add value="!"/>
347 <add value="|" /> 276 <add value="?"/>
348 <add value="{"/> 277 <add value="+"/>
349 <add value="}"/> 278 <add value="="/>
350 <add value="!"/> 279 <add value="'"/>
351 <add value="?"/> 280 </valid>
352 <add value="+"/> 281 </sanitizer>
353 <add value="="/> 282 </param>
354 <add value="'"/> 283 <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">
355 </valid> 284 <sanitizer>
356 </sanitizer> 285 <valid initial="default">
357 </param> 286 <add value="|"/>
358 <param label="Features description" 287 <add value="{"/>
359 type="text" 288 <add value="}"/>
360 name="description" 289 <add value="!"/>
361 value="jexl:get(feature,'note') || get(feature,'description')" 290 <add value="?"/>
362 help="See https://jbrowse.org/jb2/docs/config_guide/#configuration-callbacks for syntax"> 291 <add value="+"/>
363 <sanitizer> 292 <add value="="/>
364 <valid initial="default"> 293 <add value="'"/>
365 <add value="|" /> 294 </valid>
366 <add value="{"/> 295 </sanitizer>
367 <add value="}"/> 296 </param>
368 <add value="!"/> 297 </when>
369 <add value="?"/> 298 <when value="LinearArcDisplay"/>
370 <add value="+"/> 299 </conditional>
371 <add value="="/> 300 </section>
372 <add value="'"/> 301 </xml>
373 </valid>
374 </sanitizer>
375 </param>
376 </when>
377 <when value="LinearArcDisplay"/>
378 </conditional>
379 </section>
380 </xml>
381
382 <xml name="track_styling_xam"> 302 <xml name="track_styling_xam">
383 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false"> 303 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false">
384 <conditional name="track_style"> 304 <conditional name="track_style">
385 <param name="display" type="select" label="Display style" help="How the track will be displayed by default"> 305 <param name="display" type="select" label="Display style" help="How the track will be displayed by default">
386 <option value="LinearAlignmentsDisplay" selected="true">LinearAlignmentsDisplay</option> 306 <option value="LinearAlignmentsDisplay" selected="true">LinearAlignmentsDisplay</option>
391 </param> 311 </param>
392 <!-- TODO check if possible to handle more options than just the display style--> 312 <!-- TODO check if possible to handle more options than just the display style-->
393 <when value="LinearAlignmentsDisplay"/> 313 <when value="LinearAlignmentsDisplay"/>
394 <when value="LinearPileupDisplay"/> 314 <when value="LinearPileupDisplay"/>
395 <when value="LinearSNPCoverageDisplay"> 315 <when value="LinearSNPCoverageDisplay">
396 <param name="displayCrossHatches" label="Draw cross hatches" type="boolean" checked="true" truevalue="true" falsevalue="false" /> 316 <param name="displayCrossHatches" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Draw cross hatches"/>
397 <param name="minScore" label="Min score" type="integer" value="" optional="true"/> 317 <param name="minScore" type="integer" value="" optional="true" label="Min score"/>
398 <param name="maxScore" label="Max score" type="integer" value="" optional="true"/> 318 <param name="maxScore" type="integer" value="" optional="true" label="Max score"/>
399 </when> 319 </when>
400 <when value="LinearReadArcsDisplay"/> 320 <when value="LinearReadArcsDisplay"/>
401 <when value="LinearReadCloudDisplay"/> 321 <when value="LinearReadCloudDisplay"/>
402 </conditional> 322 </conditional>
403 </section> 323 </section>
404 </xml> 324 </xml>
405
406 <xml name="track_styling_vcf"> 325 <xml name="track_styling_vcf">
407 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false"> 326 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false">
408 <conditional name="track_style"> 327 <conditional name="track_style">
409 <param name="display" type="select" label="Display style" help="How the track will be displayed by default"> 328 <param name="display" type="select" label="Display style" help="How the track will be displayed by default">
410 <option value="LinearVariantDisplay" selected="true">LinearVariantDisplay</option> 329 <option value="LinearVariantDisplay" selected="true">LinearVariantDisplay</option>
415 </when> 334 </when>
416 <when value="LinearPairedArcDisplay"/> 335 <when value="LinearPairedArcDisplay"/>
417 </conditional> 336 </conditional>
418 </section> 337 </section>
419 </xml> 338 </xml>
420
421 <xml name="track_styling_bigwig"> 339 <xml name="track_styling_bigwig">
422 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false"> 340 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false">
423 <conditional name="track_style"> 341 <conditional name="track_style">
424 <param name="display" type="select" label="Display style" help="How the track will be displayed by default"> 342 <param name="display" type="select" label="Display style" help="How the track will be displayed by default">
425 <option value="LinearWiggleDisplay" selected="true">LinearWiggleDisplay</option> 343 <option value="LinearWiggleDisplay" selected="true">LinearWiggleDisplay</option>
429 <option value="local" selected="true">Local</option> 347 <option value="local" selected="true">Local</option>
430 <option value="global">Global</option> 348 <option value="global">Global</option>
431 <option value="globalsd">Global ± 3σ</option> 349 <option value="globalsd">Global ± 3σ</option>
432 <option value="localsd">Local ± 3σ</option> 350 <option value="localsd">Local ± 3σ</option>
433 </param> 351 </param>
434 <param name="resolution" label="Resolution" type="integer" value="1"/> 352 <param name="resolution" type="integer" value="1" label="Resolution"/>
435 <param name="summaryScoreMode" type="select" label="Autoscale type"> 353 <param name="summaryScoreMode" type="select" label="Autoscale type">
436 <option value="max">Max</option> 354 <option value="max">Max</option>
437 <option value="min">Min</option> 355 <option value="min">Min</option>
438 <option value="avg">Avg</option> 356 <option value="avg">Avg</option>
439 <option value="whiskers" selected="true">Whiskers (combines all three)</option> 357 <option value="whiskers" selected="true">Whiskers (combines all three)</option>
440 </param> 358 </param>
441 <param name="filled" label="Fill in histogram" type="boolean" checked="true" truevalue="true" falsevalue="false" /> 359 <param name="filled" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Fill in histogram"/>
442 <param name="scaleType" type="select" label="Autoscale type"> 360 <param name="scaleType" type="select" label="Autoscale type">
443 <option value="linear" selected="true">Linear</option> 361 <option value="linear" selected="true">Linear</option>
444 <option value="log">Log</option> 362 <option value="log">Log</option>
445 </param> 363 </param>
446 <param name="displayCrossHatches" label="Draw cross hatches" type="boolean" checked="true" truevalue="true" falsevalue="false" /> 364 <param name="displayCrossHatches" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Draw cross hatches"/>
447 <param name="minScore" label="Min score" type="integer" value="" optional="true"/> 365 <param name="minScore" type="integer" value="" optional="true" label="Min score"/>
448 <param name="maxScore" label="Max score" type="integer" value="" optional="true"/> 366 <param name="maxScore" type="integer" value="" optional="true" label="Max score"/>
449 </when> 367 </when>
450 </conditional> 368 </conditional>
451 </section> 369 </section>
452 </xml> 370 </xml>
453
454 <xml name="track_menu"> 371 <xml name="track_menu">
455 <section name="jbmenu" title="JBrowse Contextual Menu options [Advanced]" expanded="false"> 372 <section name="jbmenu" title="JBrowse Contextual Menu options [Advanced]" expanded="false">
456 <repeat name="track_menu" title="Track Menu"> 373 <repeat name="track_menu" title="Track Menu">
457 <param label="Menu action" 374 <param name="menu_action" type="select" label="Menu action" help="Action performed when user clicks on the menu">
458 type="select"
459 name="menu_action"
460 help="Action performed when user clicks on the menu">
461 <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> 375 <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>
462 <option value="newWindow">newWindow: causes the given url to be opened in a new browser window.</option> 376 <option value="newWindow">newWindow: causes the given url to be opened in a new browser window.</option>
463 <option value="navigateTo">navigateTo: opens the given url in the same browser window, navigating the user away from JBrowse.</option> 377 <option value="navigateTo">navigateTo: opens the given url in the same browser window, navigating the user away from JBrowse.</option>
464 </param> 378 </param>
465 <param label="Menu label" 379 <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)">
466 type="text" 380 <expand macro="menu_sanitize"/>
467 name="menu_label" 381 </param>
468 help="Will be displayed in the contextual menu on each feature ({name}, {id}, {type}, {start}, {end}, {strand} variables will be interpreted)"> 382 <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)">
469 <expand macro="menu_sanitize" /> 383 <expand macro="menu_sanitize"/>
470 </param> 384 </param>
471 <param label="Menu title" 385 <param name="menu_url" type="text" label="Menu url" help="Destination URL ({name}, {id}, {type}, {start}, {end}, {strand} variables will be interpreted)">
472 type="text" 386 <expand macro="menu_sanitize"/>
473 name="menu_title" 387 </param>
474 help="Will be displayed in the popup title bar if displayed ({id}, {type}, {start}, {end}, {strand} variables will be interpreted)"> 388 <param name="menu_icon" type="select" label="Menu icon" help="Icon to display next to menu label">
475 <expand macro="menu_sanitize" />
476 </param>
477 <param label="Menu url"
478 type="text"
479 name="menu_url"
480 help="Destination URL ({name}, {id}, {type}, {start}, {end}, {strand} variables will be interpreted)">
481 <expand macro="menu_sanitize" />
482 </param>
483 <param label="Menu icon"
484 type="select"
485 name="menu_icon"
486 help="Icon to display next to menu label">
487 <option value="dijitIconBookmark" selected="true">Bookmark</option> 389 <option value="dijitIconBookmark" selected="true">Bookmark</option>
488 <option value="dijitIconSave">Save</option> 390 <option value="dijitIconSave">Save</option>
489 <option value="dijitIconPrint">Print</option> 391 <option value="dijitIconPrint">Print</option>
490 <option value="dijitIconCut">Cut</option> 392 <option value="dijitIconCut">Cut</option>
491 <option value="dijitIconCopy">Copy</option> 393 <option value="dijitIconCopy">Copy</option>
519 <option value="dijitIconError">Error</option> 421 <option value="dijitIconError">Error</option>
520 </param> 422 </param>
521 </repeat> 423 </repeat>
522 </section> 424 </section>
523 </xml> 425 </xml>
524
525 <xml name="menu_sanitize"> 426 <xml name="menu_sanitize">
526 <sanitizer> 427 <sanitizer>
527 <valid> 428 <valid>
528 <add value="{"/> 429 <add value="{"/>
529 <add value="}"/> 430 <add value="}"/>
531 <add value="?"/> 432 <add value="?"/>
532 <add value="&amp;"/> 433 <add value="&amp;"/>
533 <add value="+"/> 434 <add value="+"/>
534 <add value="="/> 435 <add value="="/>
535 <add value="'"/> 436 <add value="'"/>
536 <add value='"'/> 437 <add value="&quot;"/>
537 </valid> 438 </valid>
538 </sanitizer> 439 </sanitizer>
539 </xml> 440 </xml>
540
541 <xml name="input_conditional" token_label="Track Data" token_format="data"> 441 <xml name="input_conditional" token_label="Track Data" token_format="data">
542 <conditional name="useuri"> 442 <conditional name="useuri">
543 <param name="insource" type="select" label="Define track data as a history file or an internet URI" 443 <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">
544 help="A public URI implies that all the associated tabix files are also in place. They are created for history files">
545 <option value="history" selected="true">Track data from a history file</option> 444 <option value="history" selected="true">Track data from a history file</option>
546 <option value="uri" >Tabix data URI - index files must be available at corresponding URI</option> 445 <option value="uri">Tabix data URI - index files must be available at corresponding URI</option>
547 </param> 446 </param>
548 <when value="history"> 447 <when value="history">
549 <param label="@LABEL@" format="@FORMAT@" name="annotation" multiple="True" optional="true" type="data" /> 448 <param name="annotation" type="data" format="@FORMAT@" optional="true" label="@LABEL@" multiple="True"/>
550 </when> 449 </when>
551 <when value="uri"> 450 <when value="uri">
552 <param label="@LABEL@" name="annouri" type="text" /> 451 <param name="annouri" type="text" label="@LABEL@"/>
553 <param label="Short name for track display" name="annoname" type="text" > 452 <param name="annoname" type="text" label="Short name for track display">
554 <sanitizer invalid_char="_"> 453 <sanitizer invalid_char="_">
555 <valid initial="string.printable" > 454 <valid initial="string.printable">
556 <remove value="'" /> 455 <remove value="'"/>
557 </valid> 456 </valid>
558 </sanitizer> 457 </sanitizer>
559 </param> 458 </param>
560 </when> 459 </when>
561 </conditional> 460 </conditional>
562 </xml> 461 </xml>
563 <xml name="pafref_conditional" token_label="Track Data" token_format="data"> 462 <xml name="pafref_conditional" token_label="Track Data" token_format="data">
564 <conditional name="pafuseuri"> 463 <conditional name="pafuseuri">
565 <param name="insource" type="select" label="PAF reference data from a history file or an internet URI?" 464 <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.">
566 help="Multiple references can be used for mashmap PAF. A URI source requires all the associated tabix index files to be in place.">
567 <option value="history" selected="true">PAF reference comparison genome from a history file</option> 465 <option value="history" selected="true">PAF reference comparison genome from a history file</option>
568 <option value="uri">PAF reference comparison genome tabix .gz URI with index files at the corresponding URIs</option> 466 <option value="uri">PAF reference comparison genome tabix .gz URI with index files at the corresponding URIs</option>
569 </param> 467 </param>
570 <when value="history"> 468 <when value="history">
571 <param label="@LABEL@" format="@FORMAT@" name="annotation" type="data" 469 <param name="annotation" type="data" format="@FORMAT@" label="@LABEL@" help="Add all PAF reference comparison genomes used to make the PAF" multiple="true"/>
572 help="Add all PAF reference comparison genomes used to make the PAF" multiple="true" />
573 </when> 470 </when>
574 <when value="uri"> 471 <when value="uri">
575 <repeat name="refuri" title="PAF reference comparison genome URI" min="1"> 472 <repeat name="refuri" title="PAF reference comparison genome URI" min="1">
576 <param label="@LABEL@" name="annotation" type="text" /> 473 <param name="annotation" type="text" label="@LABEL@"/>
577 <param label="Short name for this reference" name="annoname" type="text" help="Short names take less track space"> 474 <param name="annoname" type="text" label="Short name for this reference" help="Short names take less track space">
578 <sanitizer invalid_char="_"> 475 <sanitizer invalid_char="_">
579 <valid initial="string.printable" > 476 <valid initial="string.printable">
580 <remove value="'" /> 477 <remove value="'"/>
581 </valid> 478 </valid>
582 </sanitizer> 479 </sanitizer>
583 </param> 480 </param>
584 </repeat> 481 </repeat>
585 </when> 482 </when>
586 </conditional> 483 </conditional>
587 </xml> 484 </xml>
588 <xml name="citations"> 485 <xml name="citations">
589 <citations> 486 <citations>
590 <citation type="doi">10.1186/s13059-016-0924-1</citation> 487 <citation type="doi">10.1186/s13059-016-0924-1</citation>
591 <citation type="doi">10.1101/gr.094607.109</citation> 488 <citation type="doi">10.1101/gr.094607.109</citation>
592 </citations> 489 </citations>
593 </xml> 490 </xml>
594 </macros> 491 </macros>