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comparison macros.xml @ 0:61add3f58f26 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
author iuc
date Thu, 02 Oct 2025 10:19:44 +0000
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-1:000000000000 0:61add3f58f26
1 <?xml version="1.0"?>
2 <macros>
3 <token name="@TOOL_VERSION@">3.6.5</token>
4 <xml name="requirements">
5 <requirements>
6 <requirement type="package" version="@TOOL_VERSION@">jbrowse2</requirement>
7 <requirement type="package" version="1.22.1">samtools</requirement>
8 <requirement type="package" version="1.11">tabix</requirement>
9 <requirement type="package" version="3.13.7">python</requirement>
10 <requirement type="package" version="2.32.5">requests</requirement>
11 <yield/>
12 </requirements>
13 </xml>
14 <token name="@VERSION_SUFFIX@">0</token>
15
16 <xml name="general_options">
17 <section name="jbgen" title="Advanced: general JBrowse options" expanded="false">
18 <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" />
19
20 <param name="primary_color" type="color" label="Primary color" value="#0d233f"/>
21 <param name="secondary_color" type="color" label="Secondary color" value="#721e63"/>
22 <param name="tertiary_color" type="color" label="Tertiary color" value="#135560"/>
23 <param name="quaternary_color" type="color" label="Quaternary color" value="#ffb11d"/>
24
25 <param label="Font size" name="font_size" type="integer" value="10" min="6" max="50" />
26 </section>
27 </xml>
28
29 <xml name="track_metadata">
30 <section name="metadata" title="Advanced: track metadata" expanded="false">
31 <param name="galaxy_metadata" label="Show Galaxy track metadata" type="boolean" checked="true" truevalue="true" falsevalue="false" help="Make Galaxy metadata available in 'About track' window and faceted track selector" />
32 <param name="metadata_bonus" type="data" format="tsv,tabular" label="Additional track metadata" optional="true" help="Display additional track metadata from a TSV file" />
33 </section>
34 </xml>
35
36 <xml name="track_visibility">
37 <param type="select" label="Track Visibility" name="track_visibility">
38 <option value="default_off">Off when browser opens</option>
39 <option value="default_on" selected="true">On when browser opens</option>
40 </param>
41 </xml>
42
43 <xml name="track_styling_linear">
44
45 <param name="display_mode" type="select" label="Display mode">
46 <option value="normal" selected="true">normal</option>
47 <option value="compact">compact</option>
48 <option value="reducedRepresentation">reducedRepresentation</option>
49 <option value="collapse">collapse</option>
50 </param>
51
52 <param label="Show labels" name="show_labels" type="boolean" checked="true" truevalue="true" falsevalue="false" />
53
54 <param label="Features label"
55 type="text"
56 name="labels_name"
57 value="jexl:get(feature,'name') || get(feature,'id')"
58 help="See https://jbrowse.org/jb2/docs/config_guide/#configuration-callbacks for syntax">
59 <expand macro="jexl_sanitize" />
60 </param>
61
62 <param label="Show descriptions" name="show_descriptions" type="boolean" checked="true" truevalue="true" falsevalue="false" />
63
64 <param label="Features description"
65 type="text"
66 name="descriptions_name"
67 value="jexl:get(feature,'note') || get(feature,'description')"
68 help="See https://jbrowse.org/jb2/docs/config_guide/#configuration-callbacks for syntax">
69 <expand macro="jexl_sanitize" />
70 </param>
71
72 <param label="Max height" name="max_height" type="integer" value="600" min="20" help="Maximum height that the track is permitted to reach in pixels."/>
73 </xml>
74
75 <xml name="track_styling_arc">
76
77 <param name="display_mode" type="select" label="Display mode">
78 <option value="arcs" selected="true">arcs</option>
79 <option value="semicircles">semicircles</option>
80 </param>
81
82 <param label="Arcs label"
83 type="text"
84 name="labels_name"
85 value="jexl:get(feature,'score')"
86 help="See https://jbrowse.org/jb2/docs/config_guide/#configuration-callbacks for syntax">
87 <expand macro="jexl_sanitize" />
88 </param>
89 </xml>
90
91 <xml name="track_styling_feature">
92 <section name="jbstyle" title="Advanced: styling options" expanded="false">
93 <conditional name="track_style">
94 <param name="display" type="select" label="Display style" help="How the track will be displayed by default">
95 <option value="LinearBasicDisplay" selected="true">LinearBasicDisplay</option>
96 <option value="LinearArcDisplay">LinearArcDisplay</option>
97 </param>
98 <when value="LinearBasicDisplay">
99 <expand macro="track_styling_linear"/>
100 </when>
101 <when value="LinearArcDisplay">
102 <expand macro="track_styling_arc"/>
103 </when>
104 </conditional>
105 </section>
106 </xml>
107
108 <xml name="track_styling_xam">
109 <section name="jbstyle" title="Advanced: styling options" expanded="false">
110 <conditional name="track_style">
111 <param name="display" type="select" label="Display style" help="How the track will be displayed by default">
112 <option value="LinearAlignmentsDisplay" selected="true">Alignments (Pileup + SNP Coverage)</option>
113 <option value="LinearPileupDisplay">Pileup</option>
114 <option value="LinearSNPCoverageDisplay">SNP Coverage</option>
115 <option value="LinearReadArcsDisplay">Arc</option>
116 <option value="LinearReadCloudDisplay">Read Cloud</option>
117 </param>
118 <when value="LinearAlignmentsDisplay"/>
119 <!-- TODO add options from both LinearPileupDisplay and LinearSNPCoverageDisplay (doesn't work currently) -->
120 <when value="LinearPileupDisplay"/>
121 <!-- TODO add more options (doesn't work currently) -->
122 <when value="LinearSNPCoverageDisplay">
123 <!-- TODO add more options (doesn't work currently) -->
124 <param name="scale_type" type="select" label="Scale type">
125 <option value="linear" selected="true">Linear</option>
126 <option value="log">Log</option>
127 </param>
128 <param name="min_score" label="Min score" type="integer" value="" optional="true"/>
129 <param name="max_score" label="Max score" type="integer" value="" optional="true"/>
130 </when>
131 <when value="LinearReadArcsDisplay"/>
132 <!-- TODO add more options -->
133 <when value="LinearReadCloudDisplay"/>
134 <!-- TODO add more options -->
135 </conditional>
136 </section>
137 </xml>
138
139 <xml name="track_styling_vcf">
140 <section name="jbstyle" title="Advanced: styling options" expanded="false">
141 <conditional name="track_style">
142 <param name="display" type="select" label="Display style" help="How the track will be displayed by default">
143 <option value="LinearVariantDisplay" selected="true">Variant</option>
144 <option value="MultiLinearVariantDisplay">Multi-sample variant display (matrix)</option>
145 <option value="LinearVariantMatrixDisplay">Multi-sample variant display (regular)</option>
146 <option value="LinearPairedArcDisplay">Arc</option>
147 </param>
148 <when value="LinearVariantDisplay">
149 <!-- TODO does not work (jbrowse side) -->
150 <!--expand macro="track_styling_linear"/-->
151 </when>
152 <when value="MultiLinearVariantDisplay"/>
153 <when value="LinearVariantMatrixDisplay"/>
154 <when value="LinearPairedArcDisplay"/>
155 </conditional>
156 </section>
157 </xml>
158
159 <xml name="track_styling_bigwig">
160 <section name="jbstyle" title="Advanced: styling options" expanded="false">
161 <conditional name="track_style">
162 <param name="display" type="select" label="Display style" help="How the track will be displayed by default">
163 <option value="LinearWiggleDisplay" selected="true">Wiggle</option>
164 <option value="MultiLinearWiggleDisplay" selected="true">Multiple Wiggle</option>
165 </param>
166 <when value="LinearWiggleDisplay">
167 <param name="wig_renderer" type="select" label="Renderer type">
168 <option value="xyplot" selected="true">XY Plot</option>
169 <option value="density">Density</option>
170 <option value="line">Line</option>
171 </param>
172
173 <!-- TODO not working -->
174 <!--param name="autoscale" type="select" label="Autoscale type">
175 <option value="local" selected="true">Local</option>
176 <option value="global">Global</option>
177 <option value="globalsd">Global ± 3σ</option>
178 <option value="localsd">Local ± 3σ</option>
179 </param>
180 <param name="resolution" label="Resolution" type="integer" value="1"/>
181 <param name="summaryScoreMode" type="select" label="Autoscale type">
182 <option value="max">Max</option>
183 <option value="min">Min</option>
184 <option value="avg">Avg</option>
185 <option value="whiskers" selected="true">Whiskers (combines all three)</option>
186 </param>
187 <param name="filled" label="Fill in histogram" type="boolean" checked="true" truevalue="true" falsevalue="false" />
188 <param name="scaleType" type="select" label="Scale type">
189 <option value="linear" selected="true">Linear</option>
190 <option value="log">Log</option>
191 </param>
192 <param name="displayCrossHatches" label="Draw cross hatches" type="boolean" checked="true" truevalue="true" falsevalue="false" />
193 <param name="minScore" label="Min score" type="integer" value="" optional="true"/>
194 <param name="maxScore" label="Max score" type="integer" value="" optional="true"/-->
195 </when>
196 <when value="MultiLinearWiggleDisplay">
197 <param name="wig_renderer" type="select" label="Renderer type">
198 <option value="multirowxy" selected="true">Multi row XY Plot</option>
199 <option value="xyplot">Multi XY Plot</option>
200 <option value="multirowdensity">Density</option>
201 <option value="multiline">Line</option>
202 <option value="multirowline">Row line</option>
203 </param>
204 </when>
205 </conditional>
206 </section>
207 </xml>
208
209 <xml name="track_styling_maf">
210 <param name="track_display" type="hidden" value="LinearMafDisplay" />
211 </xml>
212
213 <xml name="track_styling_hic">
214 <param name="track_display" type="hidden" value="LinearHicDisplay" />
215 </xml>
216
217 <xml name="track_styling_gc">
218 <param name="track_display" type="hidden" value="LinearGCContentDisplay" />
219 </xml>
220
221 <xml name="track_styling_synteny">
222 <section name="jbstyle" title="Advanced: styling options" expanded="false">
223 <conditional name="track_style">
224 <param name="display" type="select" label="Display style" help="How the track will be displayed by default">
225 <option value="LinearBasicDisplay" selected="true">Basic track display</option>
226 <option value="LinearSyntenyDisplay" selected="true">Synteny viewer</option>
227 </param>
228 <when value="LinearBasicDisplay"/>
229 <when value="LinearSyntenyDisplay"/>
230 </conditional>
231 </section>
232 </xml>
233
234 <xml name="details_panel">
235 <section name="formatdetails" title="Advanced: feature details panel customization" expanded="false">
236 <param label="JEXL code to customize the top-level feature"
237 type="text"
238 name="formatdetails_feature"
239 optional="true"
240 help="e.g. jexl:{newfield:'Custom contents here: '+feature.name} (see https://jbrowse.org/jb2/docs/config_guides/customizing_feature_details/ for more details)">
241 <expand macro="jexl_sanitize" />
242 </param>
243 <param label="JEXL code to customize the subfeatures"
244 type="text"
245 name="formatdetails_subfeature"
246 optional="true"
247 help="e.g. jexl:{newfield:'Custom contents here: '+feature.name} (see https://jbrowse.org/jb2/docs/config_guides/customizing_feature_details/ for more details)">
248 <expand macro="jexl_sanitize" />
249 </param>
250 <param name="formatdetails_depth" label="Depth to customize the subfeatures to" type="integer" value="1"/>
251 </section>
252 </xml>
253
254 <xml name="jexl_sanitize">
255 <sanitizer>
256 <mapping initial="galaxy.util.mapped_chars">
257 <add source="&#10;" target=" " />
258 <add source="&gt;" target="__gt__" />
259 <add source="&lt;" target="__lt__" />
260 </mapping>
261 <valid initial="default">
262 <add value="|" />
263 <add value="{"/>
264 <add value="}"/>
265 <add value="!"/>
266 <add value="?"/>
267 <add value="&amp;"/>
268 <add value="+"/>
269 <add value="="/>
270 <add value="'"/>
271 <add value='"'/>
272 </valid>
273 </sanitizer>
274 </xml>
275
276 <xml name="input_conditional" token_label="Track Data" token_format="data" token_help="" token_multiple="True">
277 <conditional name="annotation_cond">
278 <param label="@LABEL@" name="annotation_source" type="select">
279 <option selected="True" value="history">Use data from history</option>
280 <option value="remote">Use a genome from a remote source (not recommended)</option>
281 </param>
282 <when value="history">
283 <param name="annotation" label="@LABEL@" format="@FORMAT@" type="data" multiple="@MULTIPLE@" help="@HELP@"/>
284 </when>
285 <when value="remote">
286 <param name="uri" type="text" label="URI pointing to a @LABEL@"
287 help="@HELP@ ⚠️ WARNING: If this URI is not available for any reason, your JBrowse track will not show up." />
288 <param name="label" type="text" label="Track label" />
289 <param name="format" type="hidden" value="@FORMAT@" />
290 </when>
291 </conditional>
292 </xml>
293
294 <xml name="input_conditional_no_remote" token_label="Track Data" token_format="data" token_help="" token_multiple="True">
295 <conditional name="annotation_cond">
296 <param label="@LABEL@" name="annotation_source" type="select">
297 <option selected="True" value="history">Use data from history</option>
298 </param>
299 <when value="history">
300 <param name="annotation" label="@LABEL@" format="@FORMAT@" type="data" multiple="@MULTIPLE@" help="@HELP@"/>
301 </when>
302 </conditional>
303 </xml>
304
305 <xml name="citations">
306 <citations>
307 <citation type="doi">10.1186/s13059-023-02914-z</citation>
308 </citations>
309 </xml>
310 </macros>