Mercurial > repos > bgruening > jbrowse2
comparison macros.xml @ 0:53c2be00bb6f draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
author | bgruening |
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date | Wed, 05 Jun 2024 08:15:49 +0000 |
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1 <macros> | |
2 <token name="@TOOL_VERSION@">2.11.1</token> | |
3 <xml name="edamInc"> | |
4 <edam_topics> | |
5 <edam_topic>topic_3307</edam_topic> | |
6 <edam_topic>topic_0092</edam_topic> | |
7 </edam_topics> | |
8 <edam_operations> | |
9 <edam_operation>operation_0573</edam_operation> | |
10 <edam_operation>operation_0564</edam_operation> | |
11 </edam_operations> | |
12 </xml> | |
13 <xml name="requirements"> | |
14 <requirements> | |
15 <requirement type="package" version="@TOOL_VERSION@">jbrowse2</requirement> | |
16 <requirement type="package" version="1.82">biopython</requirement> | |
17 <requirement type="package" version="0.7.1">bcbio-gff</requirement> | |
18 <requirement type="package" version="1.19">samtools</requirement> | |
19 <requirement type="package" version="6.0.1">pyyaml</requirement> | |
20 <requirement type="package" version="1.11">tabix</requirement> | |
21 <requirement type="package" version="4.6.0">findutils</requirement> | |
22 <requirement type="package" version="0.0.12-0">hictk</requirement> | |
23 <requirement type="package" version="3.0">zip</requirement> | |
24 <yield/> | |
25 </requirements> | |
26 </xml> | |
27 <token name="@DATA_DIR@">\$GALAXY_JBROWSE_SHARED_DIR</token> | |
28 <token name="@VERSION_SUFFIX@">0</token> | |
29 <xml name="creators"> | |
30 <creator> | |
31 <person givenName="Helena" familyName="Rasche" url="https://github.com/hexylena"/> | |
32 <person givenName="Anthony" familyName="Bretaudeau" url="https://github.com/abretaud"/> | |
33 <person givenName="Ross" familyName="Lazarus" url="https://github.com/fubar2/"/> | |
34 </creator> | |
35 </xml> | |
36 <xml name="genome_selector" token_help="" token_label="Fasta sequences" token_optional="False"> | |
37 <conditional name="reference_genome"> | |
38 <param name="genome_type_select" type="select" label="Reference genome to display" help="Built-in references"> | |
39 <option selected="True" value="indexed">Use a built-in genome</option> | |
40 <option value="history">Use a genome from history</option> | |
41 </param> | |
42 <when value="indexed"> | |
43 <param name="genomes" type="select" optional="@OPTIONAL@" label="@LABEL@" help="@HELP@"> | |
44 <options from_data_table="all_fasta"> | |
45 <filter column="2" type="sort_by"/> | |
46 <validator message="No genomes are available for the selected input dataset" type="no_options"/> | |
47 </options> | |
48 </param> | |
49 </when> | |
50 <when value="history"> | |
51 <param name="genomes" type="data" format="fasta" optional="@OPTIONAL@" label="@LABEL@" help="@HELP@" multiple="True"/> | |
52 </when> | |
53 </conditional> | |
54 </xml> | |
55 <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"> | |
56 <conditional name="@COND_NAME@" label="@COND_LABEL@"> | |
57 <param name="@SELECT_NAME@" type="select" label="@SELECT_LABEL@"> | |
58 <option value="automatic" selected="true">@AUTOMATIC_LABEL@</option> | |
59 <option value="manual">@MANUAL_LABEL@</option> | |
60 </param> | |
61 <when value="automatic"> | |
62 </when> | |
63 <when value="manual"> | |
64 <yield/> | |
65 </when> | |
66 </conditional> | |
67 </xml> | |
68 <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"> | |
69 <param name="@NAME@" type="color" value="@VALUE@" label="@LABEL@" help="@HELP@"> | |
70 <sanitizer> | |
71 <valid initial="string.letters,string.digits"> | |
72 <add value="#"/> | |
73 </valid> | |
74 </sanitizer> | |
75 </param> | |
76 </xml> | |
77 <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"> | |
78 <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@"> | |
79 <expand macro="jb_color"/> | |
80 <yield/> | |
81 </expand> | |
82 </xml> | |
83 <xml name="brewer_scheme"> | |
84 <param name="brewer_scheme" type="select" label="Brewer color Scheme"> | |
85 <option value="BrBg">BrBg: Brown - Blue Green</option> | |
86 <option value="PiYg">PiYg: Pink - Yellow Green</option> | |
87 <option value="PRGn">PRGn: Purple Red - Green</option> | |
88 <option value="PuOr">PuOr: Purple - Orange</option> | |
89 <option value="RdBu" selected="true">RdBu: Red - Blue</option> | |
90 <option value="RdGy">RdGy: Red - Gray</option> | |
91 <option value="RdYlBu">RdYlBu: Red - Yellow - Blue</option> | |
92 <option value="RdYlGn">RdYlBu: Red - Yellow - Green</option> | |
93 <option value="Spectral">Spectral</option> | |
94 </param> | |
95 </xml> | |
96 <xml name="general_options"> | |
97 <section name="jbgen" title="General JBrowse Options [Advanced]" expanded="false"> | |
98 <conditional name="ucol"> | |
99 <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"> | |
100 <option value="form" selected="true">Fill in the tool form to specify tracks for the output JBrowse2</option> | |
101 <option value="collect">Convert a collection of suitable track files</option> | |
102 </param> | |
103 <when value="collect"> | |
104 <param name="autoCollection" type="data_collection" label="Collection of bed, bam and other track files"/> | |
105 </when> | |
106 <when value="form"/> | |
107 </conditional> | |
108 <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"/> | |
109 <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"/> | |
110 <param name="session_name" type="text" value="New JBrowse2 session" label="Session name" help="Displayed at the top of the window"/> | |
111 <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"/> | |
112 <param name="primary_color" type="color" value="#0D233F" label="Primary color"> | |
113 <sanitizer> | |
114 <valid initial="string.ascii_letters,string.digits"> | |
115 <add value="#"/> | |
116 </valid> | |
117 </sanitizer> | |
118 </param> | |
119 <param name="secondary_color" type="color" value="#721E63" label="Secondary color"> | |
120 <sanitizer> | |
121 <valid initial="string.ascii_letters,string.digits"> | |
122 <add value="#"/> | |
123 </valid> | |
124 </sanitizer> | |
125 </param> | |
126 <param name="tertiary_color" type="color" value="#135560" label="Tertiary color"> | |
127 <sanitizer> | |
128 <valid initial="string.ascii_letters,string.digits"> | |
129 <add value="#"/> | |
130 </valid> | |
131 </sanitizer> | |
132 </param> | |
133 <param name="quaternary_color" type="color" value="#FFB11D" label="Quaternary color"> | |
134 <sanitizer> | |
135 <valid initial="string.ascii_letters,string.digits"> | |
136 <add value="#"/> | |
137 </valid> | |
138 </sanitizer> | |
139 </param> | |
140 <param name="font_size" type="integer" value="10" label="Font size"/> | |
141 </section> | |
142 </xml> | |
143 <xml name="color_selection_minmax"> | |
144 <section name="jbcolor" title="JBrowse Color Options [Advanced]" expanded="false"> | |
145 <!-- Abuse auto/manual for bicolor pivot. Means we'll have to handle the | |
146 auto case as well, but may be safe to just say "brewer colors? Pff, | |
147 red/blue" --> | |
148 <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"> | |
149 <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."/> | |
150 <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."/> | |
151 </expand> | |
152 <conditional name="bicolor_pivot" label="Bicolor Pivot"> | |
153 <param name="bicolor_pivot_select" type="select" label="Bicolor Pivot"> | |
154 <option value="zero" selected="true">Zero</option> | |
155 <option value="mean">Mean</option> | |
156 <option value="custom">Custom Value</option> | |
157 </param> | |
158 <when value="zero"/> | |
159 <when value="mean"/> | |
160 <when value="custom"> | |
161 <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."/> | |
162 </when> | |
163 </conditional> | |
164 </section> | |
165 </xml> | |
166 <xml name="color_selection" token_scaling_lin_select="true" token_scaling_log_select="false"> | |
167 <section name="jbcolor_scale" title="JBrowse Feature Score Scaling & Coloring Options [Advanced]" expanded="false"> | |
168 <conditional name="color_score" label="JBrowse style.color & Score relationship"> | |
169 <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"> | |
170 <option value="score">Based on score</option> | |
171 <option value="none" selected="true">Ignore score</option> | |
172 </param> | |
173 <when value="none"> | |
174 <!-- When no scaling is done, no scores available, then just let the | |
175 user choose a base color for the track --> | |
176 <expand macro="auto_color"/> | |
177 </when> | |
178 <when value="score"> | |
179 <!-- Scaling --> | |
180 <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."> | |
181 <option value="linear" selected="@SCALING_LIN_SELECT@">Linear scaling</option> | |
182 <option value="logarithmic" selected="false">Logarithmic scaling</option> | |
183 <option value="blast" selected="@SCALING_LOG_SELECT@">Blast scaling</option> | |
184 </param> | |
185 <!-- Scaling Bounds --> | |
186 <conditional name="score_scales" label="Minimum/Maximum values for track scores"> | |
187 <param name="scale_select" type="select" label="How should minimum and maximum values be determined for the scores of the features"> | |
188 <option value="automatic" selected="true">Automatically determined</option> | |
189 <option value="manual">Manually specify minimum and maximum expected scores for the feature track</option> | |
190 </param> | |
191 <when value="automatic"/> | |
192 <when value="manual"> | |
193 <param name="minimum" type="integer" value="0" label="Minimum expected score"/> | |
194 <param name="maximum" type="integer" value="100" label="Maximum expected score"/> | |
195 </when> | |
196 </conditional> | |
197 <!-- Scale color --> | |
198 <conditional name="color_scheme" label="Color Scheme for scored features"> | |
199 <param name="score_scheme" type="select" label="JBrowse style.color function's color scheme for scored values"> | |
200 <option value="opacity">Opacity (high scores = 1.0 opacity)</option> | |
201 <!--<option value="brewer">Brewer Color Schemes</option>--> | |
202 </param> | |
203 <when value="opacity"> | |
204 <!-- Single color selection mode --> | |
205 <expand macro="auto_color"/> | |
206 </when> | |
207 <!--<when value="brewer">--> | |
208 <!--[> Brewer continuum selection <]--> | |
209 <!--<expand macro="brewer_scheme" />--> | |
210 <!--</when>--> | |
211 </conditional> | |
212 </when> | |
213 </conditional> | |
214 </section> | |
215 </xml> | |
216 <xml name="track_visibility"> | |
217 <param name="track_visibility" type="select" label="Track Visibility"> | |
218 <option value="default_off">Off when browser opens</option> | |
219 <option value="default_on" selected="true">On when browser opens</option> | |
220 </param> | |
221 </xml> | |
222 <xml name="track_styling_linear"> | |
223 <param name="show_labels" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show labels"/> | |
224 <param name="show_descriptions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show descriptions"/> | |
225 <param name="display_mode" type="select" label="Display mode"> | |
226 <option value="normal" selected="true">normal</option> | |
227 <option value="compact">compact</option> | |
228 <option value="reducedRepresentation">reducedRepresentation</option> | |
229 <option value="collapse">collapse</option> | |
230 </param> | |
231 <param name="max_height" type="integer" value="600" label="Max height" help="Maximum height that the track is permitted to reach in pixels."/> | |
232 </xml> | |
233 <xml name="track_styling_vgp"> | |
234 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false"> | |
235 <param name="show_labels" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show labels"/> | |
236 <param name="show_descriptions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show descriptions"/> | |
237 <param name="display" type="select" label="Display style" help="How the track will be displayed by default"> | |
238 <option value="LinearBasicDisplay" selected="true">LinearBasicDisplay</option> | |
239 <option value="LinearPileupDisplay">LinearPileupDisplay - good for dense tracks at scale</option> | |
240 <option value="LinearArcDisplay">LinearArcDisplay</option> | |
241 </param> | |
242 </section> | |
243 </xml> | |
244 <xml name="track_styling_feature"> | |
245 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false"> | |
246 <conditional name="track_style"> | |
247 <param name="display" type="select" label="Display style" help="How the track will be displayed by default"> | |
248 <option value="LinearBasicDisplay" selected="true">LinearBasicDisplay</option> | |
249 <option value="LinearPileupDisplay">LinearPileupDisplay - good for dense tracks at scale</option> | |
250 <option value="LinearArcDisplay">LinearArcDisplay</option> | |
251 </param> | |
252 <when value="LinearPileupDisplay"> | |
253 <expand macro="track_styling_linear"/> | |
254 </when> | |
255 <when value="LinearBasicDisplay"> | |
256 <expand macro="track_styling_linear"/> | |
257 <!-- examples: https://github.com/GMOD/jbrowse-components/discussions/2729 | |
258 and https://github.com/GMOD/jbrowse-components/blob/main/plugins/svg/src/SvgFeatureRenderer/configSchema.ts#L41 --> | |
259 <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"> | |
260 <sanitizer> | |
261 <valid initial="default"> | |
262 <add value="|"/> | |
263 <add value="{"/> | |
264 <add value="}"/> | |
265 <add value="!"/> | |
266 <add value="?"/> | |
267 <add value="+"/> | |
268 <add value="="/> | |
269 <add value="'"/> | |
270 </valid> | |
271 </sanitizer> | |
272 </param> | |
273 <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"> | |
274 <sanitizer> | |
275 <valid initial="default"> | |
276 <add value="|"/> | |
277 <add value="{"/> | |
278 <add value="}"/> | |
279 <add value="!"/> | |
280 <add value="?"/> | |
281 <add value="+"/> | |
282 <add value="="/> | |
283 <add value="'"/> | |
284 </valid> | |
285 </sanitizer> | |
286 </param> | |
287 </when> | |
288 <when value="LinearArcDisplay"/> | |
289 </conditional> | |
290 </section> | |
291 </xml> | |
292 <xml name="track_styling_xam"> | |
293 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false"> | |
294 <conditional name="track_style"> | |
295 <param name="display" type="select" label="Display style" help="How the track will be displayed by default"> | |
296 <option value="LinearAlignmentsDisplay" selected="true">LinearAlignmentsDisplay</option> | |
297 <option value="LinearPileupDisplay">LinearPileupDisplay</option> | |
298 <option value="LinearSNPCoverageDisplay">LinearSNPCoverageDisplay</option> | |
299 <option value="LinearReadArcsDisplay">LinearReadArcsDisplay</option> | |
300 <option value="LinearReadCloudDisplay">LinearReadCloudDisplay</option> | |
301 </param> | |
302 <!-- TODO check if possible to handle more options than just the display style--> | |
303 <when value="LinearAlignmentsDisplay"/> | |
304 <when value="LinearPileupDisplay"/> | |
305 <when value="LinearSNPCoverageDisplay"> | |
306 <param name="displayCrossHatches" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Draw cross hatches"/> | |
307 <param name="minScore" type="integer" value="" optional="true" label="Min score"/> | |
308 <param name="maxScore" type="integer" value="" optional="true" label="Max score"/> | |
309 </when> | |
310 <when value="LinearReadArcsDisplay"/> | |
311 <when value="LinearReadCloudDisplay"/> | |
312 </conditional> | |
313 </section> | |
314 </xml> | |
315 <xml name="track_styling_vcf"> | |
316 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false"> | |
317 <conditional name="track_style"> | |
318 <param name="display" type="select" label="Display style" help="How the track will be displayed by default"> | |
319 <option value="LinearVariantDisplay" selected="true">LinearVariantDisplay</option> | |
320 <option value="LinearPairedArcDisplay">LinearPairedArcDisplay</option> | |
321 </param> | |
322 <when value="LinearVariantDisplay"> | |
323 <expand macro="track_styling_linear"/> | |
324 </when> | |
325 <when value="LinearPairedArcDisplay"/> | |
326 </conditional> | |
327 </section> | |
328 </xml> | |
329 <xml name="track_styling_bigwig"> | |
330 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false"> | |
331 <conditional name="track_style"> | |
332 <param name="display" type="select" label="Display style" help="How the track will be displayed by default"> | |
333 <option value="LinearWiggleDisplay" selected="true">LinearWiggleDisplay</option> | |
334 </param> | |
335 <when value="LinearWiggleDisplay"> | |
336 <param name="autoscale" type="select" label="Autoscale type"> | |
337 <option value="local" selected="true">Local</option> | |
338 <option value="global">Global</option> | |
339 <option value="globalsd">Global ± 3σ</option> | |
340 <option value="localsd">Local ± 3σ</option> | |
341 </param> | |
342 <param name="resolution" type="integer" value="1" label="Resolution"/> | |
343 <param name="summaryScoreMode" type="select" label="Autoscale type"> | |
344 <option value="max">Max</option> | |
345 <option value="min">Min</option> | |
346 <option value="avg">Avg</option> | |
347 <option value="whiskers" selected="true">Whiskers (combines all three)</option> | |
348 </param> | |
349 <param name="filled" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Fill in histogram"/> | |
350 <param name="scaleType" type="select" label="Autoscale type"> | |
351 <option value="linear" selected="true">Linear</option> | |
352 <option value="log">Log</option> | |
353 </param> | |
354 <param name="displayCrossHatches" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Draw cross hatches"/> | |
355 <param name="minScore" type="integer" value="" optional="true" label="Min score"/> | |
356 <param name="maxScore" type="integer" value="" optional="true" label="Max score"/> | |
357 </when> | |
358 </conditional> | |
359 </section> | |
360 </xml> | |
361 <xml name="track_menu"> | |
362 <section name="jbmenu" title="JBrowse Contextual Menu options [Advanced]" expanded="false"> | |
363 <repeat name="track_menu" title="Track Menu"> | |
364 <param name="menu_action" type="select" label="Menu action" help="Action performed when user clicks on the menu"> | |
365 <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> | |
366 <option value="newWindow">newWindow: causes the given url to be opened in a new browser window.</option> | |
367 <option value="navigateTo">navigateTo: opens the given url in the same browser window, navigating the user away from JBrowse.</option> | |
368 </param> | |
369 <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)"> | |
370 <expand macro="menu_sanitize"/> | |
371 </param> | |
372 <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)"> | |
373 <expand macro="menu_sanitize"/> | |
374 </param> | |
375 <param name="menu_url" type="text" label="Menu url" help="Destination URL ({name}, {id}, {type}, {start}, {end}, {strand} variables will be interpreted)"> | |
376 <expand macro="menu_sanitize"/> | |
377 </param> | |
378 <param name="menu_icon" type="select" label="Menu icon" help="Icon to display next to menu label"> | |
379 <option value="dijitIconBookmark" selected="true">Bookmark</option> | |
380 <option value="dijitIconSave">Save</option> | |
381 <option value="dijitIconPrint">Print</option> | |
382 <option value="dijitIconCut">Cut</option> | |
383 <option value="dijitIconCopy">Copy</option> | |
384 <option value="dijitIconClear">Clear</option> | |
385 <option value="dijitIconDelete">Delete</option> | |
386 <option value="dijitIconUndo">Undo</option> | |
387 <option value="dijitIconEdit">Edit</option> | |
388 <option value="dijitIconNewTask">New Task</option> | |
389 <option value="dijitIconEditTask">Edit Task</option> | |
390 <option value="dijitIconEditProperty">Edit Property</option> | |
391 <option value="dijitIconTask">Task</option> | |
392 <option value="dijitIconFilter">Filter</option> | |
393 <option value="dijitIconConfigure">Configure</option> | |
394 <option value="dijitIconSearch">Search</option> | |
395 <option value="dijitIconApplication">Application</option> | |
396 <option value="dijitIconChart">Chart</option> | |
397 <option value="dijitIconConnector">Connector</option> | |
398 <option value="dijitIconDatabase">Database</option> | |
399 <option value="dijitIconDocuments">Documents</option> | |
400 <option value="dijitIconMail">Mail</option> | |
401 <option value="dijitLeaf">Leaf</option> | |
402 <option value="dijitIconFile">File</option> | |
403 <option value="dijitIconFunction">Function</option> | |
404 <option value="dijitIconKey">Key</option> | |
405 <option value="dijitIconPackage">Package</option> | |
406 <option value="dijitIconSample">Sample</option> | |
407 <option value="dijitIconTable">Table</option> | |
408 <option value="dijitIconUsers">Users</option> | |
409 <option value="dijitIconFolderClosed">Folder Closed</option> | |
410 <option value="dijitIconFolderOpen">Folder Open</option> | |
411 <option value="dijitIconError">Error</option> | |
412 </param> | |
413 </repeat> | |
414 </section> | |
415 </xml> | |
416 <xml name="menu_sanitize"> | |
417 <sanitizer> | |
418 <valid> | |
419 <add value="{"/> | |
420 <add value="}"/> | |
421 <add value="!"/> | |
422 <add value="?"/> | |
423 <add value="&"/> | |
424 <add value="+"/> | |
425 <add value="="/> | |
426 <add value="'"/> | |
427 <add value="""/> | |
428 </valid> | |
429 </sanitizer> | |
430 </xml> | |
431 <xml name="input_conditional" token_label="Track Data" token_format="data"> | |
432 <conditional name="useuri"> | |
433 <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"> | |
434 <option value="history" selected="true">Track data from a history file</option> | |
435 <option value="uri">Tabix data URI - index files must be available at corresponding URI</option> | |
436 </param> | |
437 <when value="history"> | |
438 <param name="annotation" type="data" format="@FORMAT@" optional="true" label="@LABEL@" multiple="True"/> | |
439 </when> | |
440 <when value="uri"> | |
441 <param name="annouri" type="text" label="@LABEL@"/> | |
442 <param name="annoname" type="text" label="Short name for track display"> | |
443 <sanitizer invalid_char="_"> | |
444 <valid initial="string.printable"> | |
445 <remove value="'"/> | |
446 </valid> | |
447 </sanitizer> | |
448 </param> | |
449 </when> | |
450 </conditional> | |
451 </xml> | |
452 <xml name="pafref_conditional" token_label="Track Data" token_format="data"> | |
453 <conditional name="pafuseuri"> | |
454 <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."> | |
455 <option value="history" selected="true">PAF reference comparison genome from a history file</option> | |
456 <option value="uri">PAF reference comparison genome tabix .gz URI with index files at the corresponding URIs</option> | |
457 </param> | |
458 <when value="history"> | |
459 <param name="annotation" type="data" format="@FORMAT@" label="@LABEL@" help="Add all PAF reference comparison genomes used to make the PAF" multiple="true"/> | |
460 </when> | |
461 <when value="uri"> | |
462 <repeat name="refuri" title="PAF reference comparison genome URI" min="1"> | |
463 <param name="annotation" type="text" label="@LABEL@"/> | |
464 <param name="annoname" type="text" label="Short name for this reference" help="Short names take less track space"> | |
465 <sanitizer invalid_char="_"> | |
466 <valid initial="string.printable"> | |
467 <remove value="'"/> | |
468 </valid> | |
469 </sanitizer> | |
470 </param> | |
471 </repeat> | |
472 </when> | |
473 </conditional> | |
474 </xml> | |
475 <xml name="citations"> | |
476 <citations> | |
477 <citation type="doi">10.1186/s13059-016-0924-1</citation> | |
478 <citation type="doi">10.1101/gr.094607.109</citation> | |
479 </citations> | |
480 </xml> | |
481 </macros> |