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comparison jbrowse2.xml @ 62:ab0d6782a95f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
author fubar
date Thu, 28 Mar 2024 04:51:06 +0000
parents 81d535970196
children ac00dcfb5d1d
comparison
equal deleted inserted replaced
61:e7a6f7a7148d 62:ab0d6782a95f
1 <tool id="jbrowse2" name="jbrowse2" version="@TOOL_VERSION@+@WRAPPER_VERSION@_7" profile="22.05"> 1 <tool id="jbrowse2auto" name="JBrowse2auto" version="@TOOL_VERSION@+@WRAPPER_VERSION@_8" profile="22.05">
2 <description>genome browser</description> 2 <description>genome browser</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="edamInc"/> 6 <expand macro="edamInc"/>
60 #end if 60 #end if
61 #end if 61 #end if
62 ]]></command> 62 ]]></command>
63 <configfiles> 63 <configfiles>
64 <configfile name="trackxml"><![CDATA[<?xml version="1.0"?> 64 <configfile name="trackxml"><![CDATA[<?xml version="1.0"?>
65 #if $jbgen.ucol.formcoll=="form":
66 <root> 65 <root>
67 <metadata> 66 <metadata>
68 <genomes>
69 #if str($reference_genome.genome_type_select) == "uri":
70 <genome path="${reference_genome.uri}" label="${reference_genome.refname}" useuri="yes">
71 <metadata>
72 <dataset
73 dname = "${reference_genome.refname}" />
74 </metadata>
75 </genome>
76 #else if str($reference_genome.genome_type_select) == "indexed":
77 <genome path="${reference_genome.genome.fields.path}" label="${reference_genome.genome.fields.name}" useuri="no">
78 <metadata>
79 <dataset
80 dname = "${reference_genome.genome.fields.name}" />
81 </metadata>
82 </genome>
83 #else
84 <genome path="$reference_genome.genome" label="${reference_genome.genome.name}" useuri="no">
85 <metadata>
86 <dataset id="${__app__.security.encode_id($reference_genome.genome.id)}" hid="${reference_genome.genome.hid}"
87 size="${reference_genome.genome.get_size(nice_size=True)}"
88 edam_format="${reference_genome.genome.datatype.edam_format}"
89 file_ext="${reference_genome.genome.ext}"
90 dname = "${reference_genome.genome.name}" />
91 <history id="${__app__.security.encode_id($reference_genome.genome.history_id)}"
92 #if $reference_genome.genome.history.user:
93 user_email="${reference_genome.genome.history.user.email}"
94 user_id="${reference_genome.genome.history.user_id}"
95 display_name="${reference_genome.genome.history.get_display_name()}"/>
96 #else
97 user_email="anonymous"
98 user_id="-1"
99 display_name="Unnamed History"/>
100 #end if
101 <metadata
102 #for (key, value) in $reference_genome.genome.get_metadata().items():
103 #if "_types" not in $key:
104 #if isinstance($value, list):
105 #set value_str = "[%s]" % ','.join([str(val) for val in value])
106 ${key}="$value_str"
107 #else
108 ${key}="${value}"
109 #end if
110 #end if
111 #end for
112 />
113 <tool
114 tool_id="${reference_genome.genome.creating_job.tool_id}"
115 tool_version="${reference_genome.genome.creating_job.tool_version}"
116 />
117 </metadata>
118 </genome>
119 #end if
120 </genomes>
121 <general> 67 <general>
122 <defaultLocation>${jbgen.defaultLocation}</defaultLocation> 68 <defaultLocation>${jbgen.defaultLocation}</defaultLocation>
123 <zipOut>${jbgen.zipOut}</zipOut> 69 <zipOut>${jbgen.zipOut}</zipOut>
124 <analytics>${jbgen.enableAnalytics}</analytics> 70 <analytics>${jbgen.enableAnalytics}</analytics>
125 <primary_color>${jbgen.primary_color}</primary_color> 71 <primary_color>${jbgen.primary_color}</primary_color>
129 <font_size>${jbgen.font_size}</font_size> 75 <font_size>${jbgen.font_size}</font_size>
130 <session_name>${jbgen.session_name}</session_name> 76 <session_name>${jbgen.session_name}</session_name>
131 </general> 77 </general>
132 <galaxyUrl>${__app__.config.galaxy_infrastructure_url}</galaxyUrl> 78 <galaxyUrl>${__app__.config.galaxy_infrastructure_url}</galaxyUrl>
133 </metadata> 79 </metadata>
80 #if $jbgen.ucol.formcoll=="form":
81 #for $assembly in $assemblies:
82 <assembly>
83 <metadata>
84 <genomes>
85 #if str($assembly.reference_genome.genome_type_select) == "uri":
86 <genome path="${assembly.reference_genome.uri}" label="${assembly.reference_genome.refname}" useuri="yes">
87 <metadata>
88 <dataset
89 dname = "${assembly.reference_genome.refname}" />
90 </metadata>
91 </genome>
92 #else if str($assembly.reference_genome.genome_type_select) == "indexed":
93 <genome path="${assembly.reference_genome.genome.fields.path}" label="${assembly.reference_genome.genome.fields.name}" useuri="no">
94 <metadata>
95 <dataset
96 dname = "${assembly.reference_genome.genome.fields.name}" />
97 </metadata>
98 </genome>
99 #else
100 <genome path="$assembly.reference_genome.genome" label="${assembly.reference_genome.genome.name}" useuri="no">
101 <metadata>
102 #if $uglyTestingHack != "enabled":
103 <dataset id="${__app__.security.encode_id($assembly.reference_genome.genome.id)}"
104 hid="${assembly.reference_genome.genome.hid}"
105 size="${assembly.reference_genome.genome.get_size(nice_size=True)}"
106 edam_format="${assembly.reference_genome.genome.datatype.edam_format}"
107 file_ext="${assembly.reference_genome.genome.ext}"
108 dname = "${assembly.reference_genome.genome.name}"
109 />
110 <history
111 #if $assembly.reference_genome.genome.history.user:
112 user_email="${assembly.reference_genome.genome.history.user.email}"
113 user_id="${assembly.reference_genome.genome.history.user_id}"
114 display_name="${assembly.reference_genome.genome.history.get_display_name()}"/>
115 #else
116 user_email="anonymous"
117 user_id="-1"
118 display_name="Unnamed History"
119 #end if
120 id="${__app__.security.encode_id($assembly.reference_genome.genome.history_id)}"
121 />
122 <metadata
123 #for (key, value) in $assembly.reference_genome.genome.get_metadata().items():
124 #if "_types" not in $key:
125 #if isinstance($value, list):
126 #set value_str = "[%s]" % ','.join([str(val) for val in value])
127 ${key}="$value_str"
128 #else
129 ${key}="${value}"
130 #end if
131 #end if
132 #end for
133 />
134 <tool
135 tool_id="${assembly.reference_genome.genome.creating_job.tool_id}"
136 tool_version="${assembly.reference_genome.genome.creating_job.tool_version}"
137 />
138 #end if
139 </metadata>
140 </genome>
141 #end if
142 </genomes>
143
144 </metadata>
134 <tracks> 145 <tracks>
135 #for $tg in $track_groups: 146 #for $tg in $assembly.track_groups:
136 #for $track in $tg.data_tracks: 147 #for $track in $tg.data_tracks:
137 #if $track.data_format.useuri.insource == "uri": 148 #if $track.data_format.useuri.insource == "uri":
138 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}"> 149 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
139 <files> 150 <files>
140 <trackFile path="${track.data_format.useuri.annouri}" ext="${track.data_format.data_format_select}" 151 <trackFile path="${track.data_format.useuri.annouri}" ext="${track.data_format.data_format_select}"
149 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}"> 160 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
150 <files> 161 <files>
151 #for $dataset in $track.data_format.useuri.annotation: 162 #for $dataset in $track.data_format.useuri.annotation:
152 <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.name}" useuri="no"> 163 <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.name}" useuri="no">
153 <metadata> 164 <metadata>
165 #if $uglyTestingHack != "enabled":
154 <dataset id="${__app__.security.encode_id($dataset.id)}" hid="${dataset.hid}" 166 <dataset id="${__app__.security.encode_id($dataset.id)}" hid="${dataset.hid}"
155 size="${dataset.get_size(nice_size=True)}" 167 size="${dataset.get_size(nice_size=True)}"
156 edam_format="${dataset.datatype.edam_format}" 168 edam_format="${dataset.datatype.edam_format}"
157 file_ext="${dataset.ext}" /> 169 file_ext="${dataset.ext}" />
158 <history id="${__app__.security.encode_id($dataset.history_id)}" 170 <history id="${__app__.security.encode_id($dataset.history_id)}"
180 /> 192 />
181 <tool 193 <tool
182 tool_id="${dataset.creating_job.tool_id}" 194 tool_id="${dataset.creating_job.tool_id}"
183 tool_version="${dataset.creating_job.tool_version}" 195 tool_version="${dataset.creating_job.tool_version}"
184 /> 196 />
197 #end if
185 </metadata> 198 </metadata>
186 </trackFile> 199 </trackFile>
187 #end for 200 #end for
188 </files> 201 </files>
189 #end if 202 #end if
190 #end if 203 #end if
204 #if $uglyTestingHack != "enabled":
191 <options> 205 <options>
192 <style> 206 <style>
193 #if str($track.data_format.data_format_select) in ["gff", "bed", "vcf", "maf", "blastxml"]: 207 #if str($track.data_format.data_format_select) in ["gff", "bed", "vcf", "maf", "blastxml"]:
194 <type>${track.data_format.jbstyle.track_style.display}</type> 208 <type>${track.data_format.jbstyle.track_style.display}</type>
195 #if str($track.data_format.jbstyle.track_style.display) in ["LinearBasicDisplay", "LinearVariantDisplay"]: 209 #if str($track.data_format.jbstyle.track_style.display) in ["LinearBasicDisplay", "LinearVariantDisplay"]:
196 <trackShowLabels>${track.data_format.jbstyle.track_style.show_labels}</trackShowLabels> 210 <trackShowLabels>${track.data_format.jbstyle.track_style.show_labels}</trackShowLabels>
197 <trackShowDescriptions>${track.data_format.jbstyle.track_style.show_descriptions}</trackShowDescriptions> 211 <trackShowDescriptions>${track.data_format.jbstyle.track_style.show_descriptions}</trackShowDescriptions>
212 #end if
198 #end if 213 #end if
199 #end if 214 #if str($track.data_format.data_format_select) in ["bam", "cram"]:
200 #if str($track.data_format.data_format_select) in ["bam", "cram"]: 215 <type>LinearAlignmentsDisplay</type>
201 <type>LinearAlignmentsDisplay</type> 216 #end if
202 #end if 217 #if str($track.data_format.data_format_select) in ["paf"]:
203 #if str($track.data_format.data_format_select) in ["paf"]: 218 <type>LinearBasicDisplay</type>
204 <type>LinearBasicDisplay</type> 219 #end if
205 #end if 220 #if str($track.data_format.data_format_select) in ["hic"]:
206 #if str($track.data_format.data_format_select) in ["hic"]: 221 <type>LinearHicDisplay</type>
207 <type>LinearHicDisplay</type> 222 #end if
208 #end if
209 </style> 223 </style>
210 #if str($track.data_format.data_format_select) == "bam": 224 #if str($track.data_format.data_format_select) == "bam":
211 <bam> 225 <bam>
212 #for $dataset in $track.data_format.useuri.annotation: 226 #for $dataset in $track.data_format.useuri.annotation:
213 <bam_index>${dataset.metadata.bam_index}</bam_index> 227 <bam_index>${dataset.metadata.bam_index}</bam_index>
262 <query>${track.data_format.query}</query> 276 <query>${track.data_format.query}</query>
263 <query_refnames>${track.data_format.query_refnames}</query_refnames> 277 <query_refnames>${track.data_format.query_refnames}</query_refnames>
264 </sparql> 278 </sparql>
265 #end if 279 #end if
266 </options> 280 </options>
281 #end if
267 </track> 282 </track>
268 #end for 283 #end for
269 #end for 284 #end for
270 </tracks> 285 </tracks>
286 </assembly>
287 #end for
288 #end if
271 </root> 289 </root>
272 #end if
273 ]]></configfile> 290 ]]></configfile>
274 </configfiles> 291 </configfiles>
275
276 <inputs> 292 <inputs>
293 <repeat name="assemblies" min="1" title="Genome Assembly" help="When too many genomes are never enough">
277 <conditional name="reference_genome"> 294 <conditional name="reference_genome">
278 <param help="Built-in references" label="Reference genome to display" name="genome_type_select" type="select"> 295 <param help="Select a built in, history or remote tabix URI for the reference track"
296 label="Reference genome source" name="genome_type_select" type="select">
279 <option selected="True" value="indexed">Use a built-in genome</option> 297 <option selected="True" value="indexed">Use a built-in genome</option>
280 <option value="history">Use a genome from history</option> 298 <option value="history">Use a genome from history</option>
281 <option value="uri">URI for a reference in tabix .gz format </option> 299 <option value="uri">URI for a reference as tabix with predictable index file URI</option>
282 </param> 300 </param>
283 <when value="indexed"> 301 <when value="indexed">
284 <param 302 <param
285 help="If your genome of interest is not listed, contact the Galaxy team" 303 help="If not listed, add a custom genome, use a history genome or a remote URI tabix genome"
286 label="Select a reference genome" 304 label="Select a built in reference genome or custom genome"
287 name="genome" 305 name="genome"
288 type="select" 306 type="select"
289 optional="true"> 307 optional="true">
290 <options from_data_table="all_fasta"> 308 <options from_data_table="all_fasta">
291 <filter column="2" type="sort_by"/> 309 <filter column="2" type="sort_by"/>
308 label="URI pointing to tabix compressed fasta" 326 label="URI pointing to tabix compressed fasta"
309 name="uri" 327 name="uri"
310 type="text"> 328 type="text">
311 </param> 329 </param>
312 <param 330 <param
313 label="Reference key - dbkey equivalent" 331 label="Reference dbkey for tracks with this genome, such as hg38 or SacCer4"
314 name="refname" 332 name="refname"
315 type="text"> 333 type="text">
316 </param> 334 </param>
317 </when> 335 </when>
318 </conditional> 336 </conditional>
426 <expand macro="track_visibility" /> 444 <expand macro="track_visibility" />
427 </when> 445 </when>
428 </conditional> 446 </conditional>
429 </repeat> 447 </repeat>
430 </repeat> 448 </repeat>
431 449 </repeat>
432 <expand macro="general_options" /> 450 <expand macro="general_options" />
433
434 <param type="hidden" name="uglyTestingHack" value="" /> 451 <param type="hidden" name="uglyTestingHack" value="" />
435 </inputs> 452 </inputs>
436 <outputs> 453 <outputs>
437 <data format="html" name="output" label="JBrowse2"> 454 <data format="html" name="output" label="JBrowse2">
438 <change_format> 455 <change_format>
440 </change_format> 457 </change_format>
441 </data> 458 </data>
442 </outputs> 459 </outputs>
443 <tests> 460 <tests>
444 <test> 461 <test>
445 <param name="reference_genome|genome_type_select" value="history"/> 462 <repeat name="assemblies">
446 <param name="reference_genome|genome" value="merlin.fa"/> 463 <conditional name="reference_genome">
447 <repeat name="track_groups"> 464 <param name="genome_type_select" value="history"/>
448 <param name="category" value="Default" /> 465 <param name="genome" value="merlin.fa"/>
449 <repeat name="data_tracks"> 466 <param name="genome.ext" value="fasta"/>
450 <conditional name="data_format"> 467 <param name="genome.name" value="Merlin"/>
451 <param name="data_format_select" value="bigwig"/> 468 </conditional>
452 <conditional name="useuri"> 469 <repeat name="track_groups">
453 <param name="annotation" value="bw/merlin.bw"/> 470 <param name="category" value="Default" />
454 <param name="insource" value="history"/> 471 <repeat name="data_tracks">
455 </conditional> 472 <conditional name="data_format">
456 </conditional> 473 <param name="data_format_select" value="bigwig"/>
474 <conditional name="useuri">
475 <param name="annotation" value="bw/merlin.bw"/>
476 <param name="insource" value="history"/>
477 </conditional>
478 </conditional>
479 </repeat>
480 </repeat>
481 </repeat>
482 <param name="uglyTestingHack" value="enabled" />
483 <output name="output">
484 <assert_contents>
485 <has_text text="genome path="></has_text>
486 <has_text text="label="></has_text>
487 <has_text text="format="></has_text>
488 <has_text text="metadata"></has_text>
489 <has_text text="useuri="></has_text>
490 <has_text text="trackFile path="></has_text>
491 <has_text text="ext=&quot;bigwig&quot;"></has_text>
492 <has_text text="format=&quot;bigwig&quot;"></has_text>
493 </assert_contents>
494 </output>
495 </test>
496 <test>
497 <repeat name="assemblies">
498 <conditional name="reference_genome">
499 <param name="genome_type_select" value="history"/>
500 <param name="genome" value="merlin.fa"/>
501 <param name="genome.ext" value="fasta"/>
502 <param name="genome.name" value="Merlin"/>
503 </conditional>
504 <repeat name="track_groups">
505 <param name="category" value="Default" />
506 <repeat name="data_tracks">
507 <conditional name="data_format">
508 <param name="data_format_select" value="vcf"/>
509 <conditional name="useuri">
510 <param name="insource" value="history"/>
511 <param name="annotation" value="vcf/merlin.vcf"/>
512 </conditional>
513 </conditional>
514 </repeat>
457 </repeat> 515 </repeat>
458 </repeat> 516 </repeat>
459 <param name="uglyTestingHack" value="enabled" /> 517 <param name="uglyTestingHack" value="enabled" />
460 <output name="output"> 518 <output name="output">
461 <assert_contents> 519 <assert_contents>
462 <has_text text="genome path="></has_text> 520 <has_text text="genome path="></has_text>
463 <has_text text="dataset id="></has_text> 521 <has_text text="label="></has_text>
464 <has_text text="history id="></has_text> 522 <has_text text="format="></has_text>
465 <has_text text="metadata"></has_text> 523 <has_text text="metadata"></has_text>
466 <has_text text="tool_id"></has_text> 524 <has_text text="useuri="></has_text>
467 <has_text text="trackFile path="></has_text> 525 <has_text text="trackFile path="></has_text>
468 <has_text text="file_ext=&quot;bigwig&quot;"></has_text> 526 <has_text text="ext=&quot;vcf&quot; label=&quot;merlin.vcf&quot;"></has_text>
469 <has_text text="format=&quot;bigwig&quot;"></has_text>
470 </assert_contents> 527 </assert_contents>
471 </output> 528 </output>
472 </test> 529 </test>
473 <test> 530 <test>
474 <param name="reference_genome|genome_type_select" value="history"/> 531 <repeat name="assemblies">
475 <param name="reference_genome|genome" value="merlin.fa"/> 532 <conditional name="reference_genome">
476 <repeat name="track_groups"> 533 <param name="genome_type_select" value="history"/>
477 <param name="category" value="Default" /> 534 <param name="genome" value="merlin.fa"/>
478 <repeat name="data_tracks"> 535 <param name="genome.ext" value="fasta"/>
479 <conditional name="data_format"> 536 <param name="genome.name" value="Merlin"/>
480 <param name="data_format_select" value="vcf"/> 537 </conditional>
481 <conditional name="useuri"> 538 </repeat>
482 <param name="insource" value="history"/> 539 <param name="uglyTestingHack" value="enabled" />
483 <param name="annotation" value="vcf/merlin.vcf"/> 540 <output name="output">
484 </conditional> 541 <assert_contents>
485 </conditional> 542 <has_text text="genome path="></has_text>
543 <has_text text="label="></has_text>
544 <has_text text="format="></has_text>
545 <has_text text="metadata"></has_text>
546 </assert_contents>
547 </output>
548 </test>
549 <test>
550 <repeat name="assemblies">
551 <conditional name="reference_genome">
552 <param name="genome_type_select" value="history"/>
553 <param name="genome" value="merlin.fa"/>
554 <param name="genome.ext" value="fasta"/>
555 <param name="genome.name" value="Merlin"/>
556 </conditional>
557 <repeat name="track_groups">
558 <param name="category" value="Default" />
559 <repeat name="data_tracks">
560 <conditional name="data_format">
561 <param name="data_format_select" value="vcf"/>
562 <conditional name="useuri">
563 <param name="insource" value="history"/>
564 <param name="annotation" value="vcf/merlin.vcf"/>
565 </conditional>
566 </conditional>
567 </repeat>
486 </repeat> 568 </repeat>
487 </repeat> 569 </repeat>
488 <param name="uglyTestingHack" value="enabled" /> 570 <param name="uglyTestingHack" value="enabled" />
489 <output name="output"> 571 <output name="output">
490 <assert_contents> 572 <assert_contents>
491 <has_text text="genome path="></has_text> 573 <has_text text="genome path="></has_text>
492 <has_text text="dataset id="></has_text> 574 <has_text text="label="></has_text>
493 <has_text text="history id="></has_text> 575 <has_text text="format="></has_text>
494 <has_text text="metadata"></has_text> 576 <has_text text="metadata"></has_text>
495 <has_text text="tool_id"></has_text> 577 <has_text text="useuri="></has_text>
496 <has_text text="trackFile path="></has_text>
497 <has_text text="ext=&quot;vcf&quot; label=&quot;merlin.vcf&quot;"></has_text>
498 </assert_contents>
499 </output>
500 </test>
501 <test>
502 <param name="reference_genome|genome_type_select" value="history"/>
503 <param name="reference_genome|genome" value="merlin.fa"/>
504 <param name="uglyTestingHack" value="enabled" />
505 <output name="output">
506 <assert_contents>
507 <has_text text="genome path="></has_text>
508 <has_text text="dataset id="></has_text>
509 <has_text text="history id="></has_text>
510 <has_text text="metadata"></has_text>
511 <has_text text="tool_id"></has_text>
512 </assert_contents>
513 </output>
514 </test>
515 <test>
516 <param name="reference_genome|genome_type_select" value="history"/>
517 <param name="reference_genome|genome" value="merlin.fa"/>
518 <repeat name="track_groups">
519 <param name="category" value="Default" />
520 <repeat name="data_tracks">
521 <conditional name="data_format">
522 <param name="data_format_select" value="bed"/>
523 <conditional name="useuri">
524 <param name="insource" value="history"/>
525 <param name="annotation" value="bed/test-3.bed"/>
526 </conditional>
527 </conditional>
528 </repeat>
529 </repeat>
530 <param name="uglyTestingHack" value="enabled" />
531 <output name="output">
532 <assert_contents>
533 <has_text text="genome path="></has_text>
534 <has_text text="dataset id="></has_text>
535 <has_text text="history id="></has_text>
536 <has_text text="metadata"></has_text>
537 <has_text text="tool_id"></has_text>
538 <has_text text="trackFile path="></has_text> 578 <has_text text="trackFile path="></has_text>
539 <has_text text="ext=&quot;bed&quot; label=&quot;test-3.bed&quot;"></has_text> 579 <has_text text="ext=&quot;bed&quot; label=&quot;test-3.bed&quot;"></has_text>
540 </assert_contents> 580 </assert_contents>
541 </output> 581 </output>
542 </test> 582 </test>
543 <test> 583 <test>
544 <param name="reference_genome|genome_type_select" value="history"/> 584 <repeat name="assemblies">
545 <param name="reference_genome|genome" value="merlin.fa"/> 585 <conditional name="reference_genome">
546 <repeat name="track_groups"> 586 <param name="genome_type_select" value="history"/>
547 <param name="category" value="Auto Coloured" /> 587 <param name="genome" value="merlin.fa"/>
548 <repeat name="data_tracks"> 588 <param name="genome.ext" value="fasta"/>
549 <conditional name="data_format"> 589 <param name="genome.name" value="Merlin"/>
590 </conditional>
591 <repeat name="track_groups">
592 <param name="category" value="Default" />
593 <repeat name="data_tracks">
594 <conditional name="data_format">
550 <param name="data_format_select" value="gff"/> 595 <param name="data_format_select" value="gff"/>
551 <conditional name="useuri"> 596 <conditional name="useuri">
552 <param name="insource" value="history"/> 597 <param name="insource" value="history"/>
553 <param name="annotation" value="gff3/A.gff"/> 598 <param name="annotation" value="gff3/A.gff"/>
599 </conditional>
554 </conditional> 600 </conditional>
555 <conditional name="match_part"> 601 <conditional name="match_part">
556 <param name="match_part_select" value="false"/> 602 <param name="match_part_select" value="false"/>
557 </conditional> 603 </conditional>
558 <section name="jbcolor_scale"> 604 <section name="jbcolor_scale">
561 </conditional> 607 </conditional>
562 <conditional name="color"> 608 <conditional name="color">
563 <param name="color_select" value="automatic"/> 609 <param name="color_select" value="automatic"/>
564 </conditional> 610 </conditional>
565 </section> 611 </section>
566 </conditional> 612 </repeat>
567 </repeat> 613 </repeat>
568 </repeat> 614 </repeat>
569 615
570 <repeat name="track_groups"> 616 <repeat name="track_groups">
571 <param name="category" value="Ignore Scale" /> 617 <param name="category" value="Ignore Scale" />
768 <has_text text="2.gff"/> 814 <has_text text="2.gff"/>
769 </assert_contents> 815 </assert_contents>
770 </output> 816 </output>
771 </test> 817 </test>
772 <test> 818 <test>
773 <param name="reference_genome|genome_type_select" value="history"/> 819 <repeat name="assemblies">
774 <param name="reference_genome|genome" value="merlin.fa"/> 820 <conditional name="reference_genome">
775 821 <param name="genome_type_select" value="history"/>
776 <repeat name="track_groups"> 822 <param name="genome" value="merlin.fa"/>
777 <param name="category" value="With menu or index" /> 823 <param name="genome.ext" value="fasta"/>
778 <repeat name="data_tracks"> 824 <param name="genome.name" value="Merlin"/>
779 <conditional name="data_format"> 825 </conditional>
826 <repeat name="track_groups">
827 <param name="category" value="Default" />
828 <repeat name="data_tracks">
829 <conditional name="data_format">
830 <param name="data_format_select" value="gff"/>
831 <conditional name="useuri">
832 <param name="annotation" value="gff3/1.gff"/>
833 <param name="insource" value= "history"/>
834 </conditional>
835 <conditional name="match_part">
836 <param name="match_part_select" value="false"/>
837 </conditional>
838 <section name="jbcolor_scale">
839 <conditional name="color_score">
840 <param name="color_score_select" value="none"/>
841 </conditional>
842 <conditional name="color">
843 <param name="color_select" value="automatic"/>
844 </conditional>
845 </section>
846 <section name="jbmenu">
847 <repeat name="track_menu">
848 <param name="menu_action" value="iframeDialog"/>
849 <param name="menu_label" value="Some menu item"/>
850 <param name="menu_title" value="Frame title"/>
851 <param name="menu_url" value="https://example.com/#!/?id={name}&amp;q={type}&amp;z=&quot;{end}&quot;"/>
852 <param name="menu_icon" value="dijitIconNewTask"/>
853 </repeat>
854 <repeat name="track_menu">
855 <param name="menu_action" value="newWindow"/>
856 <param name="menu_label" value="Another menu item"/>
857 <param name="menu_title" value="Frame title 2"/>
858 <param name="menu_url" value="https://example.com/#!/?id={name}&amp;q={type}&amp;z=&quot;{end}&quot;"/>
859 </repeat>
860 </section>
861 </conditional>
862 </repeat>
863 <repeat name="data_tracks">
864 <conditional name="data_format">
780 <param name="data_format_select" value="gff"/> 865 <param name="data_format_select" value="gff"/>
781 <conditional name="useuri"> 866 <conditional name="useuri">
782 <param name="annotation" value="gff3/1.gff"/> 867 <param name="annotation" value="gff3/1.gff"/>
783 <param name="insource" value= "history"/> 868 <param name="insource" value= "history"/>
784 </conditional> 869 </conditional>
785 <conditional name="match_part"> 870 <conditional name="match_part">
786 <param name="match_part_select" value="false"/> 871 <param name="match_part_select" value="false"/>
787 </conditional> 872 </conditional>
788 <section name="jbcolor_scale"> 873 <section name="jbcolor_scale">
789 <conditional name="color_score"> 874 <conditional name="color_score">
790 <param name="color_score_select" value="none"/> 875 <param name="color_score_select" value="none"/>
791 </conditional> 876 </conditional>
792 <conditional name="color"> 877 <conditional name="color">
793 <param name="color_select" value="automatic"/> 878 <param name="color_select" value="automatic"/>
794 </conditional> 879 </conditional>
795 </section> 880 </section>
796 <section name="jbmenu"> 881 </conditional>
797 <repeat name="track_menu"> 882 </repeat>
798 <param name="menu_action" value="iframeDialog"/>
799 <param name="menu_label" value="Some menu item"/>
800 <param name="menu_title" value="Frame title"/>
801 <param name="menu_url" value="https://example.com/#!/?id={name}&amp;q={type}&amp;z=&quot;{end}&quot;"/>
802 <param name="menu_icon" value="dijitIconNewTask"/>
803 </repeat>
804 <repeat name="track_menu">
805 <param name="menu_action" value="newWindow"/>
806 <param name="menu_label" value="Another menu item"/>
807 <param name="menu_title" value="Frame title 2"/>
808 <param name="menu_url" value="https://example.com/#!/?id={name}&amp;q={type}&amp;z=&quot;{end}&quot;"/>
809 </repeat>
810 </section>
811 </conditional>
812 </repeat>
813 <repeat name="data_tracks">
814 <conditional name="data_format">
815 <param name="data_format_select" value="gff"/>
816 <conditional name="useuri">
817 <param name="annotation" value="gff3/1.gff"/>
818 <param name="insource" value= "history"/>
819 </conditional>
820 <param name="insource" value= "history"/>
821 <conditional name="match_part">
822 <param name="match_part_select" value="false"/>
823 </conditional>
824 <section name="jbcolor_scale">
825 <conditional name="color_score">
826 <param name="color_score_select" value="none"/>
827 </conditional>
828 <conditional name="color">
829 <param name="color_select" value="automatic"/>
830 </conditional>
831 </section>
832 </conditional>
833 </repeat>
834 </repeat> 883 </repeat>
835 884 </repeat>
836 <param name="uglyTestingHack" value="enabled" /> 885 <param name="uglyTestingHack" value="enabled" />
837 <output name="output"> 886 <output name="output">
838 <assert_contents> 887 <assert_contents>
839 <has_text text="With menu or index"/> 888 <has_text text="With menu or index"/>
840 <has_text text="gff"/> 889 <has_text text="gff"/>
841 </assert_contents> 890 </assert_contents>
842 </output> 891 </output>
843 </test> 892 </test>
893
844 <!-- TODO add a synteny test --> 894 <!-- TODO add a synteny test -->
845 <!-- TODO add a bam and a cram test --> 895 <!-- TODO add a bam and a cram test -->
846 <!-- TODO add an hic test --> 896 <!-- TODO add an hic test -->
847 <!-- TODO add a vcf_bgzip test --> 897 <!-- TODO add a vcf_bgzip test -->
848 </tests> 898 </tests>