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comparison jbrowse2.xml @ 46:4181e97c70a7 draft

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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
author fubar
date Mon, 04 Mar 2024 09:47:19 +0000
parents 0ec526d2d8c1
children 460d5b6c5d98
comparison
equal deleted inserted replaced
45:0ec526d2d8c1 46:4181e97c70a7
1 <tool id="jbrowse2" name="jbrowse2" version="@TOOL_VERSION@+@WRAPPER_VERSION@_5" profile="22.05"> 1 <tool id="jbrowse2" name="jbrowse2" version="@TOOL_VERSION@+@WRAPPER_VERSION@_6" 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"/>
15 ## but nice if users want to reproduce locally 15 ## but nice if users want to reproduce locally
16 cp '$trackxml' '$output.files_path/galaxy.xml' && 16 cp '$trackxml' '$output.files_path/galaxy.xml' &&
17 17
18 export JBROWSE2_PATH=\$(dirname \$(which jbrowse))/../opt/jbrowse2 && 18 export JBROWSE2_PATH=\$(dirname \$(which jbrowse))/../opt/jbrowse2 &&
19 19
20 ## Once that's done, we run the python script to handle the real work 20 #if $jbgen.ucol.formcoll=="collect":
21 python '$__tool_directory__/jbrowse2.py' 21 python '$__tool_directory__/autogenJB2.py'
22 --jbrowse2path \${JBROWSE2_PATH} 22 #for $key in $autoCollection.keys():
23 --outdir '$output.files_path' 23 #if $autoCollection[$key].is_collection:
24 --xml '$trackxml' && 24 #set subCol=$autoCollection[$key]
25 #if $jbgen.zipOut == "true": 25 #set pafs=[($subCol[x],$subcol[x].ext,x) for x in $subCol.keys() if $subCol[x].ext == 'paf']
26 (cd '$output.files_path' && zip -r - . ) > '$output' 26 #if len($pafs) > 0:
27 #else 27 --pafmeta '$pafs[0]'
28 cp '$output.files_path/index.html' '$output' 28 #set refs = [($pafs[0][2],$subCol[x],x) for x in $subCol.keys() if $subCol[x].ext == 'fasta']
29 #end if 29 #for $ref in $refs:
30 ## Ugly testing hack since I cannot get <extra_files> to test the files I want to test. Hmph. 30 --pafreferencemeta '$ref'
31 #if str($uglyTestingHack) == "enabled": 31 #end for
32 && cp '$trackxml' '$output' 32 #end if
33 #else if $autoCollection[$key].ext == 'fasta':
34 --referencemeta '$autoCollection[$key],$autoCollection[$key].ext,$key'
35 #else if $autoCollection[$key].ext in ['bed', 'bigwig', 'cool', 'gff', 'gff3', 'hic', 'maf', 'mcool', 'scool', 'vcf']
36 --trackmeta '$autoCollection[$key],$autoCollection[$key].ext,$key'
37 #else if $autoCollection[$key].ext in ['bam',]
38 --trackmeta '$autoCollection[$key],$autoCollection[$key].ext,$key,$autoCollection[$key].metadata.bam_index'
39 #else if $autoCollection[$key].ext in ['cram',]
40 --trackmeta '$autoCollection[$key],$autoCollection[$key].ext,$key,$autoCollection[$key].metadata.cram_index'
41 #end if
42 #end for
43 --outdir '$output.files_path'
44 --jbrowse2path \${JBROWSE2_PATH}
45 --sessName "Autogen JBrowse" &&
46 #if $jbgen.zipOut == "true":
47 (cd '$output.files_path' && zip -r - . ) > '$output'
48 #else
49 cp '$output.files_path/index.html' '$output'
50 #end if
51 #else:
52 python '$__tool_directory__/jbrowse2.py'
53 --jbrowse2path \${JBROWSE2_PATH}
54 --outdir '$output.files_path'
55 --xml '$trackxml' &&
56 #if $jbgen.zipOut == "true":
57 (cd '$output.files_path' && zip -r - . ) > '$output'
58 #else
59 cp '$output.files_path/index.html' '$output'
60 #end if
61 ## Ugly testing hack since I cannot get <extra_files> to test the files I want to test. Hmph.
62 #if str($uglyTestingHack) == "enabled":
63 && cp '$trackxml' '$output'
64 #end if
33 #end if 65 #end if
34 ]]></command> 66 ]]></command>
35 <configfiles> 67 <configfiles>
36 <configfile name="trackxml"><![CDATA[<?xml version="1.0"?> 68 <configfile name="trackxml"><![CDATA[<?xml version="1.0"?>
69 #if $jbgen.ucol.formcoll=="form":
37 <root> 70 <root>
38 <metadata> 71 <metadata>
39 <genomes> 72 <genomes>
40 #if str($reference_genome.genome_type_select) == "indexed": 73 #if str($reference_genome.genome_type_select) == "uri":
41 <genome path="${reference_genome.genome.fields.path}" label="${reference_genome.genome.fields.name}"> 74 <genome path="${reference_genome.uri}" label="${reference_genome.refname}" useuri="yes">
42 <metadata> 75 <metadata>
43 <dataset 76 <dataset
44 dname = "${reference_genome.genome.name}" /> 77 dname = "${reference_genome.refname}" />
78 </metadata>
79 </genome>
80 #else if str($reference_genome.genome_type_select) == "indexed":
81 <genome path="${reference_genome.genome.fields.path}" label="${reference_genome.genome.fields.name}" useuri="no">
82 <metadata>
83 <dataset
84 dname = "${reference_genome.genome.refname}" />
45 </metadata> 85 </metadata>
46 </genome> 86 </genome>
47 #else 87 #else
48 <genome path="$reference_genome.genome" label="${reference_genome.genome.name}"> 88 <genome path="$reference_genome.genome" label="${reference_genome.genome.name}" useuri="no">
49 <metadata> 89 <metadata>
50 <dataset id="${__app__.security.encode_id($reference_genome.genome.id)}" hid="${reference_genome.genome.hid}" 90 <dataset id="${__app__.security.encode_id($reference_genome.genome.id)}" hid="${reference_genome.genome.hid}"
51 size="${reference_genome.genome.get_size(nice_size=True)}" 91 size="${reference_genome.genome.get_size(nice_size=True)}"
52 edam_format="${reference_genome.genome.datatype.edam_format}" 92 edam_format="${reference_genome.genome.datatype.edam_format}"
53 file_ext="${reference_genome.genome.ext}" 93 file_ext="${reference_genome.genome.ext}"
96 <galaxyUrl>${__app__.config.galaxy_infrastructure_url}</galaxyUrl> 136 <galaxyUrl>${__app__.config.galaxy_infrastructure_url}</galaxyUrl>
97 </metadata> 137 </metadata>
98 <tracks> 138 <tracks>
99 #for $tg in $track_groups: 139 #for $tg in $track_groups:
100 #for $track in $tg.data_tracks: 140 #for $track in $tg.data_tracks:
101 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}"> 141 #if $track.data_format.useuri.insource == "history":
102 #if $track.data_format.data_format_select != "sparql": 142 #if $track.data_format.useuri.annotation:
143 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
103 <files> 144 <files>
104 #for $dataset in $track.data_format.annotation: 145 #for $dataset in $track.data_format.useuri.annotation:
105 #if $dataset: 146 <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.name}" useuri="no">
106 <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.name}">
107 <metadata> 147 <metadata>
148
108 <dataset id="${__app__.security.encode_id($dataset.id)}" hid="${dataset.hid}" 149 <dataset id="${__app__.security.encode_id($dataset.id)}" hid="${dataset.hid}"
109 size="${dataset.get_size(nice_size=True)}" 150 size="${dataset.get_size(nice_size=True)}"
110 edam_format="${dataset.datatype.edam_format}" 151 edam_format="${dataset.datatype.edam_format}"
111 file_ext="${dataset.ext}" /> 152 file_ext="${dataset.ext}" />
112 <history id="${__app__.security.encode_id($dataset.history_id)}" 153 <history id="${__app__.security.encode_id($dataset.history_id)}"
117 #else 158 #else
118 user_email="anonymous" 159 user_email="anonymous"
119 user_id="-1" 160 user_id="-1"
120 display_name="Unnamed History"/> 161 display_name="Unnamed History"/>
121 #end if 162 #end if
163
122 <metadata 164 <metadata
123 #for (key, value) in $dataset.get_metadata().items(): 165 #for (key, value) in $dataset.get_metadata().items():
124 #if "_types" not in $key and $value is not None and len(str($value)) < 5000: 166 #if "_types" not in $key and $value is not None and len(str($value)) < 5000:
125 #if isinstance($value, list): 167 #if isinstance($value, list):
126 #set value_str = "[%s]" % ','.join([str(val) for val in value]) 168 #set value_str = "[%s]" % ','.join([str(val) for val in value])
135 tool_id="${dataset.creating_job.tool_id}" 177 tool_id="${dataset.creating_job.tool_id}"
136 tool_version="${dataset.creating_job.tool_version}" 178 tool_version="${dataset.creating_job.tool_version}"
137 /> 179 />
138 </metadata> 180 </metadata>
139 </trackFile> 181 </trackFile>
140 #end if 182 #end for
141
142 #end for
143 </files> 183 </files>
144 #else
145 <track cat="${tg.category}" format="sparql" visibility="off">
146 #end if
147 184
148 <options> 185 <options>
149 186
150 #if str($track.data_format.data_format_select) == "bam": 187 #if str($track.data_format.data_format_select) == "bam":
151 <bam> 188 <bam>
152 #for $dataset in $track.data_format.annotation: 189 #for $dataset in $track.data_format.useuri.annotation:
153 <bam_index>${dataset.metadata.bam_index}</bam_index> 190 <bam_index>${dataset.metadata.bam_index}</bam_index>
154 #end for 191 #end for
155 </bam> 192 </bam>
156 #else if str($track.data_format.data_format_select) == "cram": 193 #else if str($track.data_format.data_format_select) == "cram":
157 <cram> 194 <cram>
158 #for $dataset in $track.data_format.annotation: 195 #for $dataset in $track.data_format.useuri.annotation:
159 <cram_index>${dataset.metadata.cram_index}</cram_index> 196 <cram_index>${dataset.metadata.cram_index}</cram_index>
160 #end for 197 #end for
161 </cram> 198 </cram>
162 #else if str($track.data_format.data_format_select) == "blastxml": 199 #else if str($track.data_format.data_format_select) == "blastxml":
163 <blast> 200 <blast>
199 <query>${track.data_format.query}</query> 236 <query>${track.data_format.query}</query>
200 <query_refnames>${track.data_format.query_refnames}</query_refnames> 237 <query_refnames>${track.data_format.query_refnames}</query_refnames>
201 </sparql> 238 </sparql>
202 #end if 239 #end if
203 </options> 240 </options>
241 </track>
242 #end if
243 #else if track.data_format.useuri.annouri:
244 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
245 <files>
246 <trackFile path="${track.data_format.useuri.annouri}" ext="${track.data_format.data_format_select}" label="${track.data_format.useuri.annoname}" useuri="yes">
247 <metadata>
248 <dataset id = "${track.data_format.useuri.annouri}" />
249 </metadata>
250 </trackFile>
251 </files>
252 <options/>
204 </track> 253 </track>
205 #end for 254 #end if
206 #end for 255 #end for
256 #end for
207 </tracks> 257 </tracks>
208 </root> 258 </root>
259 #end if
209 ]]></configfile> 260 ]]></configfile>
210 </configfiles> 261 </configfiles>
211 262
212 <inputs> 263 <inputs>
213 <conditional name="reference_genome"> 264 <conditional name="reference_genome">
214 <param help="Built-in references" label="Reference genome to display" name="genome_type_select" type="select"> 265 <param help="Built-in references" label="Reference genome to display" name="genome_type_select" type="select">
215 <option selected="True" value="indexed">Use a built-in genome</option> 266 <option selected="True" value="indexed">Use a built-in genome</option>
216 <option value="history">Use a genome from history</option> 267 <option value="history">Use a genome from history</option>
268 <option value="uri">URI for a reference in tabix .gz format </option>
217 </param> 269 </param>
218 <when value="indexed"> 270 <when value="indexed">
219 <param 271 <param
220 help="If your genome of interest is not listed, contact the Galaxy team" 272 help="If your genome of interest is not listed, contact the Galaxy team"
221 label="Select a reference genome" 273 label="Select a reference genome"
232 <param 284 <param
233 format="fasta" 285 format="fasta"
234 label="Select the reference genome" 286 label="Select the reference genome"
235 name="genome" 287 name="genome"
236 type="data"> 288 type="data">
289 </param>
290 </when>
291 <when value="uri">
292 <param
293 label="URI pointing to tabix compressed fasta"
294 name="uri"
295 type="text">
296 </param>
297 <param
298 label="Reference key - dbkey equivalent"
299 name="refname"
300 type="text">
237 </param> 301 </param>
238 </when> 302 </when>
239 </conditional> 303 </conditional>
240 304
241 <repeat name="track_groups" title="Track Group"> 305 <repeat name="track_groups" title="Track Group">
346 <expand macro="general_options" /> 410 <expand macro="general_options" />
347 411
348 <param type="hidden" name="uglyTestingHack" value="" /> 412 <param type="hidden" name="uglyTestingHack" value="" />
349 </inputs> 413 </inputs>
350 <outputs> 414 <outputs>
351 <data format="html" name="output" label="JBrowse2 on $reference_genome.genome.name"> 415 <data format="html" name="output" label="JBrowse2">
352 <change_format> 416 <change_format>
353 <when input="zipOut" value="true" format="zip" /> 417 <when input="zipOut" value="true" format="zip" />
354 </change_format> 418 </change_format>
355 </data> 419 </data>
356 </outputs> 420 </outputs>
361 <repeat name="track_groups"> 425 <repeat name="track_groups">
362 <param name="category" value="Default" /> 426 <param name="category" value="Default" />
363 <repeat name="data_tracks"> 427 <repeat name="data_tracks">
364 <conditional name="data_format"> 428 <conditional name="data_format">
365 <param name="data_format_select" value="bigwig"/> 429 <param name="data_format_select" value="bigwig"/>
366 <param name="annotation" value="bw/merlin.bw"/> 430 <conditional name="useuri">
431 <param name="annotation" value="bw/merlin.bw"/>
432 <param name="insource" value="history"/>
433 </conditional>
367 </conditional> 434 </conditional>
368 </repeat> 435 </repeat>
369 </repeat> 436 </repeat>
370 <param name="uglyTestingHack" value="enabled" /> 437 <param name="uglyTestingHack" value="enabled" />
371 <output name="output"> 438 <output name="output">
387 <repeat name="track_groups"> 454 <repeat name="track_groups">
388 <param name="category" value="Default" /> 455 <param name="category" value="Default" />
389 <repeat name="data_tracks"> 456 <repeat name="data_tracks">
390 <conditional name="data_format"> 457 <conditional name="data_format">
391 <param name="data_format_select" value="vcf"/> 458 <param name="data_format_select" value="vcf"/>
392 <param name="annotation" value="vcf/merlin.vcf"/> 459 <conditional name="useuri">
460 <param name="insource" value="history"/>
461 <param name="annotation" value="vcf/merlin.vcf"/>
462 </conditional>
393 </conditional> 463 </conditional>
394 </repeat> 464 </repeat>
395 </repeat> 465 </repeat>
396 <param name="uglyTestingHack" value="enabled" /> 466 <param name="uglyTestingHack" value="enabled" />
397 <output name="output"> 467 <output name="output">
426 <repeat name="track_groups"> 496 <repeat name="track_groups">
427 <param name="category" value="Default" /> 497 <param name="category" value="Default" />
428 <repeat name="data_tracks"> 498 <repeat name="data_tracks">
429 <conditional name="data_format"> 499 <conditional name="data_format">
430 <param name="data_format_select" value="gene_calls"/> 500 <param name="data_format_select" value="gene_calls"/>
431 <param name="annotation" value="bed/test-3.bed"/> 501 <conditional name="useuri">
502 <param name="insource" value="history"/>
503 <param name="annotation" value="bed/test-3.bed"/>
504 </conditional>
432 </conditional> 505 </conditional>
433 </repeat> 506 </repeat>
434 </repeat> 507 </repeat>
435 <param name="uglyTestingHack" value="enabled" /> 508 <param name="uglyTestingHack" value="enabled" />
436 <output name="output"> 509 <output name="output">
451 <repeat name="track_groups"> 524 <repeat name="track_groups">
452 <param name="category" value="Auto Coloured" /> 525 <param name="category" value="Auto Coloured" />
453 <repeat name="data_tracks"> 526 <repeat name="data_tracks">
454 <conditional name="data_format"> 527 <conditional name="data_format">
455 <param name="data_format_select" value="gene_calls"/> 528 <param name="data_format_select" value="gene_calls"/>
456 <param name="annotation" value="gff3/A.gff"/> 529 <conditional name="useuri">
530 <param name="insource" value="history"/>
531 <param name="annotation" value="gff3/A.gff"/>
532 </conditional>
457 <conditional name="match_part"> 533 <conditional name="match_part">
458 <param name="match_part_select" value="false"/> 534 <param name="match_part_select" value="false"/>
459 </conditional> 535 </conditional>
460 <section name="jbcolor_scale"> 536 <section name="jbcolor_scale">
461 <conditional name="color_score"> 537 <conditional name="color_score">
472 <repeat name="track_groups"> 548 <repeat name="track_groups">
473 <param name="category" value="Ignore Scale" /> 549 <param name="category" value="Ignore Scale" />
474 <repeat name="data_tracks"> 550 <repeat name="data_tracks">
475 <conditional name="data_format"> 551 <conditional name="data_format">
476 <param name="data_format_select" value="gene_calls"/> 552 <param name="data_format_select" value="gene_calls"/>
553 <conditional name="useuri">
554 <param name="insource" value="history"/>
477 <param name="annotation" value="gff3/1.gff"/> 555 <param name="annotation" value="gff3/1.gff"/>
556 </conditional>
478 <conditional name="match_part"> 557 <conditional name="match_part">
479 <param name="match_part_select" value="false"/> 558 <param name="match_part_select" value="false"/>
480 </conditional> 559 </conditional>
481 <section name="jbcolor_scale"> 560 <section name="jbcolor_scale">
482 <conditional name="color_score"> 561 <conditional name="color_score">
494 <repeat name="track_groups"> 573 <repeat name="track_groups">
495 <param name="category" value="Scaled Colour" /> 574 <param name="category" value="Scaled Colour" />
496 <repeat name="data_tracks"> 575 <repeat name="data_tracks">
497 <conditional name="data_format"> 576 <conditional name="data_format">
498 <param name="data_format_select" value="gene_calls"/> 577 <param name="data_format_select" value="gene_calls"/>
499 <param name="annotation" value="gff3/C.gff"/> 578 <conditional name="useuri">
579 <param name="insource" value= "history"/>
580 <param name="annotation" value="gff3/C.gff"/>
581 </conditional>
500 <conditional name="match_part"> 582 <conditional name="match_part">
501 <param name="match_part_select" value="false"/> 583 <param name="match_part_select" value="false"/>
502 </conditional> 584 </conditional>
503 <section name="jbcolor_scale"> 585 <section name="jbcolor_scale">
504 <conditional name="color_score"> 586 <conditional name="color_score">
518 </conditional> 600 </conditional>
519 </repeat> 601 </repeat>
520 <repeat name="data_tracks"> 602 <repeat name="data_tracks">
521 <conditional name="data_format"> 603 <conditional name="data_format">
522 <param name="data_format_select" value="gene_calls"/> 604 <param name="data_format_select" value="gene_calls"/>
523 <param name="annotation" value="gff3/B.gff"/> 605 <conditional name="useuri">
524 <conditional name="match_part"> 606 <param name="annotation" value="gff3/B.gff"/>
607 <param name="insource" value= "history"/>
608 </conditional>
609 <conditional name="match_part">
525 <param name="match_part_select" value="false"/> 610 <param name="match_part_select" value="false"/>
526 </conditional> 611 </conditional>
527 <section name="jbcolor_scale"> 612 <section name="jbcolor_scale">
528 <conditional name="color_score"> 613 <conditional name="color_score">
529 <param name="color_score_select" value="score"/> 614 <param name="color_score_select" value="score"/>
543 </conditional> 628 </conditional>
544 </repeat> 629 </repeat>
545 <repeat name="data_tracks"> 630 <repeat name="data_tracks">
546 <conditional name="data_format"> 631 <conditional name="data_format">
547 <param name="data_format_select" value="gene_calls"/> 632 <param name="data_format_select" value="gene_calls"/>
548 <param name="annotation" value="gff3/A.gff"/> 633 <conditional name="useuri">
634 <param name="annotation" value="gff3/A.gff"/>
635 <param name="insource" value= "history"/>
636 </conditional>
549 <conditional name="match_part"> 637 <conditional name="match_part">
550 <param name="match_part_select" value="false"/> 638 <param name="match_part_select" value="false"/>
551 </conditional> 639 </conditional>
552 <section name="jbcolor_scale"> 640 <section name="jbcolor_scale">
553 <conditional name="color_score"> 641 <conditional name="color_score">
569 </conditional> 657 </conditional>
570 </repeat> 658 </repeat>
571 <repeat name="data_tracks"> 659 <repeat name="data_tracks">
572 <conditional name="data_format"> 660 <conditional name="data_format">
573 <param name="data_format_select" value="gene_calls"/> 661 <param name="data_format_select" value="gene_calls"/>
574 <param name="annotation" value="gff3/1.gff"/> 662 <conditional name="useuri">
663 <param name="annotation" value="gff3/1.gff"/>
664 <param name="insource" value= "history"/>
665 </conditional>
575 <conditional name="match_part"> 666 <conditional name="match_part">
576 <param name="match_part_select" value="false"/> 667 <param name="match_part_select" value="false"/>
577 </conditional> 668 </conditional>
578 <section name="jbcolor_scale"> 669 <section name="jbcolor_scale">
579 <conditional name="color_score"> 670 <conditional name="color_score">
600 <repeat name="track_groups"> 691 <repeat name="track_groups">
601 <param name="category" value="Realistic" /> 692 <param name="category" value="Realistic" />
602 <repeat name="data_tracks"> 693 <repeat name="data_tracks">
603 <conditional name="data_format"> 694 <conditional name="data_format">
604 <param name="data_format_select" value="gene_calls"/> 695 <param name="data_format_select" value="gene_calls"/>
605 <param name="annotation" value="gff3/interpro.gff"/> 696 <conditional name="useuri">
697 <param name="annotation" value="gff3/interpro.gff"/>
698 <param name="insource" value= "history"/>
699 </conditional>
606 <conditional name="match_part"> 700 <conditional name="match_part">
607 <param name="match_part_select" value="false"/> 701 <param name="match_part_select" value="false"/>
608 </conditional> 702 </conditional>
609 <section name="jbcolor_scale"> 703 <section name="jbcolor_scale">
610 <conditional name="color_score"> 704 <conditional name="color_score">
617 </conditional> 711 </conditional>
618 </repeat> 712 </repeat>
619 <repeat name="data_tracks"> 713 <repeat name="data_tracks">
620 <conditional name="data_format"> 714 <conditional name="data_format">
621 <param name="data_format_select" value="gene_calls"/> 715 <param name="data_format_select" value="gene_calls"/>
622 <param name="annotation" value="gff3/2.gff"/> 716 <conditional name="useuri">
717 <param name="annotation" value="gff3/2.gff"/>
718 <param name="insource" value= "history"/>
719 </conditional>
623 <conditional name="match_part"> 720 <conditional name="match_part">
624 <param name="match_part_select" value="true"/> 721 <param name="match_part_select" value="true"/>
625 <param name="name" value="cDNA_match"/> 722 <param name="name" value="cDNA_match"/>
626 </conditional> 723 </conditional>
627 <section name="jbcolor_scale"> 724 <section name="jbcolor_scale">
657 <repeat name="track_groups"> 754 <repeat name="track_groups">
658 <param name="category" value="With menu or index" /> 755 <param name="category" value="With menu or index" />
659 <repeat name="data_tracks"> 756 <repeat name="data_tracks">
660 <conditional name="data_format"> 757 <conditional name="data_format">
661 <param name="data_format_select" value="gene_calls"/> 758 <param name="data_format_select" value="gene_calls"/>
662 <param name="annotation" value="gff3/1.gff"/> 759 <conditional name="useuri">
760 <param name="annotation" value="gff3/1.gff"/>
761 <param name="insource" value= "history"/>
762 </conditional>
663 <conditional name="match_part"> 763 <conditional name="match_part">
664 <param name="match_part_select" value="false"/> 764 <param name="match_part_select" value="false"/>
665 </conditional> 765 </conditional>
666 <section name="jbcolor_scale"> 766 <section name="jbcolor_scale">
667 <conditional name="color_score"> 767 <conditional name="color_score">
689 </conditional> 789 </conditional>
690 </repeat> 790 </repeat>
691 <repeat name="data_tracks"> 791 <repeat name="data_tracks">
692 <conditional name="data_format"> 792 <conditional name="data_format">
693 <param name="data_format_select" value="gene_calls"/> 793 <param name="data_format_select" value="gene_calls"/>
694 <param name="annotation" value="gff3/1.gff"/> 794 <conditional name="useuri">
795 <param name="annotation" value="gff3/1.gff"/>
796 <param name="insource" value= "history"/>
797 </conditional>
798 <param name="insource" value= "history"/>
695 <conditional name="match_part"> 799 <conditional name="match_part">
696 <param name="match_part_select" value="false"/> 800 <param name="match_part_select" value="false"/>
697 </conditional> 801 </conditional>
698 <section name="jbcolor_scale"> 802 <section name="jbcolor_scale">
699 <conditional name="color_score"> 803 <conditional name="color_score">