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comparison jbrowse2.xml @ 34:2893ef33fba9 draft

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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd
author fubar
date Sun, 25 Feb 2024 04:18:53 +0000
parents 9aedb7f1cc77
children 15da358c3108
comparison
equal deleted inserted replaced
33:9aedb7f1cc77 34:2893ef33fba9
1 <tool id="jbrowse2" name="jbrowse2" version="@TOOL_VERSION@+@WRAPPER_VERSION@_4" profile="22.05"> 1 <tool id="jbrowse2" name="jbrowse2" version="@TOOL_VERSION@+@WRAPPER_VERSION@_5" 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"/>
16 cp '$trackxml' '$output.files_path/galaxy.xml' && 16 cp '$trackxml' '$output.files_path/galaxy.xml' &&
17 python '$__tool_directory__/jbrowse2.py' 17 python '$__tool_directory__/jbrowse2.py'
18 --outdir '$output.files_path' 18 --outdir '$output.files_path'
19 --xml '$trackxml' && 19 --xml '$trackxml' &&
20 #if $jbgen.zipOut == "true": 20 #if $jbgen.zipOut == "true":
21 (cd '$output.files_path' && zip -r - . ) > JBrowse2.zip && 21 (cd '$output.files_path' && zip -r - . ) > '$output'
22 mv JBrowse2.zip '$output'
23 #else 22 #else
24 cp '$output.files_path/index.html' '$output' 23 cp '$output.files_path/index.html' '$output'
25 #end if 24 #end if
26 ## Ugly testing hack since I cannot get <extra_files> to test the files I want to test. Hmph. 25 ## Ugly testing hack since I cannot get <extra_files> to test the files I want to test. Hmph.
27 #if str($uglyTestingHack) == "enabled": 26 #if str($uglyTestingHack) == "enabled":
469 <repeat name="track_groups"> 468 <repeat name="track_groups">
470 <param name="category" value="Default" /> 469 <param name="category" value="Default" />
471 <repeat name="data_tracks"> 470 <repeat name="data_tracks">
472 <conditional name="data_format"> 471 <conditional name="data_format">
473 <param name="data_format_select" value="gene_calls"/> 472 <param name="data_format_select" value="gene_calls"/>
474 <param name="annotation" value="bed/test-3.bed,bed/test-6.bed"/> 473 <param name="annotation" value="bed/test-3.bed"/>
475 </conditional> 474 </conditional>
476 </repeat> 475 </repeat>
477 </repeat> 476 </repeat>
478 <param name="uglyTestingHack" value="enabled" /> 477 <param name="uglyTestingHack" value="enabled" />
479 <output name="output"> 478 <output name="output">
494 <repeat name="track_groups"> 493 <repeat name="track_groups">
495 <param name="category" value="Auto Coloured" /> 494 <param name="category" value="Auto Coloured" />
496 <repeat name="data_tracks"> 495 <repeat name="data_tracks">
497 <conditional name="data_format"> 496 <conditional name="data_format">
498 <param name="data_format_select" value="gene_calls"/> 497 <param name="data_format_select" value="gene_calls"/>
499 <param name="annotation" value="gff3/A.gff,gff3/B.gff,gff3/C.gff,gff3/D.gff"/> 498 <param name="annotation" value="gff3/A.gff"/>
500 <conditional name="match_part"> 499 <conditional name="match_part">
501 <param name="match_part_select" value="false"/> 500 <param name="match_part_select" value="false"/>
502 </conditional> 501 </conditional>
503 <section name="jbcolor_scale"> 502 <section name="jbcolor_scale">
504 <conditional name="color_score"> 503 <conditional name="color_score">
537 <repeat name="track_groups"> 536 <repeat name="track_groups">
538 <param name="category" value="Scaled Colour" /> 537 <param name="category" value="Scaled Colour" />
539 <repeat name="data_tracks"> 538 <repeat name="data_tracks">
540 <conditional name="data_format"> 539 <conditional name="data_format">
541 <param name="data_format_select" value="gene_calls"/> 540 <param name="data_format_select" value="gene_calls"/>
542 <param name="annotation" value="gff3/1.gff"/> 541 <param name="annotation" value="gff3/C.gff"/>
543 <conditional name="match_part"> 542 <conditional name="match_part">
544 <param name="match_part_select" value="false"/> 543 <param name="match_part_select" value="false"/>
545 </conditional> 544 </conditional>
546 <section name="jbcolor_scale"> 545 <section name="jbcolor_scale">
547 <conditional name="color_score"> 546 <conditional name="color_score">
561 </conditional> 560 </conditional>
562 </repeat> 561 </repeat>
563 <repeat name="data_tracks"> 562 <repeat name="data_tracks">
564 <conditional name="data_format"> 563 <conditional name="data_format">
565 <param name="data_format_select" value="gene_calls"/> 564 <param name="data_format_select" value="gene_calls"/>
566 <param name="annotation" value="gff3/1.gff"/> 565 <param name="annotation" value="gff3/B.gff"/>
567 <conditional name="match_part"> 566 <conditional name="match_part">
568 <param name="match_part_select" value="false"/> 567 <param name="match_part_select" value="false"/>
569 </conditional> 568 </conditional>
570 <section name="jbcolor_scale"> 569 <section name="jbcolor_scale">
571 <conditional name="color_score"> 570 <conditional name="color_score">
586 </conditional> 585 </conditional>
587 </repeat> 586 </repeat>
588 <repeat name="data_tracks"> 587 <repeat name="data_tracks">
589 <conditional name="data_format"> 588 <conditional name="data_format">
590 <param name="data_format_select" value="gene_calls"/> 589 <param name="data_format_select" value="gene_calls"/>
591 <param name="annotation" value="gff3/1.gff"/> 590 <param name="annotation" value="gff3/A.gff"/>
592 <conditional name="match_part"> 591 <conditional name="match_part">
593 <param name="match_part_select" value="false"/> 592 <param name="match_part_select" value="false"/>
594 </conditional> 593 </conditional>
595 <section name="jbcolor_scale"> 594 <section name="jbcolor_scale">
596 <conditional name="color_score"> 595 <conditional name="color_score">
684 <assert_contents> 683 <assert_contents>
685 <has_text text="Auto Coloured"/> 684 <has_text text="Auto Coloured"/>
686 <has_text text="A.gff"/> 685 <has_text text="A.gff"/>
687 <has_text text="B.gff"/> 686 <has_text text="B.gff"/>
688 <has_text text="C.gff"/> 687 <has_text text="C.gff"/>
689 <has_text text="D.gff"/> 688 <has_text text="interpro.gff"/>
690 <has_text text="Scaled Colour"/> 689 <has_text text="Scaled Colour"/>
691 <has_text text="1.gff"/> 690 <has_text text="1.gff"/>
692 <has_text text="2.gff"/> 691 <has_text text="2.gff"/>
693 </assert_contents> 692 </assert_contents>
694 </output> 693 </output>