Mercurial > repos > fubar > jbrowse2
comparison jbrowse2.xml @ 34:2893ef33fba9 draft
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 |
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| 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> |