Mercurial > repos > iuc > jbrowse
comparison jbrowse.xml @ 40:17359b808b01 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
| author | iuc |
|---|---|
| date | Fri, 21 Aug 2020 04:42:41 -0400 |
| parents | fd5dbf0f732e |
| children | 8774b28235bb |
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| 39:fd5dbf0f732e | 40:17359b808b01 |
|---|---|
| 20 | 20 |
| 21 ## Once that's done, we run the python script to handle the real work | 21 ## Once that's done, we run the python script to handle the real work |
| 22 python '$__tool_directory__/jbrowse.py' | 22 python '$__tool_directory__/jbrowse.py' |
| 23 | 23 |
| 24 --jbrowse \${JBROWSE_SOURCE_DIR} | 24 --jbrowse \${JBROWSE_SOURCE_DIR} |
| 25 #if str($standalone) == "Complete": | 25 --standalone '$standalone' |
| 26 --standalone | |
| 27 #end if | |
| 28 | 26 |
| 29 --outdir $output.files_path | 27 --outdir $output.files_path |
| 30 $trackxml && | 28 $trackxml && |
| 31 | 29 |
| 32 #if str($standalone) == "Complete": | 30 #if str($standalone) != "data": |
| 33 cp $output.files_path/index.html $output; | 31 cp $output.files_path/index.html $output; |
| 34 #else: | 32 #else: |
| 35 cp $dummyIndex $output; | 33 cp $dummyIndex $output; |
| 36 #end if | 34 #end if |
| 37 | 35 |
| 370 name="genome" | 368 name="genome" |
| 371 type="data" /> | 369 type="data" /> |
| 372 </when> | 370 </when> |
| 373 </conditional> | 371 </conditional> |
| 374 | 372 |
| 375 <param name="standalone" type="boolean" truevalue="Complete" falsevalue="Data Directory" checked="true" label="Produce Standalone Instance" help="Produce a full, working JBrowse instance or just the data directory. Data dir mode is experimental and intended to be used with Apollo"/> | 373 <param name="standalone" label="Output JBrowse" type="select"> |
| 374 <option value="complete">Complete, for viewing and further local development (JBrowse, tools, documentation, etc.)</option> | |
| 375 <option value="minimal" selected="true">Minimal for viewing (Documentation removed)</option> | |
| 376 <option value="data">Data directory only (primarily for use with Apollo, requires extra steps to serve as website)</option> | |
| 377 </param> | |
| 376 | 378 |
| 377 <param name="gencode" type="select" label="Genetic Code"> | 379 <param name="gencode" type="select" label="Genetic Code"> |
| 378 <option value="1">1. The Standard Code</option> | 380 <option value="1">1. The Standard Code</option> |
| 379 <option value="2">2. The Vertebrate Mitochondrial Code</option> | 381 <option value="2">2. The Vertebrate Mitochondrial Code</option> |
| 380 <option value="3">3. The Yeast Mitochondrial Code</option> | 382 <option value="3">3. The Yeast Mitochondrial Code</option> |
| 667 <test> | 669 <test> |
| 668 <!-- gencode --> | 670 <!-- gencode --> |
| 669 <param name="reference_genome|genome_type_select" value="history"/> | 671 <param name="reference_genome|genome_type_select" value="history"/> |
| 670 <param name="reference_genome|genome" value="merlin.fa"/> | 672 <param name="reference_genome|genome" value="merlin.fa"/> |
| 671 <param name="gencode" value="1" /> | 673 <param name="gencode" value="1" /> |
| 672 <param name="standalone" value="Data Directory" /> | 674 <param name="standalone" value="data" /> |
| 673 <param name="uglyTestingHack" value="enabled" /> | 675 <param name="uglyTestingHack" value="enabled" /> |
| 674 <output name="output" file="gencode/test-1.xml" lines_diff="16"/> | 676 <output name="output" file="gencode/test-1.xml" lines_diff="16"/> |
| 675 </test> | 677 </test> |
| 676 <test> | 678 <test> |
| 677 <param name="reference_genome|genome_type_select" value="history"/> | 679 <param name="reference_genome|genome_type_select" value="history"/> |
| 678 <param name="reference_genome|genome" value="merlin.fa"/> | 680 <param name="reference_genome|genome" value="merlin.fa"/> |
| 679 <param name="gencode" value="11" /> | 681 <param name="gencode" value="11" /> |
| 680 <param name="standalone" value="Data Directory" /> | 682 <param name="standalone" value="data" /> |
| 681 <param name="uglyTestingHack" value="enabled" /> | 683 <param name="uglyTestingHack" value="enabled" /> |
| 682 <output name="output" file="gencode/test.xml" lines_diff="16"/> | 684 <output name="output" file="gencode/test.xml" lines_diff="16"/> |
| 683 </test> | 685 </test> |
| 684 <test> | 686 <test> |
| 685 <param name="reference_genome|genome_type_select" value="history"/> | 687 <param name="reference_genome|genome_type_select" value="history"/> |
| 686 <param name="reference_genome|genome" value="merlin.fa"/> | 688 <param name="reference_genome|genome" value="merlin.fa"/> |
| 687 <param name="gencode" value="11" /> | 689 <param name="gencode" value="11" /> |
| 688 <param name="standalone" value="Data Directory" /> | 690 <param name="standalone" value="data" /> |
| 689 <repeat name="track_groups"> | 691 <repeat name="track_groups"> |
| 690 <param name="category" value="Default" /> | 692 <param name="category" value="Default" /> |
| 691 <repeat name="data_tracks"> | 693 <repeat name="data_tracks"> |
| 692 <conditional name="data_format"> | 694 <conditional name="data_format"> |
| 693 <param name="data_format_select" value="gene_calls"/> | 695 <param name="data_format_select" value="gene_calls"/> |
| 700 </test> | 702 </test> |
| 701 <test> | 703 <test> |
| 702 <param name="reference_genome|genome_type_select" value="history"/> | 704 <param name="reference_genome|genome_type_select" value="history"/> |
| 703 <param name="reference_genome|genome" value="merlin.fa"/> | 705 <param name="reference_genome|genome" value="merlin.fa"/> |
| 704 <param name="gencode" value="11" /> | 706 <param name="gencode" value="11" /> |
| 705 <param name="standalone" value="Data Directory" /> | 707 <param name="standalone" value="data" /> |
| 706 <repeat name="track_groups"> | 708 <repeat name="track_groups"> |
| 707 <param name="category" value="Auto Coloured" /> | 709 <param name="category" value="Auto Coloured" /> |
| 708 <repeat name="data_tracks"> | 710 <repeat name="data_tracks"> |
| 709 <conditional name="data_format"> | 711 <conditional name="data_format"> |
| 710 <param name="data_format_select" value="gene_calls"/> | 712 <param name="data_format_select" value="gene_calls"/> |
| 896 </test> | 898 </test> |
| 897 <test> | 899 <test> |
| 898 <param name="reference_genome|genome_type_select" value="history"/> | 900 <param name="reference_genome|genome_type_select" value="history"/> |
| 899 <param name="reference_genome|genome" value="merlin.fa"/> | 901 <param name="reference_genome|genome" value="merlin.fa"/> |
| 900 <param name="gencode" value="11" /> | 902 <param name="gencode" value="11" /> |
| 901 <param name="standalone" value="Data Directory" /> | 903 <param name="standalone" value="data" /> |
| 902 | 904 |
| 903 <repeat name="track_groups"> | 905 <repeat name="track_groups"> |
| 904 <param name="category" value="With menu or index" /> | 906 <param name="category" value="With menu or index" /> |
| 905 <repeat name="data_tracks"> | 907 <repeat name="data_tracks"> |
| 906 <conditional name="data_format"> | 908 <conditional name="data_format"> |
| 959 </test> | 961 </test> |
| 960 <test> | 962 <test> |
| 961 <param name="reference_genome|genome_type_select" value="history"/> | 963 <param name="reference_genome|genome_type_select" value="history"/> |
| 962 <param name="reference_genome|genome" value="merlin.fa"/> | 964 <param name="reference_genome|genome" value="merlin.fa"/> |
| 963 <param name="gencode" value="11" /> | 965 <param name="gencode" value="11" /> |
| 964 <param name="standalone" value="Data Directory" /> | 966 <param name="standalone" value="data" /> |
| 965 | 967 |
| 966 <repeat name="track_groups"> | 968 <repeat name="track_groups"> |
| 967 <param name="category" value="With canvas config" /> | 969 <param name="category" value="With canvas config" /> |
| 968 <repeat name="data_tracks"> | 970 <repeat name="data_tracks"> |
| 969 <conditional name="data_format"> | 971 <conditional name="data_format"> |
| 997 </test> | 999 </test> |
| 998 <test> | 1000 <test> |
| 999 <param name="reference_genome|genome_type_select" value="history"/> | 1001 <param name="reference_genome|genome_type_select" value="history"/> |
| 1000 <param name="reference_genome|genome" value="merlin.fa"/> | 1002 <param name="reference_genome|genome" value="merlin.fa"/> |
| 1001 <param name="gencode" value="11" /> | 1003 <param name="gencode" value="11" /> |
| 1002 <param name="standalone" value="Data Directory" /> | 1004 <param name="standalone" value="data" /> |
| 1003 | 1005 |
| 1004 <repeat name="track_groups"> | 1006 <repeat name="track_groups"> |
| 1005 <param name="category" value="With custom track config" /> | 1007 <param name="category" value="With custom track config" /> |
| 1006 <repeat name="data_tracks"> | 1008 <repeat name="data_tracks"> |
| 1007 <conditional name="data_format"> | 1009 <conditional name="data_format"> |
| 1049 </test> | 1051 </test> |
| 1050 <test> | 1052 <test> |
| 1051 <param name="reference_genome|genome_type_select" value="history"/> | 1053 <param name="reference_genome|genome_type_select" value="history"/> |
| 1052 <param name="reference_genome|genome" value="merlin.fa"/> | 1054 <param name="reference_genome|genome" value="merlin.fa"/> |
| 1053 <param name="gencode" value="11" /> | 1055 <param name="gencode" value="11" /> |
| 1054 <param name="standalone" value="Data Directory" /> | 1056 <param name="standalone" value="data" /> |
| 1055 | 1057 |
| 1056 <repeat name="track_groups"> | 1058 <repeat name="track_groups"> |
| 1057 <param name="category" value="Auto Coloured" /> | 1059 <param name="category" value="Auto Coloured" /> |
| 1058 <repeat name="data_tracks"> | 1060 <repeat name="data_tracks"> |
| 1059 <conditional name="data_format"> | 1061 <conditional name="data_format"> |
| 1070 <test> | 1072 <test> |
| 1071 <!-- data_table --> | 1073 <!-- data_table --> |
| 1072 <param name="reference_genome|genome_type_select" value="indexed"/> | 1074 <param name="reference_genome|genome_type_select" value="indexed"/> |
| 1073 <param name="reference_genome|genome" value="merlin"/> | 1075 <param name="reference_genome|genome" value="merlin"/> |
| 1074 <param name="gencode" value="1" /> | 1076 <param name="gencode" value="1" /> |
| 1075 <param name="standalone" value="Data Directory" /> | 1077 <param name="standalone" value="data" /> |
| 1076 <param name="uglyTestingHack" value="enabled" /> | 1078 <param name="uglyTestingHack" value="enabled" /> |
| 1077 <output name="output" file="gencode/test-data_table.xml" lines_diff="4" /> | 1079 <output name="output" file="gencode/test-data_table.xml" lines_diff="4" /> |
| 1078 </test> | 1080 </test> |
| 1079 | 1081 |
| 1080 <test> | 1082 <test> |
| 1081 <param name="reference_genome|genome_type_select" value="history"/> | 1083 <param name="reference_genome|genome_type_select" value="history"/> |
| 1082 <param name="reference_genome|genome" value="merlin.fa"/> | 1084 <param name="reference_genome|genome" value="merlin.fa"/> |
| 1083 <param name="gencode" value="11" /> | 1085 <param name="gencode" value="11" /> |
| 1084 <param name="standalone" value="Data Directory" /> | 1086 <param name="standalone" value="data" /> |
| 1085 | 1087 |
| 1086 <repeat name="track_groups"> | 1088 <repeat name="track_groups"> |
| 1087 <param name="category" value="External endpoints" /> | 1089 <param name="category" value="External endpoints" /> |
| 1088 <repeat name="data_tracks"> | 1090 <repeat name="data_tracks"> |
| 1089 <conditional name="data_format"> | 1091 <conditional name="data_format"> |