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comparison jbrowse.xml @ 40:17359b808b01 draft

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"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
comparison
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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">