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comparison jbrowse.xml @ 31:2bb2e07a7a21 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
author iuc
date Mon, 15 Apr 2019 10:31:26 -0400
parents ca2def38369c
children 0ae74c70b267
comparison
equal deleted inserted replaced
30:ca2def38369c 31:2bb2e07a7a21
207 <iconClass>${menu_item.menu_icon}</iconClass> 207 <iconClass>${menu_item.menu_icon}</iconClass>
208 #end if 208 #end if
209 </menu> 209 </menu>
210 #end for 210 #end for
211 </menus> 211 </menus>
212 #end if
213 #if str($track.data_format.data_format_select) in ["gene_calls", "pileup", "blast", "wiggle", "vcf"]:
214 <custom_config>
215 #for $custom_option in $track.data_format.jb_custom_config.option:
216 <${custom_option.opt_key}>
217 <${custom_option.opt_value.val_type}>${$custom_option.opt_value.val}</${custom_option.opt_value.val_type}>
218 </${custom_option.opt_key}>
219 #end for
220 </custom_config>
212 #end if 221 #end if
213 222
214 #if str($track.data_format.data_format_select) == "wiggle": 223 #if str($track.data_format.data_format_select) == "wiggle":
215 <wiggle> 224 <wiggle>
216 <type>${track.data_format.xyplot}</type> 225 <type>${track.data_format.xyplot}</type>
316 Bookmarks="" 325 Bookmarks=""
317 GCContent="${plugins.GCContent}" 326 GCContent="${plugins.GCContent}"
318 BlastView="${plugins.BlastView}" 327 BlastView="${plugins.BlastView}"
319 theme="" 328 theme=""
320 /> 329 />
321 </root>]]></configfile> 330 </root>
331 ]]></configfile>
322 </configfiles> 332 </configfiles>
323 <inputs> 333 <inputs>
324 <conditional name="reference_genome"> 334 <conditional name="reference_genome">
325 <param help="Built-in references" label="Reference genome to display" name="genome_type_select" type="select"> 335 <param help="Built-in references" label="Reference genome to display" name="genome_type_select" type="select">
326 <option selected="True" value="indexed">Use a built-in genome</option> 336 <option selected="True" value="indexed">Use a built-in genome</option>
429 description="Hit_titles" 439 description="Hit_titles"
430 height="600px"/> 440 height="600px"/>
431 <expand macro="color_selection" 441 <expand macro="color_selection"
432 token_scaling_lin_select="false" 442 token_scaling_lin_select="false"
433 token_scaling_log_select="true" /> 443 token_scaling_log_select="true" />
444 <expand macro="track_custom_config" />
434 <expand macro="track_menu" /> 445 <expand macro="track_menu" />
435 <expand macro="track_display" /> 446 <expand macro="track_display" />
436 </when> 447 </when>
437 <when value="vcf"> 448 <when value="vcf">
438 <expand macro="input_conditional" label="SNP Track Data" format="vcf" /> 449 <expand macro="input_conditional" label="SNP Track Data" format="vcf" />
450 <expand macro="track_custom_config" />
439 <expand macro="track_display" /> 451 <expand macro="track_display" />
440 </when> 452 </when>
441 <when value="gene_calls"> 453 <when value="gene_calls">
442 <expand macro="input_conditional" label="GFF/GFF3/BED Track Data" format="gff,gff3,bed" /> 454 <expand macro="input_conditional" label="GFF/GFF3/BED Track Data" format="gff,gff3,bed" />
443 <conditional name="match_part" label="match/match_part data"> 455 <conditional name="match_part" label="match/match_part data">
485 classname="feature" 497 classname="feature"
486 label="product,name,id" 498 label="product,name,id"
487 description="note,description" 499 description="note,description"
488 height="10px"/> 500 height="10px"/>
489 <expand macro="color_selection" /> 501 <expand macro="color_selection" />
502 <expand macro="track_custom_config" />
490 <expand macro="track_menu" /> 503 <expand macro="track_menu" />
491 <expand macro="track_display" /> 504 <expand macro="track_display" />
492 </when> 505 </when>
493 <when value="pileup"> 506 <when value="pileup">
494 <expand macro="input_conditional" label="BAM Track Data" format="bam" /> 507 <expand macro="input_conditional" label="BAM Track Data" format="bam" />
501 <param label="Maximum size of BAM chunks" 514 <param label="Maximum size of BAM chunks"
502 name="chunkSizeLimit" 515 name="chunkSizeLimit"
503 type="integer" 516 type="integer"
504 help="Maximum size in bytes of BAM chunks that the browser will try to deal with. When this is exceeded, most tracks will display 'Too much data' message." 517 help="Maximum size in bytes of BAM chunks that the browser will try to deal with. When this is exceeded, most tracks will display 'Too much data' message."
505 value="5000000" /> 518 value="5000000" />
519 <expand macro="track_custom_config" />
506 <expand macro="track_display" /> 520 <expand macro="track_display" />
507 </when> 521 </when>
508 <when value="wiggle"> 522 <when value="wiggle">
509 <expand macro="input_conditional" label="BigWig Track Data" format="bigwig" /> 523 <expand macro="input_conditional" label="BigWig Track Data" format="bigwig" />
510 524
543 557
544 <param label="Use MultiBigWig Plugin" name="MultiBigWig" truevalue="True" falsevalue="" type="boolean" 558 <param label="Use MultiBigWig Plugin" name="MultiBigWig" truevalue="True" falsevalue="" type="boolean"
545 help="MultiBigWig is a plugin to group multiple big-wig tracks in a more aesthetically pleasing format and to show data in a higher density display." /> 559 help="MultiBigWig is a plugin to group multiple big-wig tracks in a more aesthetically pleasing format and to show data in a higher density display." />
546 560
547 <expand macro="color_selection_minmax" /> 561 <expand macro="color_selection_minmax" />
562 <expand macro="track_custom_config" />
548 <expand macro="track_display" /> 563 <expand macro="track_display" />
549 </when> 564 </when>
550 <when value="rest"> 565 <when value="rest">
551 <param type="text" label="REST Endpoint" name="url" /> 566 <param type="text" label="REST Endpoint" name="url" />
552 <param type="text" label="Track Label" name="label" value="REST Genes" /> 567 <param type="text" label="Track Label" name="label" value="REST Genes" />
640 <param name="reference_genome|genome_type_select" value="history"/> 655 <param name="reference_genome|genome_type_select" value="history"/>
641 <param name="reference_genome|genome" value="merlin.fa"/> 656 <param name="reference_genome|genome" value="merlin.fa"/>
642 <param name="gencode" value="1" /> 657 <param name="gencode" value="1" />
643 <param name="standalone" value="Data Directory" /> 658 <param name="standalone" value="Data Directory" />
644 <param name="uglyTestingHack" value="enabled" /> 659 <param name="uglyTestingHack" value="enabled" />
645 <output name="output" file="gencode/test-1.xml" lines_diff="14"/> 660 <output name="output" file="gencode/test-1.xml" lines_diff="16"/>
646 </test> 661 </test>
647 <test> 662 <test>
648 <param name="reference_genome|genome_type_select" value="history"/> 663 <param name="reference_genome|genome_type_select" value="history"/>
649 <param name="reference_genome|genome" value="merlin.fa"/> 664 <param name="reference_genome|genome" value="merlin.fa"/>
650 <param name="gencode" value="11" /> 665 <param name="gencode" value="11" />
651 <param name="standalone" value="Data Directory" /> 666 <param name="standalone" value="Data Directory" />
652 <param name="uglyTestingHack" value="enabled" /> 667 <param name="uglyTestingHack" value="enabled" />
653 <output name="output" file="gencode/test.xml" lines_diff="14"/> 668 <output name="output" file="gencode/test.xml" lines_diff="16"/>
654 </test> 669 </test>
655 <test> 670 <test>
656 <param name="reference_genome|genome_type_select" value="history"/> 671 <param name="reference_genome|genome_type_select" value="history"/>
657 <param name="reference_genome|genome" value="merlin.fa"/> 672 <param name="reference_genome|genome" value="merlin.fa"/>
658 <param name="gencode" value="11" /> 673 <param name="gencode" value="11" />
844 </conditional> 859 </conditional>
845 </repeat> 860 </repeat>
846 </repeat> 861 </repeat>
847 862
848 <param name="uglyTestingHack" value="enabled" /> 863 <param name="uglyTestingHack" value="enabled" />
849 <output name="output" file="gff3/test.xml" lines_diff="256" /> 864 <output name="output" file="gff3/test.xml" lines_diff="170" />
850 </test> 865 </test>
851 <test> 866 <test>
852 <param name="reference_genome|genome_type_select" value="history"/> 867 <param name="reference_genome|genome_type_select" value="history"/>
853 <param name="reference_genome|genome" value="merlin.fa"/> 868 <param name="reference_genome|genome" value="merlin.fa"/>
854 <param name="gencode" value="11" /> 869 <param name="gencode" value="11" />
907 </conditional> 922 </conditional>
908 </repeat> 923 </repeat>
909 </repeat> 924 </repeat>
910 925
911 <param name="uglyTestingHack" value="enabled" /> 926 <param name="uglyTestingHack" value="enabled" />
912 <output name="output" file="menus/test.xml" lines_diff="24"/> 927 <output name="output" file="menus/test.xml" lines_diff="44"/>
913 </test> 928 </test>
914 <test> 929 <test>
915 <param name="reference_genome|genome_type_select" value="history"/> 930 <param name="reference_genome|genome_type_select" value="history"/>
916 <param name="reference_genome|genome" value="merlin.fa"/> 931 <param name="reference_genome|genome" value="merlin.fa"/>
917 <param name="gencode" value="11" /> 932 <param name="gencode" value="11" />
925 <param name="annotation" value="gff3/1.gff"/> 940 <param name="annotation" value="gff3/1.gff"/>
926 <conditional name="match_part"> 941 <conditional name="match_part">
927 <param name="match_part_select" value="false"/> 942 <param name="match_part_select" value="false"/>
928 </conditional> 943 </conditional>
929 <conditional name="track_config"> 944 <conditional name="track_config">
945 <param name="track_class" value="JBrowse/View/Track/CanvasFeatures"/>
930 <section name="canvas_options"> 946 <section name="canvas_options">
931 <param name="transcriptType" value="transcript"/> 947 <param name="transcriptType" value="transcript"/>
932 <param name="subParts" value="exon"/> 948 <param name="subParts" value="exon"/>
933 <param name="impliedUTRs" value="true"/> 949 <param name="impliedUTRs" value="true"/>
934 </section> 950 </section>
944 </conditional> 960 </conditional>
945 </repeat> 961 </repeat>
946 </repeat> 962 </repeat>
947 963
948 <param name="uglyTestingHack" value="enabled" /> 964 <param name="uglyTestingHack" value="enabled" />
949 <output name="output" file="track_config/test.xml" lines_diff="26"/> 965 <output name="output" file="track_config/test.xml" lines_diff="30"/>
950 </test> 966 </test>
951 <test> 967 <test>
952 <param name="reference_genome|genome_type_select" value="history"/> 968 <param name="reference_genome|genome_type_select" value="history"/>
953 <param name="reference_genome|genome" value="merlin.fa"/> 969 <param name="reference_genome|genome" value="merlin.fa"/>
954 <param name="gencode" value="11" /> 970 <param name="gencode" value="11" />
955 <param name="standalone" value="Data Directory" /> 971 <param name="standalone" value="Data Directory" />
956 972
957 <repeat name="track_groups"> 973 <repeat name="track_groups">
974 <param name="category" value="With custom track config" />
975 <repeat name="data_tracks">
976 <conditional name="data_format">
977 <param name="data_format_select" value="gene_calls"/>
978 <param name="annotation" value="gff3/1.gff"/>
979 <conditional name="match_part">
980 <param name="match_part_select" value="false"/>
981 </conditional>
982 <section name="jb_custom_config">
983 <repeat name="option">
984 <param name="opt_key" value="displayMode"/>
985 <conditional name="opt_value">
986 <param name="val_type" value="text"/>
987 <param name="val" value="collapsed"/>
988 </conditional>
989 </repeat>
990 <repeat name="option">
991 <param name="opt_key" value="histograms.height"/>
992 <conditional name="opt_value">
993 <param name="val_type" value="integer"/>
994 <param name="val" value="150"/>
995 </conditional>
996 </repeat>
997 <repeat name="option">
998 <param name="opt_key" value="maxFeatureScreenDensity"/>
999 <conditional name="opt_value">
1000 <param name="val_type" value="float"/>
1001 <param name="val" value="0.1"/>
1002 </conditional>
1003 </repeat>
1004 <repeat name="option">
1005 <param name="opt_key" value="style.strandArrow"/>
1006 <conditional name="opt_value">
1007 <param name="val_type" value="boolean"/>
1008 <param name="val" value="false"/>
1009 </conditional>
1010 </repeat>
1011 </section>
1012 </conditional>
1013 </repeat>
1014 </repeat>
1015
1016 <param name="uglyTestingHack" value="enabled" />
1017 <output name="output" file="custom_config/test.xml" lines_diff="30"/>
1018 </test>
1019 <test>
1020 <param name="reference_genome|genome_type_select" value="history"/>
1021 <param name="reference_genome|genome" value="merlin.fa"/>
1022 <param name="gencode" value="11" />
1023 <param name="standalone" value="Data Directory" />
1024
1025 <repeat name="track_groups">
958 <param name="category" value="Auto Coloured" /> 1026 <param name="category" value="Auto Coloured" />
959 <repeat name="data_tracks"> 1027 <repeat name="data_tracks">
960 <conditional name="data_format"> 1028 <conditional name="data_format">
961 <param name="data_format_select" value="pileup"/> 1029 <param name="data_format_select" value="pileup"/>
962 <param name="annotation" value="bam/merlin-sample.bam"/> 1030 <param name="annotation" value="bam/merlin-sample.bam"/>
963 </conditional> 1031 </conditional>
964 </repeat> 1032 </repeat>
965 </repeat> 1033 </repeat>
966 1034
967 <param name="uglyTestingHack" value="enabled" /> 1035 <param name="uglyTestingHack" value="enabled" />
968 <output name="output" file="bam/test.xml" lines_diff="48"/> 1036 <output name="output" file="bam/test.xml" lines_diff="42"/>
969 </test> 1037 </test>
970 1038
971 <test> 1039 <test>
972 <!-- data_table --> 1040 <!-- data_table -->
973 <param name="reference_genome|genome_type_select" value="indexed"/> 1041 <param name="reference_genome|genome_type_select" value="indexed"/>
974 <param name="reference_genome|genome" value="merlin"/> 1042 <param name="reference_genome|genome" value="merlin"/>
975 <param name="gencode" value="1" /> 1043 <param name="gencode" value="1" />
976 <param name="standalone" value="Data Directory" /> 1044 <param name="standalone" value="Data Directory" />
977 <param name="uglyTestingHack" value="enabled" /> 1045 <param name="uglyTestingHack" value="enabled" />
978 <output name="output" file="gencode/test-data_table.xml" lines_diff="6" /> 1046 <output name="output" file="gencode/test-data_table.xml" lines_diff="4" />
979 </test> 1047 </test>
980 1048
981 <test> 1049 <test>
982 <param name="reference_genome|genome_type_select" value="history"/> 1050 <param name="reference_genome|genome_type_select" value="history"/>
983 <param name="reference_genome|genome" value="merlin.fa"/> 1051 <param name="reference_genome|genome" value="merlin.fa"/>
1020 </conditional> 1088 </conditional>
1021 </repeat> 1089 </repeat>
1022 </repeat> 1090 </repeat>
1023 1091
1024 <param name="uglyTestingHack" value="enabled" /> 1092 <param name="uglyTestingHack" value="enabled" />
1025 <output name="output" file="endpoints/test.xml" lines_diff="48"/> 1093 <output name="output" file="endpoints/test.xml" lines_diff="16"/>
1026 </test> 1094 </test>
1027 </tests> 1095 </tests>
1028 <help><![CDATA[ 1096 <help><![CDATA[
1029 JBrowse-in-Galaxy 1097 JBrowse-in-Galaxy
1030 ================= 1098 =================