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comparison jbrowse.xml @ 42:6cd09d7b5f37 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
author iuc
date Sat, 06 Feb 2021 12:01:13 +0000
parents 8774b28235bb
children
comparison
equal deleted inserted replaced
41:8774b28235bb 42:6cd09d7b5f37
681 <param name="reference_genome|genome_type_select" value="history"/> 681 <param name="reference_genome|genome_type_select" value="history"/>
682 <param name="reference_genome|genome" value="merlin.fa"/> 682 <param name="reference_genome|genome" value="merlin.fa"/>
683 <param name="gencode" value="1" /> 683 <param name="gencode" value="1" />
684 <param name="standalone" value="data" /> 684 <param name="standalone" value="data" />
685 <param name="uglyTestingHack" value="enabled" /> 685 <param name="uglyTestingHack" value="enabled" />
686 <output name="output" file="gencode/test-1.xml" lines_diff="16"/> 686 <output name="output">
687 <assert_contents>
688 <has_text text="&lt;gencode&gt;1&lt;/gencode&gt;"></has_text>
689 <has_text text="genome path="></has_text>
690 <has_text text="dataset id="></has_text>
691 <has_text text="history id="></has_text>
692 <has_text text="metadata"></has_text>
693 <has_text text="tool_id"></has_text>
694
695 </assert_contents>
696 </output>
687 </test> 697 </test>
688 <test> 698 <test>
689 <param name="reference_genome|genome_type_select" value="history"/> 699 <param name="reference_genome|genome_type_select" value="history"/>
690 <param name="reference_genome|genome" value="merlin.fa"/> 700 <param name="reference_genome|genome" value="merlin.fa"/>
691 <param name="gencode" value="11" /> 701 <param name="gencode" value="11" />
692 <param name="standalone" value="data" /> 702 <param name="standalone" value="data" />
693 <param name="uglyTestingHack" value="enabled" /> 703 <param name="uglyTestingHack" value="enabled" />
694 <output name="output" file="gencode/test.xml" lines_diff="16"/> 704 <output name="output">
705 <assert_contents>
706 <has_text text="&lt;gencode&gt;11&lt;/gencode&gt;"></has_text>
707 <has_text text="genome path="></has_text>
708 <has_text text="dataset id="></has_text>
709 <has_text text="history id="></has_text>
710 <has_text text="metadata"></has_text>
711 <has_text text="tool_id"></has_text>
712 </assert_contents>
713 </output>
695 </test> 714 </test>
696 <test> 715 <test>
697 <param name="reference_genome|genome_type_select" value="history"/> 716 <param name="reference_genome|genome_type_select" value="history"/>
698 <param name="reference_genome|genome" value="merlin.fa"/> 717 <param name="reference_genome|genome" value="merlin.fa"/>
699 <param name="gencode" value="11" /> 718 <param name="gencode" value="11" />
706 <param name="annotation" value="bed/test-3.bed,bed/test-6.bed"/> 725 <param name="annotation" value="bed/test-3.bed,bed/test-6.bed"/>
707 </conditional> 726 </conditional>
708 </repeat> 727 </repeat>
709 </repeat> 728 </repeat>
710 <param name="uglyTestingHack" value="enabled" /> 729 <param name="uglyTestingHack" value="enabled" />
711 <output name="output" file="bed/test.xml" lines_diff="32"/> 730 <output name="output">
731 <assert_contents>
732 <has_text text="&lt;gencode&gt;11&lt;/gencode&gt;"></has_text>
733 <has_text text="genome path="></has_text>
734 <has_text text="dataset id="></has_text>
735 <has_text text="history id="></has_text>
736 <has_text text="metadata"></has_text>
737 <has_text text="tool_id"></has_text>
738 <has_text text="trackFile path="></has_text>
739 <has_text text="ext=&quot;bed&quot; label=&quot;test-3.bed&quot;"></has_text>
740 <has_text text="NeatHTMLFeatures"></has_text>
741 </assert_contents>
742 </output>
712 </test> 743 </test>
713 <test> 744 <test>
714 <param name="reference_genome|genome_type_select" value="history"/> 745 <param name="reference_genome|genome_type_select" value="history"/>
715 <param name="reference_genome|genome" value="merlin.fa"/> 746 <param name="reference_genome|genome" value="merlin.fa"/>
716 <param name="gencode" value="11" /> 747 <param name="gencode" value="11" />
902 </conditional> 933 </conditional>
903 </repeat> 934 </repeat>
904 </repeat> 935 </repeat>
905 936
906 <param name="uglyTestingHack" value="enabled" /> 937 <param name="uglyTestingHack" value="enabled" />
907 <output name="output" file="gff3/test.xml" lines_diff="260" /> 938 <output name="output">
939 <assert_contents>
940 <has_text text="Auto Coloured"/>
941 <has_text text="A.gff"/>
942 <has_text text="B.gff"/>
943 <has_text text="C.gff"/>
944 <has_text text="D.gff"/>
945 <has_text text="Scaled Colour"/>
946 <has_text text="1.gff"/>
947 <has_text text="2.gff"/>
948 </assert_contents>
949 </output>
908 </test> 950 </test>
909 <test> 951 <test>
910 <param name="reference_genome|genome_type_select" value="history"/> 952 <param name="reference_genome|genome_type_select" value="history"/>
911 <param name="reference_genome|genome" value="merlin.fa"/> 953 <param name="reference_genome|genome" value="merlin.fa"/>
912 <param name="gencode" value="11" /> 954 <param name="gencode" value="11" />
965 </conditional> 1007 </conditional>
966 </repeat> 1008 </repeat>
967 </repeat> 1009 </repeat>
968 1010
969 <param name="uglyTestingHack" value="enabled" /> 1011 <param name="uglyTestingHack" value="enabled" />
970 <output name="output" file="menus/test.xml" lines_diff="44"/> 1012 <output name="output">
1013 <assert_contents>
1014 <has_text text="With menu or index"/>
1015 <has_text text="Some menu item"/>
1016 <has_text text="Frame title"/>
1017 <has_text text="dijitIconNewTask"/>
1018 </assert_contents>
1019 </output>
971 </test> 1020 </test>
972 <test> 1021 <test>
973 <param name="reference_genome|genome_type_select" value="history"/> 1022 <param name="reference_genome|genome_type_select" value="history"/>
974 <param name="reference_genome|genome" value="merlin.fa"/> 1023 <param name="reference_genome|genome" value="merlin.fa"/>
975 <param name="gencode" value="11" /> 1024 <param name="gencode" value="11" />
1003 </conditional> 1052 </conditional>
1004 </repeat> 1053 </repeat>
1005 </repeat> 1054 </repeat>
1006 1055
1007 <param name="uglyTestingHack" value="enabled" /> 1056 <param name="uglyTestingHack" value="enabled" />
1008 <output name="output" file="track_config/test.xml" lines_diff="30"/> 1057 <output name="output">
1058 <assert_contents>
1059 <has_text text="With canvas config"></has_text>
1060 <has_text text="&lt;transcriptType&gt;transcript&lt;/transcriptType&gt;"></has_text>
1061 <has_text text="&lt;subParts&gt;exon&lt;/subParts&gt;"></has_text>
1062 </assert_contents>
1063 </output>
1009 </test> 1064 </test>
1010 <test> 1065 <test>
1011 <param name="reference_genome|genome_type_select" value="history"/> 1066 <param name="reference_genome|genome_type_select" value="history"/>
1012 <param name="reference_genome|genome" value="merlin.fa"/> 1067 <param name="reference_genome|genome" value="merlin.fa"/>
1013 <param name="gencode" value="11" /> 1068 <param name="gencode" value="11" />
1055 </conditional> 1110 </conditional>
1056 </repeat> 1111 </repeat>
1057 </repeat> 1112 </repeat>
1058 1113
1059 <param name="uglyTestingHack" value="enabled" /> 1114 <param name="uglyTestingHack" value="enabled" />
1060 <output name="output" file="custom_config/test.xml" lines_diff="30"/> 1115 <output name="output">
1116 <assert_contents>
1117 <has_text text="1.gff"/>
1118 <has_text text="collapsed"/>
1119 <has_text text="150"/>
1120 <has_text text="maxFeatureScreenDensity"/>
1121 <has_text text="style.strandArrow"/>
1122 </assert_contents>
1123 </output>
1061 </test> 1124 </test>
1062 <test> 1125 <test>
1063 <param name="reference_genome|genome_type_select" value="history"/> 1126 <param name="reference_genome|genome_type_select" value="history"/>
1064 <param name="reference_genome|genome" value="merlin.fa"/> 1127 <param name="reference_genome|genome" value="merlin.fa"/>
1065 <param name="gencode" value="11" /> 1128 <param name="gencode" value="11" />
1074 </conditional> 1137 </conditional>
1075 </repeat> 1138 </repeat>
1076 </repeat> 1139 </repeat>
1077 1140
1078 <param name="uglyTestingHack" value="enabled" /> 1141 <param name="uglyTestingHack" value="enabled" />
1079 <output name="output" file="bam/test.xml" lines_diff="42"/> 1142 <output name="output">
1143 <assert_contents>
1144 <has_text text="merlin-sample.bam"/>
1145 <has_text text="sort_order=&quot;coordinate&quot;"/>
1146 <has_text text="bam_index"/>
1147 </assert_contents>
1148 </output>
1080 </test> 1149 </test>
1081 1150
1082 <test> 1151 <test>
1083 <!-- data_table --> 1152 <!-- data_table -->
1084 <param name="reference_genome|genome_type_select" value="indexed"/> 1153 <param name="reference_genome|genome_type_select" value="indexed"/>
1085 <param name="reference_genome|genome" value="merlin"/> 1154 <param name="reference_genome|genome" value="merlin"/>
1086 <param name="gencode" value="1" /> 1155 <param name="gencode" value="1" />
1087 <param name="standalone" value="data" /> 1156 <param name="standalone" value="data" />
1088 <param name="uglyTestingHack" value="enabled" /> 1157 <param name="uglyTestingHack" value="enabled" />
1089 <output name="output" file="gencode/test-data_table.xml" lines_diff="4" /> 1158 <output name="output">
1159 <assert_contents>
1160 <has_text text="merlin.fa"/>
1161 </assert_contents>
1162 </output>
1090 </test> 1163 </test>
1091 1164
1092 <test> 1165 <test>
1093 <param name="reference_genome|genome_type_select" value="history"/> 1166 <param name="reference_genome|genome_type_select" value="history"/>
1094 <param name="reference_genome|genome" value="merlin.fa"/> 1167 <param name="reference_genome|genome" value="merlin.fa"/>
1131 </conditional> 1204 </conditional>
1132 </repeat> 1205 </repeat>
1133 </repeat> 1206 </repeat>
1134 1207
1135 <param name="uglyTestingHack" value="enabled" /> 1208 <param name="uglyTestingHack" value="enabled" />
1136 <output name="output" file="endpoints/test.xml" lines_diff="16"/> 1209 <output name="output">
1210 <assert_contents>
1211 <has_text text="http://example.org.external/sparql/"/>
1212 </assert_contents>
1213 </output>
1137 </test> 1214 </test>
1138 </tests> 1215 </tests>
1139 <help><![CDATA[ 1216 <help><![CDATA[
1140 JBrowse-in-Galaxy 1217 JBrowse-in-Galaxy
1141 ================= 1218 =================