| Previous changeset 87:de8fb46bc3ef (2024-04-10) Next changeset 89:408781c080fc (2024-04-17) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9 |
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modified:
jbrowse2.xml test-data/jbrowse2_result02.zip |
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| diff -r de8fb46bc3ef -r efd1d41f11b4 jbrowse2.xml --- a/jbrowse2.xml Wed Apr 10 07:33:52 2024 +0000 +++ b/jbrowse2.xml Sun Apr 14 03:49:10 2024 +0000 |
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| b'@@ -1,4 +1,4 @@\n- <tool id="jbrowse2" name="JBrowse2" version="@TOOL_VERSION@+@WRAPPER_VERSION@_12" profile="22.05">\n+ <tool id="jbrowse2" name="JBrowse2" version="@TOOL_VERSION@+@WRAPPER_VERSION@_14" profile="22.05">\n <description>genome browser</description>\n <macros>\n <import>macros.xml</import>\n@@ -99,7 +99,7 @@\n #else\n <genome path="$assembly.reference_genome.genome" label="${assembly.reference_genome.genome.name}" useuri="no">\n <metadata>\n- #if $uglyTestingHack != "enabled":\n+\n <dataset id="${__app__.security.encode_id($assembly.reference_genome.genome.id)}"\n hid="${assembly.reference_genome.genome.hid}"\n size="${assembly.reference_genome.genome.get_size(nice_size=True)}"\n@@ -135,34 +135,38 @@\n tool_id="${assembly.reference_genome.genome.creating_job.tool_id}"\n tool_version="${assembly.reference_genome.genome.creating_job.tool_version}"\n />\n- #end if\n+\n </metadata>\n </genome>\n #end if\n </genomes>\n-\n </metadata>\n <tracks>\n #for $tg in $assembly.track_groups:\n #for $track in $tg.data_tracks:\n+ #set input_exists = "False"\n #if $track.data_format.useuri.insource == "uri":\n- <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">\n- <files>\n- <trackFile path="${track.data_format.useuri.annouri}" ext="${track.data_format.data_format_select}"\n- label="${track.data_format.useuri.annoname}" useuri="yes">\n- <metadata>\n- <dataset id = "${track.data_format.useuri.annouri}" />\n- </metadata>\n- </trackFile>\n- </files>\n+ #if $track.data_format.useuri.annouri:\n+ #set input_exists = "True"\n+ <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">\n+ <files>\n+ <trackFile path="${track.data_format.useuri.annouri}" ext="${track.data_format.data_format_select}"\n+ label="${track.data_format.useuri.annoname}" useuri="yes">\n+ <metadata>\n+ <dataset id = "${track.data_format.useuri.annouri}" />\n+ </metadata>\n+ </trackFile>\n+ </files>\n+ #end if\n #else if $track.data_format.useuri.insource == "history":\n #if $track.data_format.useuri.annotation:\n+ #set input_exists = "True"\n <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">\n <files>\n #for $dataset in $track.data_format.useuri.annotation:\n <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.name}" useuri="no">\n <metadata>\n- #if $uglyTestingHack != "enabled":\n+\n <dataset id="${__app__.security.encode_id($dataset.id)}" hid="${dataset.hid}"\n size="${dataset.get_size(nice_size=True)}"\n edam_format="${dataset.datatype.edam_format}"\n@@ -194,113 +198,112 @@\n '..b'set of tracks for each of multiple genome reference fasta files">\n <conditional name="reference_genome">\n <param help="Select a built in, history or remote tabix URI for the reference track"\n label="Reference genome source" name="genome_type_select" type="select">\n- <option selected="True" value="indexed">Use a built-in genome</option>\n- <option value="history">Use a genome from history</option>\n- <option value="uri">URI for a reference as tabix with predictable index file URI</option>\n+ <option selected="True" value="indexed">Use a Galaxy server built-in genome</option>\n+ <option value="history">Use a genome fasta file from the current history</option>\n+ <option value="uri">Provide a URI (e.g. "https://..." for a genome reference as tabix bgzip with predictable index file URI</option>\n </param>\n <when value="indexed">\n <param\n@@ -380,7 +384,6 @@\n </param>\n <when value="blastxml">\n <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml" />\n-\n <param label="Features used in Blast Search"\n help="in GFF3. This is used so we know where to map features. E.g. where results of which CDS Protein32 match up to. The query IDs in your blast results should MATCH some feature\n IDs in your GFF3 file. This is an optional field and is most useful if using JBrowse to display protein blast results on a DNA genome. blastn results don\'t need this,\n@@ -389,7 +392,6 @@\n name="blast_parent"\n optional="true"\n type="data"/>\n-\n <param label="Minimum Gap Size"\n help="before a new match_part feature is created"\n name="min_gap"\n@@ -459,7 +461,6 @@\n format="fasta" help="Paf from these as the reference(s), using the common reference as the reads to map"/>\n <expand macro="track_visibility" />\n </when>\n-\n <when value="hic">\n <expand macro="input_conditional" label="Binary Juicebox HiC data" format="hic,juicebox_hic" />\n <expand macro="track_visibility" />\n@@ -564,6 +565,15 @@\n </conditional>\n </conditional>\n </repeat>\n+ <repeat name="data_tracks">\n+ <conditional name="data_format">\n+ <param name="data_format_select" value="bam"/>\n+ <conditional name="useuri">\n+ <param name="insource" value="history"/>\n+ <param name="annotation" value=""/>\n+ </conditional>\n+ </conditional>\n+ </repeat>\n </repeat>\n </repeat>\n <repeat name="assemblies">\n@@ -658,8 +668,8 @@\n <has_archive_member path="merlin-sample.bam_5.bam"/>\n <has_archive_member path="merlinlastz.maf_6.maf.sorted.bed.gz.tbi"/>\n <has_archive_member path="merlin.blastxml_7.blastxml.gz"/>\n- <has_archive_member path="dm3test.cool_8.cool.hic"/>\n- <has_archive_member path="peach-grape-map.paf_9.paf"/>\n+ <has_archive_member path="dm3test.cool_9.cool.hic"/>\n+ <has_archive_member path="peach-grape-map.paf_10.paf"/>\n <has_archive_member path="Merlin.fa.gz.fai"/>\n <has_archive_member path="config.json">\n <has_json_property_with_text property="name" text="Merlin" />\n' |
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| diff -r de8fb46bc3ef -r efd1d41f11b4 test-data/jbrowse2_result02.zip |
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| Binary file test-data/jbrowse2_result02.zip has changed |