Mercurial > repos > fubar > jbrowse2
diff jbrowse2.xml @ 59:f807e219cec3 draft
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit faada92caf5aaabe58e52b161687a30d542a07b9
| author | fubar |
|---|---|
| date | Fri, 22 Mar 2024 22:04:08 +0000 |
| parents | 0e592dcaeb7f |
| children | 81d535970196 |
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--- a/jbrowse2.xml Thu Mar 21 09:06:52 2024 +0000 +++ b/jbrowse2.xml Fri Mar 22 22:04:08 2024 +0000 @@ -139,16 +139,17 @@ #for $tg in $track_groups: #for $track in $tg.data_tracks: #if $track.data_format.useuri.insource == "uri": - <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}"> - <files> - <trackFile path="${track.data_format.useuri.annouri}" ext="${track.data_format.data_format_select}" label="${track.data_format.useuri.annoname}" useuri="yes"> - <metadata> - <dataset id = "${track.data_format.useuri.annouri}" /> - </metadata> - </trackFile> - </files> - <options/> - </track> + <track cat="${tg.category}" format="paf" visibility="${track.data_format.track_visibility}"> + <files> + <trackFile path="${ $track.data_format.useuri.insource.annouri}" ext="paf" + label="${track.data_format.useuri.insource.annoname}" useuri="yes"> + <metadata> + <dataset id = "${track.data_format.useuri.insource.annouri}" /> + </metadata> + </trackFile> + </files> + <options/> + </track> #else if $track.data_format.useuri.insource == "history": #if $track.data_format.useuri.annotation: <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}"> @@ -203,7 +204,10 @@ #end if #end if #if str($track.data_format.data_format_select) in ["bam", "cram"]: - <type>"LinearAlignmentsDisplay"</type> + <type>LinearAlignmentsDisplay</type> + #end if + #if str($track.data_format.data_format_select) in ["paf"]: + <type>LinearBasicDisplay</type> #end if </style> #if str($track.data_format.data_format_select) == "bam": @@ -235,13 +239,13 @@ #else if str($track.data_format.data_format_select) == "paf": <paf> <genome> - #for gnome in $track.data_format.synteny_genome: - $gnome, + #for refgenome in $track.data_format.pafuseuri.refgenomes: + $refgenome.annotation, #end for </genome> <genome_label> - #for gnome in $track.data_format.synteny_genome: - $gnome.name, + #for refgenome in $track.data_format.pafuseuri.refgenomes: + $refgenome.annoname, #end for </genome_label> </paf> @@ -327,17 +331,17 @@ <repeat name="data_tracks" title="Annotation Track"> <conditional name="data_format" label="Track Data Selection Options"> <param type="select" label="Track Type" name="data_format_select"> - <option value="bam">BAM Pileup track</option> + <option value="bam">BAM track. Recommend convert to faster BED unless mapping annotation needed</option> <option value="bed">BED track</option> <option value="bigwig">BigWig track</option> - <option value="blastxml">Blast XML track - converted to GFF</option> + <option value="blastxml">Blast XML track (as GFF3)</option> + <option value="cram">CRAM track. Currently not advantageous over BAM in Galaxy. Convert to BED like BAM.</option> + <option value="gff">GFF/GFF3 track</option> <option value="cool">HiC as cool/mcool/scool format files</option> - <option value="cram">CRAM</option> - <option value="gff">GFF/GFF3 feature track</option> <option value="hic">HiC as juicebox_hic format file. Tabular hic_matrix will NOT work.</option> <option value="maf">Multiple alignment format. Reference name must match the MAF name exactly to work correctly</option> <option value="paf">PAF - approximate mapping positions between two set of sequences</option> - <option value="vcf">VCF SNP</option> + <option value="vcf">VCF SNP track</option> </param> <when value="blastxml"> <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml" /> @@ -411,12 +415,10 @@ <expand macro="track_visibility" /> </when> <when value="paf"> - <param label="Comparison genome sequence" help="Paf from these as the reference(s), using the common reference as the reads to map" - format="fasta" - name="synteny_genome" - type="data" - multiple="True"/> - <expand macro="input_conditional" label="Synteny data" format="paf" help="Make paf with mashmap or minimap2 mapping real reference onto desired syntenic references"/> + <expand macro="input_conditional" label="PAF format synteny mapping data" format="paf" + help="PAF made with mashmap or minimap2 mapping the real reference as a query on the comparison genomes as references"/> + <expand macro="pafref_conditional" label="Comparison genome sequence(s)" + format="fasta" help="Paf from these as the reference(s), using the common reference as the reads to map"/> <expand macro="track_visibility" /> </when>