diff jbrowse2.xml @ 30:8f02a84ee278 draft

planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919

--- a/jbrowse2.xml	Fri Feb 16 00:04:37 2024 +0000
+++ b/jbrowse2.xml	Wed Feb 21 02:57:30 2024 +0000
@@ -93,7 +93,7 @@
         <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
             #if $track.data_format.data_format_select != "sparql":
             <files>
-              #for $dataset in $track.data_format.annotation:
+              #set dataset = $track.data_format.annotation
               <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.element_identifier}">
                 <metadata>
                   <dataset id="${__app__.security.encode_id($dataset.id)}" hid="${dataset.hid}"
@@ -128,7 +128,6 @@
                       />
                 </metadata>
               </trackFile>
-              #end for
             </files>
             #end if
 
@@ -138,17 +137,13 @@
             #if str($track.data_format.data_format_select) == "pileup":
                 <pileup>
                     <bam_indices>
-                        #for $dataset in $track.data_format.annotation:
                         <bam_index>${dataset.metadata.bam_index}</bam_index>
-                        #end for
                     </bam_indices>
                 </pileup>
             #else if str($track.data_format.data_format_select) == "cram":
                 <cram>
                     <cram_indices>
-                        #for $dataset in $track.data_format.annotation:
                         <cram_index>${dataset.metadata.cram_index}</cram_index>
-                        #end for
                     </cram_indices>
                 </cram>
             #else if str($track.data_format.data_format_select) == "blast":
@@ -234,11 +229,11 @@
                         <option value="pileup">BAM Pileup track</option>
                         <option value="wiggle">BigWig track</option>
                         <option value="blast">Blast XML track - converted to GFF</option>
-                        <option value="cool">cool/mcool/scool data in hdf5 data</option>
+                        <option value="cool">HiC as cool/mcool/scool format files</option>
                         <option value="cram">CRAM</option>
                         <option value="gene_calls" selected="true">GFF/GFF3/BED feature track</option>
-                        <option value="hic">HiC (compressed binary) track. Existing cool format must be converted to binary hic - hic_matrix will NOT work.</option>
-                        <option value="maf">Multiple alignment format track. Reference name must match the MAF name exactly to work correctly</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="sparql">SPARQL</option>
                        <option value="vcf">VCF SNP annotation</option>