diff jbrowse2.xml @ 27:4ff1ed2065cc draft

planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit d733fb18a02929c9e9959ad30bd0f1368118e924-dirty

--- a/jbrowse2.xml	Sat Feb 03 22:22:07 2024 +0000
+++ b/jbrowse2.xml	Wed Feb 07 22:37:10 2024 +0000
@@ -165,11 +165,11 @@
                     <match>${track.data_format.match_part.name}</match>
                   #end if
                 </gff>
-            #else if str($track.data_format.data_format_select) == "synteny":
-                <synteny>
+            #else if str($track.data_format.data_format_select) == "paf":
+                <paf>
                     <genome>${track.data_format.synteny_genome}</genome>
                     <genome_label>${track.data_format.synteny_genome.name}</genome_label>
-                </synteny>
+                </paf>
             #else if str($track.data_format.data_format_select) == "hic":
                 <hic>
                 </hic>
@@ -283,7 +283,7 @@
                                     name="name"
                                     type="text"
                                     value="match"
-                                    help="Match_parts have several options for the parent feature type, such as cDNA_match, match, translated_nucleotide_match, etc. Please select the appropriate one here. You can leave empty to try autodetection (only works with CanvasFeatures track type)."
+                                    help="Match_parts have options for the parent feature type, such as cDNA_match, match, translated_nucleotide_match, etc. Please select the appropriate one here. You can leave empty to try autodetection (only works with CanvasFeatures track type)."
                                     optional="True"/>
                             </when>
                             <when value="false" />
@@ -316,7 +316,7 @@
                     </when>
 
                     <when value="hic">
-                        <expand macro="input_conditional" label="HiC data" format="hic" />
+                        <expand macro="input_conditional" label="Binary Juicebox HiC data" format="hic,juicebox_hic" />
                         <expand macro="track_visibility" />
                     </when>
                     <when value="cool">