# HG changeset patch
# User fubar
# Date 1707345430 0
# Node ID 4ff1ed2065cc9dca65c40cb807187201da11edd8
# Parent  e578621acb13f032ec893b4b2fb74cbcb5fa3ff3
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit d733fb18a02929c9e9959ad30bd0f1368118e924-dirty

diff -r e578621acb13 -r 4ff1ed2065cc jbrowse2.py
--- a/jbrowse2.py	Sat Feb 03 22:22:07 2024 +0000
+++ b/jbrowse2.py	Wed Feb 07 22:37:10 2024 +0000
@@ -1224,7 +1224,7 @@
                 self.add_paf(
                     dataset_path,
                     outputTrackConfig,
-                    track["conf"]["options"]["synteny"],
+                    track["conf"]["options"]["paf"],
                 )
             else:
                 log.warn("Do not know how to handle %s", dataset_ext)
@@ -1279,6 +1279,7 @@
         if data.get("defaultLocation", ""):
             ddl = data["defaultLocation"]
             loc_match = re.search(r"^([^:]+):([\d,]*)\.*([\d,]*)$", ddl)
+            # allow commas like 100,000 but ignore as integer
             if loc_match:
                 refName = loc_match.group(1)
                 drdict["refName"] = refName
@@ -1291,12 +1292,6 @@
                     "@@@ regexp could not match contig:start..end in the supplied location %s - please fix"
                     % ddl
                 )
-        elif self.genome_firstcontig is not None:
-            drdict["refName"] = self.genome_firstcontig
-            logging.info(
-                "@@@ no defaultlocation found for default session - using %s as first contig found"
-                % self.genome_firstcontig
-            )
 
         if drdict.get("refName", None):
             # TODO displayedRegions is not just zooming to the region, it hides the rest of the chromosome
diff -r e578621acb13 -r 4ff1ed2065cc jbrowse2.xml
--- 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">
diff -r e578621acb13 -r 4ff1ed2065cc macros.xml
--- a/macros.xml	Sat Feb 03 22:22:07 2024 +0000
+++ b/macros.xml	Wed Feb 07 22:37:10 2024 +0000
@@ -29,7 +29,7 @@
     <token name="@ATTRIBUTION@"><![CDATA[
 **Attribution**
 This Galaxy tool relies on the JBrowse2, maintained by the GMOD Community. The Galaxy wrapper is maintained by Ross Lazarus
-until the IUC have their own.
+until the IUC complete their own.
 ]]>
     </token>
     <xml name="genome_selector"