# HG changeset patch
# User fubar
# Date 1708834733 0
# Node ID 2893ef33fba9e2b57b7738f15b5d06292e9ebaa7
# Parent  9aedb7f1cc7752a1cf9cc6bc0294a47af5986763
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd

diff -r 9aedb7f1cc77 -r 2893ef33fba9 jbrowse2.py
--- a/jbrowse2.py	Sat Feb 24 10:44:01 2024 +0000
+++ b/jbrowse2.py	Sun Feb 25 04:18:53 2024 +0000
@@ -17,7 +17,7 @@
 logging.basicConfig(level=logging.INFO)
 log = logging.getLogger("jbrowse")
 
-JB2VER = "v2.10.1"
+JB2VER = "v2.10.2"
 # version pinned for cloning
 
 TODAY = datetime.datetime.now().strftime("%Y-%m-%d")
@@ -450,7 +450,7 @@
             if len(genome_name.split()) > 1:
                 genome_name = genome_name.split()[0]
                 # spaces and cruft break scripts when substituted
-            if genome_name not  in self.genome_names:
+            if genome_name not in self.genome_names:
                 # ignore dupes - can have multiple pafs with same references?
                 fapath = genome_node["path"]
                 assem = self.make_assembly(fapath, genome_name)
@@ -1015,16 +1015,16 @@
     def add_paf(self, data, trackData, pafOpts, **kwargs):
         tname = trackData["name"]
         tId = trackData["label"]
-        pgnames = [x.strip() for x in pafOpts["genome_label"].split(',')]
-        pgpaths =  [x.strip() for x in pafOpts["genome"].split(',')]
-        passnames = [self.genome_name] # always first
+        pgnames = [x.strip() for x in pafOpts["genome_label"].split(",")]
+        pgpaths = [x.strip() for x in pafOpts["genome"].split(",")]
+        passnames = [self.genome_name]  # always first
         for i, gname in enumerate(pgnames):
             if len(gname.split()) > 1:
                 gname = gname.split()[0]
                 # trouble from spacey names in command lines avoidance
                 if gname not in self.genome_names:
                     passnames.append(gname)
-                   # ignore if already there - eg for duplicates among pafs.
+                    # ignore if already there - eg for duplicates among pafs.
                     asstrack = self.make_assembly(pgpaths[i], gname)
                     self.genome_names.append(gname)
                     if self.config_json.get("assemblies", None):
@@ -1126,7 +1126,7 @@
             # Unsanitize labels (element_identifiers are always sanitized by Galaxy)
             for key, value in mapped_chars.items():
                 track_human_label = track_human_label.replace(value, key)
-            track_human_label = track_human_label.replace(" ","_")
+            track_human_label = track_human_label.replace(" ", "_")
             outputTrackConfig = {
                 "category": category,
                 "style": {},
@@ -1149,7 +1149,7 @@
                     dataset_ext,
                     outputTrackConfig,
                 )
-            elif dataset_ext in ("hic","juicebox_hic"):
+            elif dataset_ext in ("hic", "juicebox_hic"):
                 self.add_hic(
                     dataset_path,
                     outputTrackConfig,
@@ -1540,9 +1540,7 @@
     default_session_data["session_name"] = root.find(
         "metadata/general/session_name"
     ).text
-    jc.zipOut =  root.find(
-        "metadata/general/zipOut"
-    ).text == "true"
+    jc.zipOut = root.find("metadata/general/zipOut").text == "true"
     general_data = {
         "analytics": root.find("metadata/general/analytics").text,
         "primary_color": root.find("metadata/general/primary_color").text,
diff -r 9aedb7f1cc77 -r 2893ef33fba9 jbrowse2.xml
--- a/jbrowse2.xml	Sat Feb 24 10:44:01 2024 +0000
+++ b/jbrowse2.xml	Sun Feb 25 04:18:53 2024 +0000
@@ -1,4 +1,4 @@
- <tool id="jbrowse2" name="jbrowse2" version="@TOOL_VERSION@+@WRAPPER_VERSION@_4" profile="22.05">
+ <tool id="jbrowse2" name="jbrowse2" version="@TOOL_VERSION@+@WRAPPER_VERSION@_5" profile="22.05">
     <description>genome browser</description>
     <macros>
         <import>macros.xml</import>
@@ -18,8 +18,7 @@
 --outdir '$output.files_path'
 --xml '$trackxml' &&
 #if $jbgen.zipOut == "true":
-    (cd '$output.files_path' && zip -r - . ) > JBrowse2.zip &&
-    mv JBrowse2.zip '$output'
+    (cd '$output.files_path' && zip -r - . ) > '$output'
 #else
   cp '$output.files_path/index.html' '$output'
 #end if
@@ -471,7 +470,7 @@
                 <repeat name="data_tracks">
                     <conditional name="data_format">
                         <param name="data_format_select" value="gene_calls"/>
-                        <param name="annotation" value="bed/test-3.bed,bed/test-6.bed"/>
+                        <param name="annotation" value="bed/test-3.bed"/>
                     </conditional>
                 </repeat>
             </repeat>
@@ -496,7 +495,7 @@
                 <repeat name="data_tracks">
                     <conditional name="data_format">
                         <param name="data_format_select" value="gene_calls"/>
-                        <param name="annotation" value="gff3/A.gff,gff3/B.gff,gff3/C.gff,gff3/D.gff"/>
+                        <param name="annotation" value="gff3/A.gff"/>
                         <conditional name="match_part">
                             <param name="match_part_select" value="false"/>
                         </conditional>
@@ -539,7 +538,7 @@
                 <repeat name="data_tracks">
                     <conditional name="data_format">
                         <param name="data_format_select" value="gene_calls"/>
-                        <param name="annotation" value="gff3/1.gff"/>
+                        <param name="annotation" value="gff3/C.gff"/>
                         <conditional name="match_part">
                             <param name="match_part_select" value="false"/>
                         </conditional>
@@ -563,7 +562,7 @@
                 <repeat name="data_tracks">
                     <conditional name="data_format">
                         <param name="data_format_select" value="gene_calls"/>
-                        <param name="annotation" value="gff3/1.gff"/>
+                        <param name="annotation" value="gff3/B.gff"/>
                         <conditional name="match_part">
                             <param name="match_part_select" value="false"/>
                         </conditional>
@@ -588,7 +587,7 @@
                 <repeat name="data_tracks">
                     <conditional name="data_format">
                         <param name="data_format_select" value="gene_calls"/>
-                        <param name="annotation" value="gff3/1.gff"/>
+                        <param name="annotation" value="gff3/A.gff"/>
                         <conditional name="match_part">
                             <param name="match_part_select" value="false"/>
                         </conditional>
@@ -686,7 +685,7 @@
                         <has_text text="A.gff"/>
                         <has_text text="B.gff"/>
                         <has_text text="C.gff"/>
-                        <has_text text="D.gff"/>
+                        <has_text text="interpro.gff"/>
                         <has_text text="Scaled Colour"/>
                         <has_text text="1.gff"/>
                         <has_text text="2.gff"/>
diff -r 9aedb7f1cc77 -r 2893ef33fba9 more
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/more	Sun Feb 25 04:18:53 2024 +0000
@@ -0,0 +1,58 @@
+jbrowse2.py:2:80: E501 line too long (94 > 79 characters)
+jbrowse2.py:84:80: E501 line too long (124 > 79 characters)
+jbrowse2.py:85:80: E501 line too long (83 > 79 characters)
+jbrowse2.py:88:80: E501 line too long (83 > 79 characters)
+jbrowse2.py:102:80: E501 line too long (86 > 79 characters)
+jbrowse2.py:234:80: E501 line too long (87 > 79 characters)
+jbrowse2.py:261:80: E501 line too long (84 > 79 characters)
+jbrowse2.py:266:80: E501 line too long (84 > 79 characters)
+jbrowse2.py:267:80: E501 line too long (85 > 79 characters)
+jbrowse2.py:275:80: E501 line too long (85 > 79 characters)
+jbrowse2.py:283:80: E501 line too long (85 > 79 characters)
+jbrowse2.py:295:80: E501 line too long (84 > 79 characters)
+jbrowse2.py:348:80: E501 line too long (87 > 79 characters)
+jbrowse2.py:351:80: E501 line too long (83 > 79 characters)
+jbrowse2.py:357:80: E501 line too long (107 > 79 characters)
+jbrowse2.py:367:80: E501 line too long (118 > 79 characters)
+jbrowse2.py:392:80: E501 line too long (82 > 79 characters)
+jbrowse2.py:461:80: E501 line too long (80 > 79 characters)
+jbrowse2.py:554:80: E501 line too long (101 > 79 characters)
+jbrowse2.py:558:80: E501 line too long (90 > 79 characters)
+jbrowse2.py:560:80: E501 line too long (94 > 79 characters)
+jbrowse2.py:562:80: E501 line too long (94 > 79 characters)
+jbrowse2.py:563:80: E501 line too long (123 > 79 characters)
+jbrowse2.py:597:80: E501 line too long (133 > 79 characters)
+jbrowse2.py:605:80: E501 line too long (124 > 79 characters)
+jbrowse2.py:624:80: E501 line too long (87 > 79 characters)
+jbrowse2.py:783:80: E501 line too long (81 > 79 characters)
+jbrowse2.py:784:80: E501 line too long (97 > 79 characters)
+jbrowse2.py:790:80: E501 line too long (102 > 79 characters)
+jbrowse2.py:791:80: E501 line too long (101 > 79 characters)
+jbrowse2.py:792:80: E501 line too long (99 > 79 characters)
+jbrowse2.py:794:80: E501 line too long (84 > 79 characters)
+jbrowse2.py:830:80: E501 line too long (83 > 79 characters)
+jbrowse2.py:831:80: E501 line too long (93 > 79 characters)
+jbrowse2.py:837:80: E501 line too long (102 > 79 characters)
+jbrowse2.py:838:80: E501 line too long (101 > 79 characters)
+jbrowse2.py:839:80: E501 line too long (99 > 79 characters)
+jbrowse2.py:841:80: E501 line too long (86 > 79 characters)
+jbrowse2.py:843:80: E501 line too long (81 > 79 characters)
+jbrowse2.py:925:80: E501 line too long (82 > 79 characters)
+jbrowse2.py:1126:80: E501 line too long (84 > 79 characters)
+jbrowse2.py:1193:80: E501 line too long (81 > 79 characters)
+jbrowse2.py:1206:80: E501 line too long (80 > 79 characters)
+jbrowse2.py:1243:80: E501 line too long (146 > 79 characters)
+jbrowse2.py:1245:80: E501 line too long (83 > 79 characters)
+jbrowse2.py:1260:80: E501 line too long (123 > 79 characters)
+jbrowse2.py:1295:80: E501 line too long (107 > 79 characters)
+jbrowse2.py:1301:80: E501 line too long (106 > 79 characters)
+jbrowse2.py:1309:80: E501 line too long (80 > 79 characters)
+jbrowse2.py:1314:80: E501 line too long (87 > 79 characters)
+jbrowse2.py:1347:80: E501 line too long (82 > 79 characters)
+jbrowse2.py:1354:80: E501 line too long (80 > 79 characters)
+jbrowse2.py:1408:80: E501 line too long (86 > 79 characters)
+jbrowse2.py:1432:80: E501 line too long (117 > 79 characters)
+jbrowse2.py:1494:80: E501 line too long (94 > 79 characters)
+jbrowse2.py:1504:80: E501 line too long (88 > 79 characters)
+jbrowse2.py:1517:80: E501 line too long (86 > 79 characters)
+jbrowse2.py:1549:80: E501 line too long (80 > 79 characters)