Mercurial > repos > fubar > jbrowse2

changeset 64:497fd2d27aa2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976-dirty
author fubar
date Thu, 28 Mar 2024 09:15:57 +0000
parents ac00dcfb5d1d
children c81902830900
files jbrowse2.py jbrowse2.xml
diffstat 2 files changed, 20 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/jbrowse2.py	Thu Mar 28 07:46:04 2024 +0000
+++ b/jbrowse2.py	Thu Mar 28 09:15:57 2024 +0000
@@ -1141,7 +1141,8 @@
                     self.config_json["assemblies"] = [
                         asstrack,
                     ]
-        url = "%s.paf" % (trackData["label"])
+        lab = trackData["label"]
+        url = "%s.paf" % (lab)
         dest = "%s/%s" % (self.outdir, url)
         self.symlink_or_copy(os.path.realpath(data), dest)
         trackDict = {
@@ -1157,12 +1158,27 @@
                 "pafLocation": {"uri": url},
                 "assemblyNames": passnames,
             },
+            "displays": [
+                {"type": "DotplotDisplay", "displayId": "%s-DotplotDisplay" % lab},
+                {
+                    "type": "LinearComparativeDisplay",
+                    "displayId": "%s-LinearComparativeDisplay" % lab,
+                },
+                {
+                    "type": "LinearSyntenyDisplay",
+                    "displayId": "%s-LinearSyntenyDisplay" % lab,
+                },
+                {
+                    "type": "LGVSyntenyDisplay",
+                    "displayId": "%s-LGVSyntenyDisplay" % lab,
+                },
+            ],
         }
         style_json = {
             "displays": [
                 {
-                    "type": "LinearBasicDisplay",
-                    "displayId": "%s-LinearBasicyDisplay" % trackDict["trackId"],
+                    "type": "SyntenyDisplay",
+                    "displayId": "%s-SyntenyDisplay" % lab,
                 }
             ]
         }
--- a/jbrowse2.xml	Thu Mar 28 07:46:04 2024 +0000
+++ b/jbrowse2.xml	Thu Mar 28 09:15:57 2024 +0000
@@ -1,4 +1,4 @@
- <tool id="jbrowse2auto" name="JBrowse2auto" version="@TOOL_VERSION@+@WRAPPER_VERSION@_8" profile="22.05">
+ <tool id="jbrowse2" name="JBrowse2" version="@TOOL_VERSION@+@WRAPPER_VERSION@_8" profile="22.05">
     <description>genome browser</description>
     <macros>
         <import>macros.xml</import>