# HG changeset patch
# User bgruening
# Date 1722134563 0
# Node ID 878c27dfea9d3c58ebd3ace6480a89bd4d86c80b
# Parent  56f9a6e0fe80bfcc7454c7ce768825e64388478b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 45375b64cbc99173525a2b374d71a13e650ce1b0

diff -r 56f9a6e0fe80 -r 878c27dfea9d autogenJB2.py
--- a/autogenJB2.py	Thu Jul 04 08:40:21 2024 +0000
+++ b/autogenJB2.py	Sun Jul 28 02:42:43 2024 +0000
@@ -92,6 +92,11 @@
             # foo.paf must have a foo_paf.fasta or fasta.gz to match
             tnames = [x[2] for x in listtracks]
             texts = [x[1] for x in listtracks]
+            if len(listtracks) == 0:
+                sys.stderr.write(
+                    "Please add at least one track (bam,bed,bigwig,blastxml,cram,gff,hic,maf,paf or vcf) to the collection. No suitable track files for autogenJB2 - nothing to process"
+                )
+                sys.exit(5)
             for i, track in enumerate(listtracks):
                 track_conf = {
                     "trackfiles": [],
@@ -224,5 +229,5 @@
             # jc.text_index() not sure what broke here.
     else:
         sys.stderr.write(
-            "Collection has no suitable trackfiles for autogenJB2 - nothing to process"
+            "Please add a fasta genome reference to the collection. No suitable reference fasta for autogenJB2 - nothing to process"
         )
diff -r 56f9a6e0fe80 -r 878c27dfea9d jbrowse2.xml
--- a/jbrowse2.xml	Thu Jul 04 08:40:21 2024 +0000
+++ b/jbrowse2.xml	Sun Jul 28 02:42:43 2024 +0000
@@ -5,7 +5,7 @@
     </macros>
     <expand macro="edamInc"/>
     <xrefs>
-        <xref type="bio.tools">jbrowse2</xref>
+        <xref type="bio.tools">jbrowse_2</xref>
     </xrefs>
     <expand macro="requirements"/>
     <required_files>
diff -r 56f9a6e0fe80 -r 878c27dfea9d macros.xml
--- a/macros.xml	Thu Jul 04 08:40:21 2024 +0000
+++ b/macros.xml	Sun Jul 28 02:42:43 2024 +0000
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">2.12.3</token>
+    <token name="@TOOL_VERSION@">2.13.0</token>
     <xml name="edamInc">
         <edam_topics>
             <edam_topic>topic_3307</edam_topic>