Repository 'apollo_feat_from_gff3'
hg clone https://toolshed.g2.bx.psu.edu/repos/gga/apollo_feat_from_gff3

Changeset 17:250745643de2 (2023-01-11)
Previous changeset 16:12ebb583b8a3 (2021-12-10)
Commit message:
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 12282c16658b37858f49944796fd95515ef0fc0b
modified:
create_features_from_gff3.xml
create_or_update_organism.py
webapollo.py
b
diff -r 12ebb583b8a3 -r 250745643de2 create_features_from_gff3.xml
--- a/create_features_from_gff3.xml Fri Dec 10 09:52:37 2021 +0000
+++ b/create_features_from_gff3.xml Wed Jan 11 11:47:48 2023 +0000
b
@@ -32,7 +32,7 @@
       <test>
           <conditional name="org_source">
               <param name="source_select" value="direct"/>
-              <param name="org_raw" value="Test org" />
+              <param name="org_raw" value="test_organism" />
           </conditional>
           <param name="gff3_data" value="merlin.gff"/>
           <output name="output" file="load_gff3/output.txt" compare="sim_size"/>
b
diff -r 12ebb583b8a3 -r 250745643de2 create_or_update_organism.py
--- a/create_or_update_organism.py Fri Dec 10 09:52:37 2021 +0000
+++ b/create_or_update_organism.py Wed Jan 11 11:47:48 2023 +0000
b
@@ -88,7 +88,7 @@
 
     # Cleanup if existing
     if not IsRemote():
-        if(os.path.exists(args.jbrowse)):
+        if os.path.exists(args.jbrowse):
             shutil.rmtree(args.jbrowse)
         # Copy files
         shutil.copytree(args.jbrowse_src, args.jbrowse, symlinks=True)
b
diff -r 12ebb583b8a3 -r 250745643de2 webapollo.py
--- a/webapollo.py Fri Dec 10 09:52:37 2021 +0000
+++ b/webapollo.py Wed Jan 11 11:47:48 2023 +0000
[
@@ -5,9 +5,15 @@
 import json
 import logging
 import os
+import sys
 import time
 from abc import abstractmethod
 
+if sys.version_info.major == 3 and sys.version_info.minor >= 10:
+    from collections.abc import MutableMapping
+else:
+    from collections import MutableMapping
+
 import requests
 
 from six.moves.builtins import next
@@ -29,7 +35,7 @@
 # of https://github.com/tkem/cachetools/    #
 #############################################
 
-class DefaultMapping(collections.MutableMapping):
+class DefaultMapping(MutableMapping):
 
     __slots__ = ()
 
@@ -436,7 +442,6 @@
     def __init__(self):
 
         if 'ARROW_GLOBAL_CONFIG_PATH' in os.environ:
-
             with open(os.environ['ARROW_GLOBAL_CONFIG_PATH'], 'r') as config:
                 conf = yaml.safe_load(config)
                 try: