Merge branch 'release_18.09'

doc/schema_template.md

@@ -73,6 +73,7 @@ $tag:tool|outputs|collection|discover_datasets://complexType[@name='OutputCollec
 $tag:tool|tests://complexType[@name='Tests']
 $tag:tool|tests|test://complexType[@name='Test']
 $tag:tool|tests|test|param://complexType[@name='TestParam']
+$tag:tool|tests|test|param|collection://complexType[@name='TestCollection']
 $tag:tool|tests|test|repeat://complexType[@name='TestRepeat']
 $tag:tool|tests|test|section://complexType[@name='TestSection']
 $tag:tool|tests|test|conditional://complexType[@name='TestConditional']

lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt

@@ -93,7 +93,7 @@ oslo.utils==3.37.0; python_version != '3.3.*'
 packaging==17.1
 paramiko==2.4.2
 parsley==1.3
-paste==2.0.3
+paste==3.0.4
 pastedeploy==1.5.2
 pastescript==2.0.2
 pbr==4.2.0

lib/galaxy/jobs/__init__.py

@@ -1198,9 +1198,6 @@ def enqueue(self):
         self.sa_session.flush()
 
     def _set_object_store_ids(self, job):
-        if self.app.config.legacy_eager_objectstore_initialization:
-            return
-
         if job.object_store_id:
             # We aren't setting this during job creation anymore, but some existing
             # jobs may have this set. Skip this following code if that is the case.

lib/galaxy/tools/xsd/galaxy.xsd

@@ -347,7 +347,7 @@ Read more about configuring Galaxy to run Docker jobs
     </xs:attribute>
     <xs:attribute name="split_inputs" type="xs:string">
       <xs:annotation>
-        <xs:documentation xml:lang="en">A comma separated list of data inputs to split for job parallelization.</xs:documentation>
+        <xs:documentation xml:lang="en">A comma-separated list of data inputs to split for job parallelization.</xs:documentation>
       </xs:annotation>
     </xs:attribute>
     <xs:attribute name="split_size" type="xs:string">
@@ -362,7 +362,7 @@ Read more about configuring Galaxy to run Docker jobs
     </xs:attribute>
     <xs:attribute name="shared_inputs" type="xs:string">
       <xs:annotation>
-        <xs:documentation xml:lang="en">A comma separated list of data inputs that should not be split for this tool, Galaxy will infer this if not present and so this potentially never needs to be set.</xs:documentation>
+        <xs:documentation xml:lang="en">A comma-separated list of data inputs that should not be split for this tool, Galaxy will infer this if not present and so this potentially never needs to be set.</xs:documentation>
       </xs:annotation>
     </xs:attribute>
   </xs:complexType>
@@ -1107,6 +1107,11 @@ non-optional composite inputs must be specified as part of the ``param``.
         <xs:documentation xml:lang="en">Type of collection to create.</xs:documentation>
       </xs:annotation>
     </xs:attribute>
+    <xs:attribute name="tags" type="xs:string">
+      <xs:annotation>
+        <xs:documentation xml:lang="en">Comma separated list of tags to apply to the dataset (only works for elements of collections - e.g. ``element`` XML tags).</xs:documentation>
+      </xs:annotation>
+    </xs:attribute>
   </xs:complexType>
   <xs:complexType name="TestOutput">
     <xs:annotation>
@@ -2355,7 +2360,7 @@ file. Use the file extension.</xs:documentation>
 This is only valid if ``type`` is ``data_collection``. Restrict the kind of
 collection that can be consumed by this parameter (e.g. ``paired``,
 ``list:paired``, ``list``). Multiple such collection types can be specified here
-as a comma separated list.
+as a comma-separated list.
 
               ]]></xs:documentation>
           </xs:annotation>