From 0ecb4e7c595f7fb6cd6e648c4d770e1e97530424 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 7 Nov 2018 10:15:55 +0100
Subject: [PATCH 1/4] List tags as attribute of TestCollection

---
 lib/galaxy/tools/xsd/galaxy.xsd | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/lib/galaxy/tools/xsd/galaxy.xsd b/lib/galaxy/tools/xsd/galaxy.xsd
index 93cb78ee2ff..47341a32327 100644
--- a/lib/galaxy/tools/xsd/galaxy.xsd
+++ b/lib/galaxy/tools/xsd/galaxy.xsd
@@ -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>

From bff5d51245f76bfc0bbe5b71237b3709d9ff7079 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 7 Nov 2018 19:34:40 +0100
Subject: [PATCH 2/4] Use comma-separated instead of comma separated

---
 lib/galaxy/tools/xsd/galaxy.xsd | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/tools/xsd/galaxy.xsd b/lib/galaxy/tools/xsd/galaxy.xsd
index 47341a32327..2f50147a545 100644
--- a/lib/galaxy/tools/xsd/galaxy.xsd
+++ b/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>
@@ -2360,7 +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>

From 5e098857e5dee703741e070e24a40235fb5deff2 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 7 Nov 2018 20:08:21 +0100
Subject: [PATCH 3/4] Display test collection input in documentation

---
 doc/schema_template.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/doc/schema_template.md b/doc/schema_template.md
index dbf34c1859d..0b27c4a004b 100644
--- a/doc/schema_template.md
+++ b/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']

From 4760a0ac0f48b106f9a1cee348deeccc223eb64a Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 22 Aug 2018 17:33:51 +0200
Subject: [PATCH 4/4] Fix recursion issue in gff_filter_by_feature_count

---
 lib/galaxy/datatypes/util/gff_util.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/datatypes/util/gff_util.py b/lib/galaxy/datatypes/util/gff_util.py
index e81296a8cf7..421a5886c75 100644
--- a/lib/galaxy/datatypes/util/gff_util.py
+++ b/lib/galaxy/datatypes/util/gff_util.py
@@ -188,7 +188,7 @@ class GFFReaderWrapper(NiceReaderWrapper):
         if not self.seed_interval:
             while not self.seed_interval:
                 try:
-                    self.seed_interval = GenomicIntervalReader.next(self)
+                    self.seed_interval = super(GenomicIntervalReader, self).__next__()
                 except ParseError as e:
                     handle_parse_error(e)
                 # TODO: When no longer supporting python 2.4 use finally:
@@ -215,7 +215,7 @@ class GFFReaderWrapper(NiceReaderWrapper):
         feature_intervals.append(self.seed_interval)
         while True:
             try:
-                interval = GenomicIntervalReader.next(self)
+                interval = super(GenomicIntervalReader, self).__next__()
                 raw_size += len(self.current_line)
             except StopIteration as e:
                 # No more intervals to read, but last feature needs to be