Merge pull request #889 from mvdbeek/sync_galaxy_xsd

Sync galaxy xsd and fix tests

Author: jmchilton

planemo/training/__init__.py

@@ -5,7 +5,7 @@
 from .tutorial import Tutorial
 
 
-class Training:
+class Training(object):
     """Class to describe a training."""
 
     def __init__(self, kwds):

planemo/training/tool_input.py

@@ -23,7 +23,7 @@
 SPACE = '    '
 
 
-class ToolInput():
+class ToolInput(object):
     """Class to describe a tool input / parameter and its value from a workflow."""
 
     def __init__(self, tool_inp_desc, wf_param_values, wf_steps, level, should_be_there=False, force_default=False):

planemo/training/topic.py

@@ -72,7 +72,7 @@
 """
 
 
-class Topic:
+class Topic(object):
     """Class to describe a training topic."""
 
     def __init__(self, name="new_topic", target="use", title="The new topic", summary="Summary", parent_dir="topics"):

planemo/training/tutorial.py

@@ -191,7 +191,7 @@
 """
 
 
-class Tutorial:
+class Tutorial(object):
     """Class to describe a training tutorial."""
 
     def __init__(self, training, topic, name="new_tuto", title="The new tutorial", zenodo_link=""):

planemo/training/utils.py

@@ -5,7 +5,7 @@
 import oyaml as yaml
 
 
-class Requirement:
+class Requirement(object):
     """Class to describe a training requirement."""
 
     def __init__(self, title="", req_type="internal", link="/introduction/"):
@@ -29,7 +29,7 @@ def export_to_ordered_dict(self):
         return req
 
 
-class Reference:
+class Reference(object):
     """Class to describe a training reference."""
 
     def __init__(self, authors="authors et al", title="the title", link="link", summary="Why this reference is useful"):

planemo/virtualenv.py

@@ -9,7 +9,7 @@
 from galaxy.tools.deps.commands import which
 
 
-DEFAULT_PYTHON_VERSION = "2.7"
+DEFAULT_PYTHON_VERSION = os.environ.get("PLANEMO_DEFAULT_PYTHON_VERSION", "2.7")
 
 
 def create_and_exit(virtualenv_path, **kwds):

planemo/xml/xsd/tool/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>
@@ -1074,6 +1074,11 @@ referenced input dataset. This is only valid if the corresponding parameter is
 of ``type`` ``data``.</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="TestCompositeData">
     <xs:annotation>
@@ -1102,6 +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>
@@ -2350,7 +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>

requirements.txt

@@ -1,19 +1,19 @@
 aenum
 BeautifulSoup4
+bioblend>=0.10.0
 Click
 configparser
-six>=1.7.0
-pyaml
-pyyaml
-oyaml
-bioblend>=0.10.0
+cwltool==1.0.20180820141117
 docutils
-jinja2
-glob2
-virtualenv
-lxml
-gxformat2>=0.2.0
 ephemeris>=0.8
 galaxy-lib>=18.5.15
+glob2
+gxformat2>=0.2.0
 html5lib>=0.9999999,!=0.99999999,!=0.999999999,!=1.0b10,!=1.0b09
-cwltool==1.0.20180820141117
+jinja2
+lxml
+oyaml
+pyaml
+pyyaml
+six>=1.7.0
+virtualenv

tox.ini

@@ -20,6 +20,7 @@ setenv =
     quick: PLANEMO_SKIP_GALAXY_TESTS=1
     py27: PLANEMO_SKIP_PYTHON3=1
     py36: PLANEMO_SKIP_PYTHON2=1
+    py36: PLANEMO_DEFAULT_PYTHON_VERSION=3
     gx: NOSE_ATTR=tests_galaxy_branch
     master: PLANEMO_TEST_GALAXY_BRANCH=master
     dev: PLANEMO_TEST_GALAXY_BRANCH=dev