Merge branch 'release_16.07' into dev

Conflicts:
	run.sh
	static/scripts/bundled/analysis.bundled.js
	static/scripts/bundled/analysis.bundled.js.map
	static/scripts/bundled/libs.bundled.js
	static/scripts/bundled/libs.bundled.js.map

lib/galaxy/jobs/runners/slurm.py

@@ -43,7 +43,7 @@ class SlurmJobRunner( DRMAAJobRunner ):
             cmd = [ 'scontrol', '-o' ]
             if '.' in ajs.job_id:
                 # custom slurm-drmaa-with-cluster-support job id syntax
-                job_id, cluster = ajs.job_id.split('.', maxsplit=1)
+                job_id, cluster = ajs.job_id.split('.', 1)
                 cmd.extend( [ '-M', cluster ] )
             else:
                 job_id = ajs.job_id

lib/galaxy/tools/actions/__init__.py

@@ -611,7 +611,7 @@ class DefaultToolAction( object ):
         """
         if output.actions:
             for action in output.actions.actions:
-                if action.tag == "metadata":
+                if action.tag == "metadata" and action.default:
                     metadata_new_value = fill_template( action.default, context=params ).split(",")
                     dataset.metadata.__setattr__(str(action.name), metadata_new_value)
 

lib/galaxy/util/template.py

@@ -1,7 +1,16 @@
+"""Entry point for the usage of Cheetah templating within Galaxy."""
 from Cheetah.Template import Template
 
 
 def fill_template( template_text, context=None, **kwargs ):
+    """Fill a cheetah template out for specified context.
+
+    If template_text is None, an exception will be thrown, if context
+    is None (the default) - keyword arguments to this function will be used
+    as the context.
+    """
+    if template_text is None:
+        raise TypeError("Template text specified as None to fill_template.")
     if not context:
         context = kwargs
     return str( Template( source=template_text, searchList=[context] ) )

lib/galaxy/webapps/galaxy/api/history_contents.py

@@ -312,7 +312,7 @@ class HistoryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrar
         return rval
 
     def __create_dataset_collection( self, trans, history, payload, **kwd ):
-        source = kwd.get("source", "new_collection")
+        source = kwd.get( "source", payload.get( "source", "new_collection" ) )
         service = trans.app.dataset_collections_service
         if source == "new_collection":
             create_params = api_payload_to_create_params( payload )

test/functional/tools/dbkey_output_action.xml

@@ -0,0 +1,36 @@
+<tool id="dbkey_output_action" name="dbkey_output_action" version="0.1.0">
+    <command>echo foo > $mapped_reads</command>
+    <inputs>
+        <param name="input" type="data" />
+        <param name="index" type="select" label="Using reference genome">
+          <options from_data_table="test_fasta_indexes">
+            <filter type="data_meta" ref="input" key="dbkey" column="1" />
+            <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" />
+          </options>
+        </param>
+    </inputs>
+    <outputs>
+        <data format="txt" name="mapped_reads">
+            <actions>
+                <action type="metadata" name="dbkey">
+                    <option type="from_data_table" name="test_fasta_indexes" column="1" offset="0">
+                        <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
+                        <filter type="param_value" ref="index" column="0"/>
+                    </option>
+                </action>
+            </actions>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="simple_line.txt" dbkey="hg18" />
+            <param name="index" value="hg18"/>
+            <output name="mapped_reads">
+                <metadata name="dbkey" value="hg18" />
+                <assert_contents>
+                    <has_text text="foo" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+</tool>

test/functional/tools/samples_tool_conf.xml

@@ -21,6 +21,7 @@
   <tool file="inputs_as_json.xml" />
   <tool file="dbkey_filter_input.xml" />
   <tool file="dbkey_filter_multi_input.xml" />
+  <tool file="dbkey_output_action.xml" />
   <tool file="composite_output.xml" />
   <tool file="composite_output_tests.xml" />
   <tool file="unicode_stream.xml" />