Test cases demonstrating output collections in tools and workflows and a little YAML DSL for building Galaxy workflows.

gistfile1.py

    def test_workflow_run_output_collections(self):
        workflow_id = self._upload_yaml_workflow("""
- label: text_input
  type: input
- label: split_up
  tool_id: collection_creates_pair
  state:
    input1:
      $link: text_input
- tool_id: collection_paired_test
  state:
    f1:
      $link: split_up#paired_output
""")
        history_id = self.dataset_populator.new_history()
        hda1 = self.dataset_populator.new_dataset( history_id, content="a\nb\nc\nd\n" )
        inputs = {
            '0': self._ds_entry(hda1),
        }
        self.__invoke_workflow( history_id, workflow_id, inputs )
        time.sleep( 5 )
        self.dataset_populator.wait_for_history( history_id, assert_ok=True )
        self.assertEquals("a\nc\nb\nd\n", self.dataset_populator.get_history_dataset_content( history_id, hid=0 ) )

    def test_workflow_run_output_collection_mapping(self):
        workflow_id = self._upload_yaml_workflow("""
- type: input_collection
- tool_id: collection_creates_pair
  state:
    input1:
      $link: 0
- tool_id: collection_paired_test
  state:
    f1:
      $link: 1#paired_output
- tool_id: cat_list
  state:
    input1:
      $link: 2#out1
""")
        history_id = self.dataset_populator.new_history()
        hdca1 = self.dataset_collection_populator.create_list_in_history( history_id, contents=["a\nb\nc\nd\n", "e\nf\ng\nh\n"] ).json()
        self.dataset_populator.wait_for_history( history_id, assert_ok=True )
        inputs = {
            '0': self._ds_entry(hdca1),
        }
        self.__invoke_workflow( history_id, workflow_id, inputs )
        time.sleep( 5 )
        self.dataset_populator.wait_for_history( history_id, assert_ok=True )
        self.assertEquals("a\nc\nb\nd\ne\ng\nf\nh\n", self.dataset_populator.get_history_dataset_content( history_id, hid=0 ) )