diff --git a/lib/galaxy_test/api/test_workflows.py b/lib/galaxy_test/api/test_workflows.py index 34959006e46a..6fc213cdc5e3 100644 --- a/lib/galaxy_test/api/test_workflows.py +++ b/lib/galaxy_test/api/test_workflows.py @@ -2741,45 +2741,6 @@ def test_run_subworkflow_replacement_parameters(self): details = self.dataset_populator.get_history_dataset_details(history_id) assert details["name"] == "moocow suffix" - def test_placements_from_text_inputs_nested(self): - with self.dataset_populator.test_history() as history_id: - run_def = """ -class: GalaxyWorkflow -inputs: - replacemeouter: text -steps: - nested_workflow: - run: - class: GalaxyWorkflow - inputs: - replacemeinner: text - outputs: - workflow_output_1: - outputSource: create_2/out_file1 - workflow_output_2: - outputSource: create_2/out_file2 - steps: - create_2: - tool_id: create_2 - state: - sleep_time: 0 - outputs: - out_file1: - rename: "${replacemeinner} name" - out_file2: - rename: "${replacemeinner} name 2" - in: - replacemeinner: replacemeouter - -test_data: - replacemeouter: - value: moocow - type: raw -""" - self._run_jobs(run_def, history_id=history_id) - details = self.dataset_populator.get_history_dataset_details(history_id) - assert details["name"] == "moocow name 2", details["name"] - @skip_without_tool("random_lines1") def test_run_runtime_parameters_after_pause(self): with self.dataset_populator.test_history() as history_id: @@ -2839,44 +2800,6 @@ def run_test(workflow_text): run_test(NESTED_WORKFLOW_AUTO_LABELS_MODERN_SYNTAX) - @skip_without_tool("cat1") - @skip_without_tool("collection_paired_test") - def test_workflow_run_zip_collections(self): - with self.dataset_populator.test_history() as history_id: - workflow_id = self._upload_yaml_workflow( - """ -class: GalaxyWorkflow -inputs: - test_input_1: data - test_input_2: data -steps: - first_cat: - tool_id: cat1 - in: - input1: test_input_1 - zip_it: - tool_id: "__ZIP_COLLECTION__" - in: - input_forward: first_cat/out_file1 - input_reverse: test_input_2 - concat_pair: - tool_id: collection_paired_test - in: - f1: zip_it/output -""" - ) - hda1 = self.dataset_populator.new_dataset(history_id, content="samp1\t10.0\nsamp2\t20.0\n") - hda2 = self.dataset_populator.new_dataset(history_id, content="samp1\t20.0\nsamp2\t40.0\n") - self.dataset_populator.wait_for_history(history_id, assert_ok=True) - inputs = { - "0": self._ds_entry(hda1), - "1": self._ds_entry(hda2), - } - invocation_id = self.__invoke_workflow(workflow_id, inputs=inputs, history_id=history_id) - self.workflow_populator.wait_for_invocation_and_jobs(history_id, workflow_id, invocation_id) - content = self.dataset_populator.get_history_dataset_content(history_id) - assert content.strip() == "samp1\t10.0\nsamp2\t20.0\nsamp1\t20.0\nsamp2\t40.0" - @skip_without_tool("collection_paired_test") def test_workflow_flatten(self): with self.dataset_populator.test_history() as history_id: diff --git a/lib/galaxy_test/workflow/zip_collection.gxwf-tests.yml b/lib/galaxy_test/workflow/zip_collection.gxwf-tests.yml new file mode 100644 index 000000000000..e0e4ffc5ba69 --- /dev/null +++ b/lib/galaxy_test/workflow/zip_collection.gxwf-tests.yml @@ -0,0 +1,10 @@ +- doc: | + Test simple use of __ZIP_COLLECTION__ in a workflow. + job: + test_input_1: "samp1\t10.0\nsamp2\t20.0\n" + test_input_2: "samp1\t20.0\nsamp2\t40.0\n" + outputs: + out: + asserts: + - that: has_text + text: "samp1\t10.0\nsamp2\t20.0\nsamp1\t20.0\nsamp2\t40.0" diff --git a/lib/galaxy_test/workflow/zip_collection.gxwf.yml b/lib/galaxy_test/workflow/zip_collection.gxwf.yml new file mode 100644 index 000000000000..151e0ffd1aa6 --- /dev/null +++ b/lib/galaxy_test/workflow/zip_collection.gxwf.yml @@ -0,0 +1,21 @@ +class: GalaxyWorkflow +inputs: + test_input_1: data + test_input_2: data +outputs: + out: + outputSource: concat_pair/out1 +steps: + first_cat: + tool_id: cat + in: + input1: test_input_1 + zip_it: + tool_id: "__ZIP_COLLECTION__" + in: + input_forward: first_cat/out_file1 + input_reverse: test_input_2 + concat_pair: + tool_id: collection_paired_test + in: + f1: zip_it/output