From cdd15204349abbca96167eaaaffc0214bdfdafc3 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Tue, 9 Oct 2018 08:54:24 -0400 Subject: [PATCH] Rework most test workflows to label maps for step definitions --- test/api/test_workflows.py | 485 +++++++++++++-------------- test/api/test_workflows_from_yaml.py | 71 ++-- test/base/workflow_fixtures.py | 136 ++++---- 3 files changed, 341 insertions(+), 351 deletions(-) diff --git a/test/api/test_workflows.py b/test/api/test_workflows.py index 14ea5f5601c..dd397c5fdc5 100644 --- a/test/api/test_workflows.py +++ b/test/api/test_workflows.py @@ -38,18 +38,20 @@ outputs: outer_output: outputSource: second_cat/out_file1 steps: - - tool_id: cat1 - label: first_cat + first_cat: + tool_id: cat1 in: input1: outer_input - - run: + nested_workflow: + run: class: GalaxyWorkflow inputs: - id: inner_input outputs: - source: 1#out_file1 steps: - - tool_id: random_lines1 + random: + tool_id: random_lines1 state: num_lines: 1 input: @@ -57,11 +59,10 @@ steps: seed_source: seed_source_selector: set_seed seed: asdf - label: nested_workflow in: inner_input: first_cat/out_file1 - - tool_id: cat1 - label: second_cat + second_cat: + tool_id: cat1 state: input1: $link: nested_workflow#1:out_file1 @@ -500,26 +501,23 @@ steps: workflow_id = self._upload_yaml_workflow(""" class: GalaxyWorkflow inputs: - - id: outer_input + outer_input: data steps: - - run: + inner_workflow: + run: class: GalaxyWorkflow inputs: - - id: inner_input + inner_input: type: collection collection_type: "list:paired" outputs: - - id: workflow_output - source: collection_type_source#list_output + workflow_output: + outputSource: collection_type_source/list_output steps: - - label: text_input1 - type: input_collection - collection_type: "list:paired" - - tool_id: collection_type_source - label: collection_type_source + collection_type_source: + tool_id: collection_type_source in: input_collect: inner_input - label: inner_workflow in: inner_input: outer_input """) @@ -586,7 +584,8 @@ steps: workflow_version_01 = self._upload_yaml_workflow(""" class: GalaxyWorkflow steps: - - tool_id: multiple_versions + multiple: + tool_id: multiple_versions tool_version: "0.1" state: inttest: 0 @@ -598,7 +597,8 @@ steps: workflow_version_02 = self._upload_yaml_workflow(""" class: GalaxyWorkflow steps: - - tool_id: multiple_versions + multiple: + tool_id: multiple_versions tool_version: "0.2" state: inttest: 1 @@ -634,11 +634,13 @@ steps: workflow_id = self._upload_yaml_workflow(""" class: GalaxyWorkflow steps: - - tool_id: job_properties + job_props: + tool_id: job_properties state: thebool: true failbool: true - - tool_id: identifier_multiple_in_conditional + identifier: + tool_id: identifier_multiple_in_conditional state: outer_cond: cond_param_outer: true @@ -670,14 +672,15 @@ steps: workflow_id = self._upload_yaml_workflow(""" class: GalaxyWorkflow steps: - - tool_id: job_properties + job_props: + tool_id: job_properties state: thebool: true failbool: true - - tool_id: identifier_collection - state: - input1: - $link: 0#list_output + identifier: + tool_id: identifier_collection + in: + input1: job_props/list_output """) with self.dataset_populator.test_history() as history_id: invocation_id = self.__invoke_workflow(history_id, workflow_id) @@ -704,16 +707,16 @@ steps: job_summary = self._run_jobs(""" class: GalaxyWorkflow inputs: - - id: input_datasets - type: collection + input_datasets: collection steps: - - label: fail_identifier_1 + fail_identifier_1: tool_id: fail_identifier state: failbool: true in: input1: input_datasets - - tool_id: identifier_collection + identifier: + tool_id: identifier_collection in: input1: fail_identifier_1/out_file1 test_data: @@ -784,27 +787,20 @@ test_data: 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 + test_input_3: data steps: - - label: test_input_1 - type: input - - label: test_input_2 - type: input - - label: test_input_3 - type: input - - label: split_up + split_up: tool_id: collection_split_on_column - state: - input1: - $link: test_input_2 - - label: min_repeat + in: + input1: test_input_2 + min_repeat: tool_id: min_repeat - state: - queries: - - input: - $link: test_input_1 - queries2: - - input2: - $link: split_up#split_output + in: + queries_0|input: test_input_1 + queries2_0|input2: split_up/split_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") @@ -829,33 +825,27 @@ steps: with self.dataset_populator.test_history() as history_id: workflow_id = self._upload_yaml_workflow(""" class: GalaxyWorkflow +inputs: + text_input1: data + text_input2: data steps: - - label: text_input1 - type: input - - label: text_input2 - type: input - - label: cat_inputs + cat_inputs: tool_id: cat1 - state: - input1: - $link: text_input1 - queries: - - input2: - $link: text_input2 - - label: split_up_1 + in: + input1: text_input1 + queries_0|input2: text_input2 + split_up_1: tool_id: collection_split_on_column - state: - input1: - $link: cat_inputs#out_file1 - - label: split_up_2 + in: + input1: cat_inputs/out_file1 + split_up_2: tool_id: collection_split_on_column - state: - input1: - $link: split_up_1#split_output - - tool_id: cat - state: - input1: - $link: split_up_2#split_output + in: + input1: split_up_1/split_output + cat_output: + tool_id: cat + in: + input1: split_up_2/split_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\t30.0\nsamp2\t40.0\n") @@ -875,25 +865,20 @@ steps: with self.dataset_populator.test_history() as history_id: self._run_jobs(""" class: GalaxyWorkflow +inputs: + input_fastqs: collection + reference: data steps: - - label: input_fastqs - type: input_collection - - label: reference - type: input - - label: map_over_mapper + map_over_mapper: tool_id: mapper - state: - input1: - $link: input_fastqs - reference: - $link: reference - - label: pileup + in: + input1: input_fastqs + reference: reference + pileup: tool_id: pileup - state: - input1: - $link: map_over_mapper#out_file1 - reference: - $link: reference + in: + input1: map_over_mapper/out_file1 + reference: reference test_data: input_fastqs: type: list @@ -1018,16 +1003,16 @@ inputs: test_input_1: data test_input_2: data steps: - - label: first_cat + first_cat: tool_id: cat1 in: input1: test_input_1 - - label: zip_it + zip_it: tool_id: "__ZIP_COLLECTION__" in: input_forward: first_cat/out_file1 input_reverse: test_input_2 - - label: concat_pair + concat_pair: tool_id: collection_paired_test in: f1: zip_it/output @@ -1050,12 +1035,13 @@ steps: self._run_jobs(""" class: GalaxyWorkflow steps: - - tool_id: 'collection_creates_dynamic_nested' - label: 'nested' + nested: + tool_id: collection_creates_dynamic_nested state: sleep_time: 0 foo: 'dummy' - - tool_id: '__FLATTEN__' + flatten: + tool_id: '__FLATTEN__' state: input: $link: nested#list_output @@ -1083,19 +1069,20 @@ inputs: input_c: collection steps: - - label: mixed_collection + mixed_collection: tool_id: exit_code_from_file state: input: $link: input_c - - label: filtered_collection + filtered_collection: tool_id: "__FILTER_FAILED_DATASETS__" state: input: $link: mixed_collection#out_file1 - - tool_id: cat1 + cat: + tool_id: cat1 state: input1: $link: filtered_collection @@ -1141,8 +1128,8 @@ outputs: wf_output_1: outputSource: first_cat/out_file1 steps: - - tool_id: cat1 - label: first_cat + first_cat: + tool_id: cat1 in: input1: input1 """, test_data={"input1": "hello world"}, history_id=history_id) @@ -1170,8 +1157,8 @@ outputs: wf_output_1: outputSource: first_cat/out_file1 steps: - - tool_id: cat - label: first_cat + first_cat: + tool_id: cat in: input1: input1 """, test_data=""" @@ -1210,8 +1197,8 @@ outputs: wf_output_1: outputSource: first_cat/out_file1 steps: - - tool_id: cat - label: first_cat + first_cat: + tool_id: cat in: input1: input1 """, test_data=""" @@ -1252,7 +1239,7 @@ outputs: wf_output_1: outputSource: split_up/paired_output steps: - - label: split_up + split_up: tool_id: collection_creates_pair in: input1: text_input @@ -1334,11 +1321,12 @@ outputs: outer_output: outputSource: second_cat/out_file1 steps: - - tool_id: cat1 - label: first_cat + first_cat: + tool_id: cat1 in: input1: outer_input - - run: + nested_workflow: + run: class: GalaxyWorkflow inputs: inner_input: data @@ -1346,8 +1334,8 @@ steps: workflow_output: outputSource: random_lines/out_file1 steps: - - tool_id: random_lines1 - label: random_lines + random_lines: + tool_id: random_lines1 state: num_lines: 2 input: @@ -1355,15 +1343,14 @@ steps: seed_source: seed_source_selector: set_seed seed: asdf - label: nested_workflow in: inner_input: first_cat/out_file1 - - tool_id: split - label: split + split: + tool_id: split in: input1: nested_workflow/workflow_output - - tool_id: cat_list - label: second_cat + second_cat: + tool_id: cat_list in: input1: split/output @@ -1392,11 +1379,12 @@ outputs: outer_output: outputSource: second_cat/out_file1 steps: - - tool_id: cat1 - label: first_cat + first_cat: + tool_id: cat1 in: input1: outer_input - - run: + nested_workflow: + run: class: GalaxyWorkflow inputs: inner_input: data @@ -1404,8 +1392,8 @@ steps: workflow_output: outputSource: inner_cat/out_file1 steps: - - tool_id: random_lines1 - label: random_lines + random_lines: + tool_id: random_lines1 state: num_lines: 2 input: @@ -1413,20 +1401,18 @@ steps: seed_source: seed_source_selector: set_seed seed: asdf - - tool_id: split - label: split + split: + tool_id: split in: input1: random_lines/out_file1 - - tool_id: cat1 - label: inner_cat + inner_cat: + tool_id: cat1 in: input1: split/output - - label: nested_workflow in: inner_input: first_cat/out_file1 - - tool_id: cat_list - label: second_cat + second_cat: + tool_id: cat_list in: input1: nested_workflow/workflow_output """, test_data=""" @@ -1449,11 +1435,12 @@ outputs: outer_output: outputSource: second_cat/out_file1 steps: - - tool_id: cat1 - label: first_cat + first_cat: + tool_id: cat1 in: input1: outer_input - - run: + nested_workflow: + run: class: GalaxyWorkflow inputs: inner_input: data @@ -1461,8 +1448,8 @@ steps: workflow_output: outputSource: split/output steps: - - tool_id: random_lines1 - label: random_lines + random_lines: + tool_id: random_lines1 state: num_lines: 2 input: @@ -1470,15 +1457,14 @@ steps: seed_source: seed_source_selector: set_seed seed: asdf - - tool_id: split - label: split + split: + tool_id: split in: input1: random_lines/out_file1 - label: nested_workflow in: inner_input: first_cat/out_file1 - - tool_id: cat_list - label: second_cat + second_cat: + tool_id: cat_list in: input1: nested_workflow/workflow_output """, test_data=""" @@ -1501,12 +1487,12 @@ outputs: count_list: outputSource: count_list/out_file1 steps: - - tool_id: empty_list - label: empty_list + empty_list: + tool_id: empty_list in: input1: input1 - - tool_id: random_lines1 - label: random_lines + random_lines: + tool_id: random_lines1 state: num_lines: 2 input: @@ -1514,8 +1500,8 @@ steps: seed_source: seed_source_selector: set_seed seed: asdf - - tool_id: count_list - label: count_list + count_list: + tool_id: count_list in: input1: random_lines/out_file1 """, test_data=""" @@ -1533,7 +1519,8 @@ class: GalaxyWorkflow inputs: text_input1: collection steps: - - tool_id: collection_type_source_map_over + map_over: + tool_id: collection_type_source_map_over in: input_collect: text_input1 """, test_data=""" @@ -1557,12 +1544,12 @@ outputs: count_multi_file: outputSource: count_multi_file/out_file1 steps: - - tool_id: empty_list - label: empty_list + empty_list: + tool_id: empty_list in: input1: input1 - - tool_id: random_lines1 - label: random_lines + random_lines: + tool_id: random_lines1 state: num_lines: 2 input: @@ -1570,8 +1557,8 @@ steps: seed_source: seed_source_selector: set_seed seed: asdf - - tool_id: count_multi_file - label: count_multi_file + count_multi_file: + tool_id: count_multi_file in: input1: random_lines/out_file1 """, test_data=""" @@ -1731,12 +1718,12 @@ inputs: type: collection collection_type: list steps: - - tool_id: cat - label: first_cat + first_cat: + tool_id: cat in: input1: input1 - - tool_id: cat - label: second_cat + second_cat: + tool_id: cat in: input1: first_cat/out_file1 """) @@ -1770,29 +1757,29 @@ class: GalaxyWorkflow inputs: test_input: data steps: -- label: first_cat - tool_id: cat1 - in: - input1: test_input -- label: the_pause - type: pause - in: - input: first_cat/out_file1 -- label: second_cat - tool_id: cat1 - in: - input1: the_pause -- label: third_cat - tool_id: random_lines1 - in: - $step: second_cat - state: - num_lines: 1 - input: - $link: test_input - seed_source: - seed_source_selector: set_seed - seed: asdf + first_cat: + tool_id: cat1 + in: + input1: test_input + the_pause: + type: pause + in: + input: first_cat/out_file1 + second_cat: + tool_id: cat1 + in: + input1: the_pause + third_cat: + tool_id: random_lines1 + in: + $step: second_cat + state: + num_lines: 1 + input: + $link: test_input + seed_source: + seed_source_selector: set_seed + seed: asdf """, test_data={"test_input": "hello world"}, history_id=history_id, wait=False, round_trip_format_conversion=True) history_id = run_summary.history_id workflow_id = run_summary.workflow_id @@ -1817,18 +1804,18 @@ class: GalaxyWorkflow inputs: text_input: text steps: -- tool_id: validation_repeat - state: - r2: - - text: - $link: text_input + validation: + tool_id: validation_repeat + state: + r2: + - text: + $link: text_input """, test_data=""" text_input: value: "abd" type: raw """, history_id=history_id, wait=True, round_trip_format_conversion=True) - time.sleep(10) - self.workflow_populator.wait_for_invocation(run_summary.workflow_id, run_summary.invocation_id) + self.wait_for_invocation_and_jobs(history_id, run_summary.workflow_id, run_summary.invocation_id) jobs = self._history_jobs(history_id) assert len(jobs) == 1 @@ -1839,11 +1826,12 @@ class: GalaxyWorkflow inputs: text_input: text steps: -- tool_id: validation_repeat - state: - r2: - - text: - $link: text_input + validation: + tool_id: validation_repeat + state: + r2: + - text: + $link: text_input """, test_data=""" text_input: value: "" @@ -1858,16 +1846,16 @@ inputs: data_input: data text_input: text steps: -- label: randomlines - tool_id: random_lines1 - state: - num_lines: 1 - input: - $link: data_input - seed_source: - seed_source_selector: set_seed - seed: - $link: text_input + randomlines: + tool_id: random_lines1 + state: + num_lines: 1 + input: + $link: data_input + seed_source: + seed_source_selector: set_seed + seed: + $link: text_input """, test_data=""" data_input: value: 1.bed @@ -2041,8 +2029,8 @@ outputs: wf_output_1: outputSource: output_filter/out_1 steps: - - tool_id: output_filter - label: output_filter + output_filter: + tool_id: output_filter state: produce_out_1: False filter_text_1: '1' @@ -2063,8 +2051,8 @@ inputs: type: collection collection_type: list steps: - - tool_id: cat - label: first_cat + first_cat: + tool_id: cat in: input1: input1 outputs: @@ -2098,8 +2086,8 @@ inputs: type: collection collection_type: list steps: - - tool_id: cat - label: first_cat + first_cat: + tool_id: cat in: input1: input1 outputs: @@ -2151,7 +2139,8 @@ input1: class: GalaxyWorkflow inputs: [] steps: - - tool_id: create_2 + create_2: + tool_id: create_2 state: sleep_time: 0 outputs: @@ -2183,8 +2172,8 @@ class: GalaxyWorkflow inputs: input1: data steps: - - tool_id: fail_identifier - label: first_fail + first_fail: + tool_id: fail_identifier state: failbool: true input1: @@ -2192,7 +2181,8 @@ steps: outputs: out_file1: rename: "cat1 out" - - tool_id: cat + cat: + tool_id: cat in: input1: first_fail/out_file1 outputs: @@ -2230,8 +2220,8 @@ class: GalaxyWorkflow inputs: input1: data steps: - - tool_id: cat - label: first_cat + first_cat: + tool_id: cat in: input1: input1 outputs: @@ -2256,8 +2246,8 @@ inputs: input1: data input2: data steps: - - tool_id: cat - label: first_cat + first_cat: + tool_id: cat state: input1: $link: input1 @@ -2290,7 +2280,8 @@ inputs: fasta_input: data fastq_input: data steps: - - tool_id: mapper2 + mapping: + tool_id: mapper2 state: fastq_input: fastq_input_selector: single @@ -2328,7 +2319,8 @@ inputs: fasta_input: data fastq_inputs: data steps: - - tool_id: mapper2 + mapping: + tool_id: mapper2 state: fastq_input: fastq_input_selector: paired_collection @@ -2370,7 +2362,8 @@ class: GalaxyWorkflow inputs: input1: data steps: - - tool_id: collection_creates_pair + create_pair: + tool_id: collection_creates_pair state: input1: $link: input1 @@ -2398,8 +2391,8 @@ inputs: type: data_collection_input collection_type: list steps: - - tool_id: cat - label: first_cat + first_cat: + tool_id: cat in: input1: input1 outputs: @@ -2431,7 +2424,7 @@ class: GalaxyWorkflow inputs: input1: data steps: - - label: first_cat + first_cat: tool_id: cat in: input1: input1 @@ -2442,7 +2435,7 @@ steps: - "group:condition:treated" - "group:type:single-read" - "machine:illumina" - - label: second_cat + second_cat: tool_id: cat in: input1: first_cat/out_file1 @@ -2474,7 +2467,8 @@ class: GalaxyWorkflow inputs: input1: data steps: - - tool_id: collection_creates_pair + create_pair: + tool_id: collection_creates_pair in: input1: input1 outputs: @@ -2502,8 +2496,8 @@ inputs: type: collection collection_type: list steps: - - tool_id: cat - label: first_cat + first_cat: + tool_id: cat in: input1: input1 outputs: @@ -2533,15 +2527,16 @@ class: GalaxyWorkflow inputs: input1: data steps: - - tool_id: cat - label: first_cat + first_cat: + tool_id: cat in: input1: input1 outputs: out_file1: add_tags: - "name:foo" - - tool_id: collection_creates_pair + create_pair: + tool_id: collection_creates_pair in: input1: first_cat#out_file1 outputs: @@ -2603,15 +2598,15 @@ class: GalaxyWorkflow inputs: test_input: data steps: - - label: first_cat + first_cat: tool_id: cat1 in: input1: test_input - - label: the_pause + the_pause: type: pause in: input: first_cat/out_file1 - - label: second_cat + second_cat: tool_id: cat1 in: input1: the_pause @@ -2659,16 +2654,16 @@ outputs: wf_output_1: outputSource: third_cat/out_file1 steps: - - tool_id: cat1 - label: first_cat + first_cat: + tool_id: cat1 in: input1: input1 - - tool_id: cat1 - label: second_cat + second_cat: + tool_id: cat1 in: input1: first_cat/out_file1 - - tool_id: cat1 - label: third_cat + third_cat: + tool_id: cat1 in: input1: second_cat/out_file1 outputs: @@ -2765,10 +2760,11 @@ steps: workflow_id = self._upload_yaml_workflow(""" class: GalaxyWorkflow steps: - - tool_id: validation_repeat - state: - r2: - - text: "abd" + validation: + tool_id: validation_repeat + state: + r2: + - text: "abd" """) workflow_request = dict( history="hist_id=%s" % history_id, @@ -2792,10 +2788,11 @@ steps: self._run_jobs(""" class: GalaxyWorkflow steps: - - tool_id: validation_repeat - state: - r2: - - text: "" + validation: + tool_id: validation_repeat + state: + r2: + - text: "" """, history_id=history_id, wait=False, expected_response=400) def _run_validation_workflow_with_substitions(self, substitions): @@ -2958,7 +2955,7 @@ class: GalaxyWorkflow inputs: input_c: collection steps: - - label: cat1 + cat1: tool_id: cat1 in: input1: input_c diff --git a/test/api/test_workflows_from_yaml.py b/test/api/test_workflows_from_yaml.py index ff67c99b3bc..9a10f32bea2 100644 --- a/test/api/test_workflows_from_yaml.py +++ b/test/api/test_workflows_from_yaml.py @@ -125,11 +125,12 @@ class: GalaxyWorkflow inputs: outer_input: data steps: - - tool_id: cat1 - label: first_cat + first_cat: + tool_id: cat1 in: input1: outer_input - - run: + nested_workflow: + run: class: GalaxyWorkflow inputs: inner_input: data @@ -142,7 +143,6 @@ steps: seed_source: seed_source_selector: set_seed seed: asdf - label: nested_workflow in: inner_input: first_cat/out_file1 """, client_convert=False) @@ -200,18 +200,18 @@ $graph: inputs: outer_input: data steps: - - tool_id: cat - label: outer_cat - in: - input1: outer_input - - run: '#nested' - label: nested_workflow_1 - in: - inner_input: outer_cat/out_file1 - - run: '#nested' - label: nested_workflow_2 - in: - inner_input: nested_workflow_1/inner_output + outer_cat: + tool_id: cat + in: + input1: outer_input + nested_workflow_1: + run: '#nested' + in: + inner_input: outer_cat/out_file1 + nested_workflow_2: + run: '#nested' + in: + inner_input: nested_workflow_1/inner_output """ history_id = self.dataset_populator.new_history() self._run_jobs(duplicate_subworkflow_invocate_wf, test_data={"outer_input": "hello world"}, history_id=history_id, client_convert=False) @@ -222,18 +222,18 @@ $graph: workflow_id = self._upload_yaml_workflow(""" class: GalaxyWorkflow steps: - - label: test_input + test_input: type: input - - label: first_cat + first_cat: tool_id: cat1 state: input1: $link: test_input - - label: the_pause + the_pause: type: pause in: input: first_cat/out_file1 - - label: second_cat + second_cat: tool_id: cat1 in: input1: the_pause @@ -243,25 +243,22 @@ steps: def test_implicit_connections(self): workflow_id = self._upload_yaml_workflow(""" class: GalaxyWorkflow +inputs: + test_input: data steps: - - label: test_input - type: input - - label: first_cat + first_cat: tool_id: cat1 - state: - input1: - $link: test_input - - label: the_pause + in: + input1: test_input + the_pause: type: pause - connect: - input: - - first_cat#out_file1 - - label: second_cat + in: + input: first_cat/out_file1 + second_cat: tool_id: cat1 - state: - input1: - $link: the_pause - - label: third_cat + in: + input1: the_pause + third_cat: tool_id: cat1 connect: $step: second_cat @@ -276,7 +273,7 @@ steps: self._run_jobs(""" class: GalaxyWorkflow steps: - - label: test_input + test_input: tool_id: disambiguate_cond state: p3: @@ -291,7 +288,7 @@ steps: self._run_jobs(""" class: GalaxyWorkflow steps: - - label: test_input + test_input: tool_id: disambiguate_cond state: p3: diff --git a/test/base/workflow_fixtures.py b/test/base/workflow_fixtures.py index 59e7d43876d..519dd750131 100644 --- a/test/base/workflow_fixtures.py +++ b/test/base/workflow_fixtures.py @@ -5,7 +5,8 @@ class: GalaxyWorkflow doc: | Simple workflow that no-op cats a file and then selects 10 random lines. inputs: - - id: the_input + the_input: + type: data doc: input doc steps: - tool_id: cat1 @@ -32,8 +33,8 @@ class: GalaxyWorkflow inputs: input1: data steps: - - tool_id: cat - label: first_cat + first_cat: + tool_id: cat in: input1: input1 queries_0|input2: input1 @@ -45,7 +46,8 @@ class: GalaxyWorkflow inputs: input1: data steps: - - tool_id: multiple_versions + mul_versions: + tool_id: multiple_versions tool_version: "0.0.1" state: inttest: 8 @@ -57,7 +59,8 @@ class: GalaxyWorkflow inputs: input1: data steps: - - tool_id: multiple_versions + mul_versions: + tool_id: multiple_versions tool_version: "0.0.1" state: inttest: "moocow" @@ -69,11 +72,12 @@ class: GalaxyWorkflow inputs: text_input: data steps: - - label: split_up + split_up: tool_id: collection_creates_pair in: input1: text_input - - tool_id: collection_paired_test + paired: + tool_id: collection_paired_test in: f1: split_up/paired_output test_data: @@ -87,25 +91,21 @@ test_data: WORKFLOW_WITH_DYNAMIC_OUTPUT_COLLECTION = """ class: GalaxyWorkflow +inputs: + text_input1: data + text_input2: data steps: - - label: text_input1 - type: input - - label: text_input2 - type: input - - label: cat_inputs + cat_inputs: tool_id: cat1 - state: - input1: - $link: text_input1 - queries: - - input2: - $link: text_input2 - - label: split_up + in: + input1: text_input1 + queries_0|input2: text_input2 + split_up: tool_id: collection_split_on_column - state: - input1: - $link: cat_inputs#out_file1 - - tool_id: cat_list + in: + input1: cat_inputs/out_file1 + cat_list: + tool_id: cat_list in: input1: split_up/split_output test_data: @@ -125,8 +125,8 @@ inputs: type: collection collection_type: list steps: - - tool_id: cat - label: cat + cat: + tool_id: cat in: input1: input1 """ @@ -156,7 +156,7 @@ class: GalaxyWorkflow inputs: input_c: collection steps: - - label: apply + apply: tool_id: __APPLY_RULES__ state: input: @@ -170,8 +170,8 @@ steps: mapping: - type: list_identifiers columns: [0, 1] - - tool_id: random_lines1 - label: random_lines + random_lines: + tool_id: random_lines1 state: num_lines: 1 input: @@ -195,7 +195,7 @@ class: GalaxyWorkflow inputs: input_c: collection steps: - - label: apply + apply: tool_id: __APPLY_RULES__ state: input: @@ -209,8 +209,8 @@ steps: mapping: - type: list_identifiers columns: [0, 1] - - tool_id: collection_creates_list - label: copy_list + copy_list: + tool_id: collection_creates_list in: input1: apply/output test_data: @@ -232,11 +232,12 @@ outputs: outer_output: outputSource: second_cat/out_file1 steps: - - tool_id: cat1 - label: first_cat + first_cat: + tool_id: cat1 in: input1: outer_input - - run: + nested_workflow: + run: class: GalaxyWorkflow inputs: inner_input: data @@ -244,8 +245,8 @@ steps: workflow_output: outputSource: random_lines/out_file1 steps: - - tool_id: random_lines1 - label: random_lines + random_lines: + tool_id: random_lines1 state: num_lines: 1 input: @@ -253,17 +254,13 @@ steps: seed_source: seed_source_selector: set_seed seed: asdf - label: nested_workflow in: inner_input: first_cat/out_file1 - - tool_id: cat1 - label: second_cat - state: - input1: - $link: nested_workflow#workflow_output - queries: - - input2: - $link: nested_workflow#workflow_output + second_cat: + tool_id: cat1 + in: + input1: nested_workflow/workflow_output + queries_0|input2: nested_workflow/workflow_output """ @@ -275,7 +272,8 @@ outputs: outer_output: outputSource: nested_workflow/workflow_output steps: - - run: + nested_workflow: + run: class: GalaxyWorkflow inputs: inner_input: data @@ -293,7 +291,6 @@ steps: seed_source: seed_source_selector: set_seed seed: asdf - label: nested_workflow in: inner_input: outer_input """ @@ -304,15 +301,16 @@ class: GalaxyWorkflow inputs: input1: data steps: - - tool_id: cat1 - label: first_cat + first_cat: + tool_id: cat1 outputs: out_file1: hide: true rename: "the new value" in: input1: input1 - - tool_id: cat1 + second_cat: + tool_id: cat1 in: input1: first_cat/out_file1 """ @@ -323,7 +321,8 @@ class: GalaxyWorkflow inputs: input1: data steps: - - tool_id: random_lines1 + random: + tool_id: random_lines1 runtime_inputs: - num_lines state: @@ -340,11 +339,12 @@ class: GalaxyWorkflow inputs: input1: data steps: - - label: the_pause + the_pause: type: pause in: input: input1 - - tool_id: random_lines1 + random: + tool_id: random_lines1 runtime_inputs: - num_lines state: @@ -360,8 +360,8 @@ class: GalaxyWorkflow inputs: input1: data steps: - - tool_id: cat - label: first_cat + first_cat: + tool_id: cat state: input1: $link: input1 @@ -380,11 +380,10 @@ class: GalaxyWorkflow inputs: input1: data steps: - - tool_id: cat - label: first_cat - state: - input1: - $link: input1 + first_cat: + tool_id: cat + in: + input1: input1 outputs: out_file1: rename: "${replaceme} suffix" @@ -398,7 +397,8 @@ outputs: outer_output: outputSource: nested_workflow/workflow_output steps: - - run: + nested_workflow: + run: class: GalaxyWorkflow inputs: inner_input: data @@ -413,7 +413,6 @@ steps: outputs: out_file1: rename: "${replaceme} suffix" - label: nested_workflow in: inner_input: outer_input """ @@ -426,12 +425,9 @@ outputs: wf_output_1: outputSource: first_cat/out_file1 steps: - - tool_id: cat1 - label: first_cat - state: - input1: - $link: input1 - queries: - - input2: - $link: input1 + first_cat: + tool_id: cat1 + in: + input1: input1 + queries_0|input2: input1 """