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Rework most test workflows to label maps for step definitions

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This commit is contained in:
John Chilton
2018-10-12 13:41:13 -04:00
parent 14978355ee
commit cdd1520434
3 changed files with 341 additions and 351 deletions
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test/api/test_workflows.py
+241 -244
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@@ -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
test/api/test_workflows_from_yaml.py
+34 -37
View File
@@ -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:
test/base/workflow_fixtures.py
+66 -70
View File
@@ -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
"""