mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
434 lines
7.6 KiB
Python
434 lines
7.6 KiB
Python
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WORKFLOW_SIMPLE_CAT_AND_RANDOM_LINES = """
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class: GalaxyWorkflow
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doc: |
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Simple workflow that no-op cats a file and then selects 10 random lines.
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inputs:
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the_input:
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type: data
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doc: input doc
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steps:
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- tool_id: cat1
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doc: cat doc
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in:
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input1: the_input
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- tool_id: cat1
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in:
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input1: 1/out_file1
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- tool_id: random_lines1
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label: random_line_label
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state:
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num_lines: 10
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seed_source:
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seed_source_selector: set_seed
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seed: asdf
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in:
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input: 2/out_file1
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"""
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WORKFLOW_SIMPLE_CAT_TWICE = """
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class: GalaxyWorkflow
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inputs:
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input1: data
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steps:
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first_cat:
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tool_id: cat
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in:
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input1: input1
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queries_0|input2: input1
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"""
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WORKFLOW_WITH_OLD_TOOL_VERSION = """
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class: GalaxyWorkflow
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inputs:
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input1: data
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steps:
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mul_versions:
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tool_id: multiple_versions
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tool_version: "0.0.1"
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state:
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inttest: 8
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"""
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WORKFLOW_WITH_INVALID_STATE = """
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class: GalaxyWorkflow
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inputs:
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input1: data
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steps:
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mul_versions:
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tool_id: multiple_versions
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tool_version: "0.0.1"
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state:
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inttest: "moocow"
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"""
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WORKFLOW_WITH_OUTPUT_COLLECTION = """
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class: GalaxyWorkflow
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inputs:
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text_input: data
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steps:
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split_up:
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tool_id: collection_creates_pair
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in:
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input1: text_input
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paired:
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tool_id: collection_paired_test
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in:
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f1: split_up/paired_output
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test_data:
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text_input: |
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a
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b
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c
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d
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"""
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WORKFLOW_WITH_DYNAMIC_OUTPUT_COLLECTION = """
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class: GalaxyWorkflow
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inputs:
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text_input1: data
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text_input2: data
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steps:
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cat_inputs:
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tool_id: cat1
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in:
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input1: text_input1
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queries_0|input2: text_input2
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split_up:
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tool_id: collection_split_on_column
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in:
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input1: cat_inputs/out_file1
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cat_list:
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tool_id: cat_list
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in:
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input1: split_up/split_output
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test_data:
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text_input1: |
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samp1\t10.0
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samp2\t20.0
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text_input2: |
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samp1\t30.0
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samp2\t40.0
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"""
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WORKFLOW_SIMPLE_MAPPING = """
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class: GalaxyWorkflow
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inputs:
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input1:
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type: collection
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collection_type: list
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steps:
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cat:
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tool_id: cat
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in:
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input1: input1
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"""
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WORKFLOW_WITH_OUTPUT_COLLECTION_MAPPING = """
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class: GalaxyWorkflow
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steps:
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- type: input_collection
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- tool_id: collection_creates_pair
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state:
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input1:
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$link: 0
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- tool_id: collection_paired_test
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state:
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f1:
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$link: 1#paired_output
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- tool_id: cat_list
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state:
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input1:
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$link: 2#out1
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"""
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WORKFLOW_WITH_RULES_1 = """
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class: GalaxyWorkflow
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inputs:
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input_c: collection
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steps:
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apply:
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tool_id: __APPLY_RULES__
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state:
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input:
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$link: input_c
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rules:
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rules:
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- type: add_column_metadata
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value: identifier0
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- type: add_column_metadata
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value: identifier0
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mapping:
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- type: list_identifiers
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columns: [0, 1]
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random_lines:
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tool_id: random_lines1
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state:
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num_lines: 1
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input:
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$link: apply#output
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seed_source:
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seed_source_selector: set_seed
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seed: asdf
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test_data:
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input_c:
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type: list
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elements:
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- identifier: i1
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content: "0"
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- identifier: i2
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content: "1"
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"""
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WORKFLOW_WITH_RULES_2 = """
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class: GalaxyWorkflow
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inputs:
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input_c: collection
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steps:
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apply:
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tool_id: __APPLY_RULES__
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state:
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input:
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$link: input_c
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rules:
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rules:
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- type: add_column_metadata
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value: identifier0
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- type: add_column_metadata
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value: identifier0
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mapping:
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- type: list_identifiers
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columns: [0, 1]
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copy_list:
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tool_id: collection_creates_list
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in:
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input1: apply/output
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test_data:
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input_c:
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type: list
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elements:
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- identifier: i1
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content: "0"
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- identifier: i2
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content: "1"
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"""
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WORKFLOW_NESTED_SIMPLE = """
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class: GalaxyWorkflow
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inputs:
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outer_input: data
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outputs:
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outer_output:
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outputSource: second_cat/out_file1
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steps:
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first_cat:
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tool_id: cat1
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in:
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input1: outer_input
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nested_workflow:
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run:
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class: GalaxyWorkflow
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inputs:
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inner_input: data
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outputs:
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workflow_output:
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outputSource: random_lines/out_file1
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steps:
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random_lines:
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tool_id: random_lines1
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state:
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num_lines: 1
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input:
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$link: inner_input
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seed_source:
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seed_source_selector: set_seed
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seed: asdf
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in:
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inner_input: first_cat/out_file1
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second_cat:
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tool_id: cat1
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in:
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input1: nested_workflow/workflow_output
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queries_0|input2: nested_workflow/workflow_output
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"""
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WORKFLOW_NESTED_RUNTIME_PARAMETER = """
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class: GalaxyWorkflow
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inputs:
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outer_input: data
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outputs:
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outer_output:
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outputSource: nested_workflow/workflow_output
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steps:
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nested_workflow:
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run:
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class: GalaxyWorkflow
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inputs:
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inner_input: data
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outputs:
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workflow_output:
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outputSource: random_lines#out_file1
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steps:
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- tool_id: random_lines1
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label: random_lines
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runtime_inputs:
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- num_lines
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state:
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input:
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$link: inner_input
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seed_source:
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seed_source_selector: set_seed
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seed: asdf
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in:
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inner_input: outer_input
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"""
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WORKFLOW_WITH_OUTPUT_ACTIONS = """
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class: GalaxyWorkflow
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inputs:
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input1: data
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steps:
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first_cat:
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tool_id: cat1
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outputs:
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out_file1:
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hide: true
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rename: "the new value"
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in:
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input1: input1
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second_cat:
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tool_id: cat1
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in:
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input1: first_cat/out_file1
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"""
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WORKFLOW_RUNTIME_PARAMETER_SIMPLE = """
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class: GalaxyWorkflow
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inputs:
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input1: data
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steps:
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random:
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tool_id: random_lines1
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runtime_inputs:
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- num_lines
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state:
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input:
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$link: input1
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seed_source:
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seed_source_selector: set_seed
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seed: asdf
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"""
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WORKFLOW_RUNTIME_PARAMETER_AFTER_PAUSE = """
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class: GalaxyWorkflow
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inputs:
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input1: data
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steps:
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the_pause:
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type: pause
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in:
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input: input1
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random:
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tool_id: random_lines1
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runtime_inputs:
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- num_lines
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state:
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input:
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$link: the_pause
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seed_source:
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seed_source_selector: set_seed
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seed: asdf
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"""
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WORKFLOW_RENAME_ON_INPUT = """
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class: GalaxyWorkflow
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inputs:
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input1: data
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steps:
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first_cat:
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tool_id: cat
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state:
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input1:
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$link: input1
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outputs:
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out_file1:
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rename: "#{input1 | basename} suffix"
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test_data:
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input1:
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value: 1.fasta
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type: File
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name: fasta1
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"""
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WORKFLOW_RENAME_ON_REPLACEMENT_PARAM = """
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class: GalaxyWorkflow
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inputs:
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input1: data
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steps:
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first_cat:
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tool_id: cat
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in:
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input1: input1
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outputs:
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out_file1:
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rename: "${replaceme} suffix"
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"""
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WORKFLOW_NESTED_REPLACEMENT_PARAMETER = """
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class: GalaxyWorkflow
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inputs:
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outer_input: data
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outputs:
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outer_output:
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outputSource: nested_workflow/workflow_output
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steps:
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nested_workflow:
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run:
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class: GalaxyWorkflow
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inputs:
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inner_input: data
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outputs:
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workflow_output:
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outputSource: first_cat/out_file1
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steps:
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- tool_id: cat
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label: first_cat
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in:
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input1: inner_input
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outputs:
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out_file1:
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rename: "${replaceme} suffix"
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in:
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inner_input: outer_input
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"""
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WORKFLOW_WITH_OUTPUTS = """
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class: GalaxyWorkflow
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inputs:
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input1: data
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outputs:
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wf_output_1:
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outputSource: first_cat/out_file1
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steps:
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first_cat:
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tool_id: cat1
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in:
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input1: input1
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queries_0|input2: input1
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"""
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