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Source code for galaxy_test.base.workflow_fixtures
import json
from typing import Any
WORKFLOW_SIMPLE = """
class: GalaxyWorkflow
name: Simple Workflow
inputs:
input1: data
outputs:
wf_output_1:
outputSource: first_cat/out_file1
steps:
first_cat:
tool_id: cat1
in:
input1: input1
"""
WORKFLOW_SIMPLE_CAT_AND_RANDOM_LINES = """
class: GalaxyWorkflow
doc: |
Simple workflow that no-op cats a file and then selects 10 random lines.
creator:
- class: Person
name: John Chilton
email: jmchilton@gmail.com
identifier: https://orcid.org/0000-0002-6794-0756
inputs:
the_input:
type: data
doc: input doc
steps:
- tool_id: cat1
doc: cat doc
in:
input1: the_input
- tool_id: cat1
in:
input1: 1/out_file1
- tool_id: random_lines1
label: random_line_label
state:
num_lines: 10
seed_source:
seed_source_selector: set_seed
seed: asdf
in:
input: 2/out_file1
"""
WORKFLOW_SIMPLE_CAT_TWICE = """
class: GalaxyWorkflow
inputs:
input1: data
steps:
first_cat:
tool_id: cat
in:
input1: input1
queries_0|input2: input1
"""
WORKFLOW_WITH_OLD_TOOL_VERSION = """
class: GalaxyWorkflow
inputs:
input1: data
steps:
mul_versions:
tool_id: multiple_versions
tool_version: "0.0.1"
state:
inttest: 8
"""
WORKFLOW_SELECT_FROM_OPTIONAL_DATASET = """
class: GalaxyWorkflow
steps:
select_from_dataset_optional:
tool_id: select_from_dataset_optional
state:
select_single: null
"""
# Throwing a bunch of broken steps in to get a really long modal and sure it
# is scrollable.
WORKFLOW_WITH_INVALID_STATE = """
class: GalaxyWorkflow
inputs:
input1: data
steps:
mul_versions_1:
tool_id: multiple_versions
tool_version: "0.0.1"
state:
inttest: "moocow"
'another bad step':
tool_id: multiple_versions
tool_version: "0.0.3c"
state:
inttest: "moocow"
'another bad step':
tool_id: multiple_versions
tool_version: "0.0.3c"
state:
inttest: "moocow"
'another bad step2':
tool_id: multiple_versions
tool_version: "0.0.3c"
state:
inttest: "moocow"
'another bad step3':
tool_id: multiple_versions
tool_version: "0.0.3c"
state:
inttest: "moocow"
'another bad step4':
tool_id: multiple_versions
tool_version: "0.0.3c"
state:
inttest: "moocow"
'another bad step5':
tool_id: multiple_versions
tool_version: "0.0.3c"
state:
inttest: "moocow"
'another bad step6':
tool_id: multiple_versions
tool_version: "0.0.3c"
state:
inttest: "moocow"
'another bad step7':
tool_id: multiple_versions
tool_version: "0.0.3c"
state:
inttest: "moocow"
'another bad step8':
tool_id: multiple_versions
tool_version: "0.0.3c"
state:
inttest: "moocow"
'another bad step9':
tool_id: multiple_versions
tool_version: "0.0.3c"
state:
inttest: "moocow"
'another bad step10':
tool_id: multiple_versions
tool_version: "0.0.3c"
state:
inttest: "moocow"
'another bad step11':
tool_id: multiple_versions
tool_version: "0.0.3c"
state:
inttest: "moocow"
'another bad step12':
tool_id: multiple_versions
tool_version: "0.0.3c"
state:
inttest: "moocow"
'another bad step13':
tool_id: multiple_versions
tool_version: "0.0.3c"
state:
inttest: "moocow"
'another bad step14':
tool_id: multiple_versions
tool_version: "0.0.3c"
state:
inttest: "moocow"
"""
WORKFLOW_WITH_OUTPUT_COLLECTION = """
class: GalaxyWorkflow
inputs:
text_input: data
steps:
split_up:
tool_id: collection_creates_pair
in:
input1: text_input
paired:
tool_id: collection_paired_test
in:
f1: split_up/paired_output
test_data:
text_input: |
a
b
c
d
"""
WORKFLOW_WITH_MAPPED_OUTPUT_COLLECTION = """
class: GalaxyWorkflow
inputs:
input1:
type: data_collection_input
collection_type: list
outputs:
wf_output_1:
outputSource: first_cat/out_file1
steps:
first_cat:
tool_id: cat
in:
input1: input1
"""
WORKFLOW_WITH_DYNAMIC_OUTPUT_COLLECTION = """
class: GalaxyWorkflow
inputs:
text_input1: data
text_input2: data
steps:
cat_inputs:
tool_id: cat1
in:
input1: text_input1
queries_0|input2: text_input2
split_up:
tool_id: collection_split_on_column
in:
input1: cat_inputs/out_file1
cat_list:
tool_id: cat_list
in:
input1: split_up/split_output
test_data:
text_input1: |
samp1\t10.0
samp2\t20.0
text_input2: |
samp1\t30.0
samp2\t40.0
"""
WORKFLOW_WHEN_NOT_CONNECTED = """
class: GalaxyWorkflow
inputs:
some_file:
type: data
should_run:
type: boolean
steps:
cat1:
tool_id: cat1
in:
input1: some_file
when: $(inputs.when)
"""
WORKFLOW_SIMPLE_MAPPING = """
class: GalaxyWorkflow
inputs:
input1:
type: collection
collection_type: list
steps:
cat:
tool_id: cat
in:
input1: input1
"""
WORKFLOW_WITH_OUTPUT_COLLECTION_MAPPING = """
class: GalaxyWorkflow
inputs:
input_collection: collection
steps:
- 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
"""
WORKFLOW_WITH_RULES_1 = """
class: GalaxyWorkflow
inputs:
input_c: collection
steps:
apply:
tool_id: __APPLY_RULES__
state:
input:
$link: input_c
rules:
rules:
- type: add_column_metadata
value: identifier0
- type: add_column_metadata
value: identifier0
mapping:
- type: list_identifiers
columns: [0, 1]
random_lines:
tool_id: random_lines1
state:
num_lines: 1
input:
$link: apply/output
seed_source:
seed_source_selector: set_seed
seed: asdf
test_data:
input_c:
collection_type: list
elements:
- identifier: i1
content: "0"
- identifier: i2
content: "1"
"""
WORKFLOW_WITH_RULES_2 = """
class: GalaxyWorkflow
inputs:
input_c: collection
steps:
apply:
tool_id: __APPLY_RULES__
state:
input:
$link: input_c
rules:
rules:
- type: add_column_metadata
value: identifier0
- type: add_column_metadata
value: identifier0
mapping:
- type: list_identifiers
columns: [0, 1]
copy_list:
tool_id: collection_creates_list
in:
input1: apply/output
test_data:
input_c:
type: list
elements:
- identifier: i1
content: "0"
- identifier: i2
content: "1"
"""
WORKFLOW_NESTED_SIMPLE = """
class: GalaxyWorkflow
inputs:
outer_input: data
outputs:
outer_output:
outputSource: second_cat/out_file1
steps:
first_cat:
tool_id: cat1
in:
input1: outer_input
nested_workflow:
run:
class: GalaxyWorkflow
inputs:
inner_input: data
outputs:
workflow_output:
outputSource: random_lines/out_file1
steps:
random_lines:
tool_id: random_lines1
state:
num_lines: 1
input:
$link: inner_input
seed_source:
seed_source_selector: set_seed
seed: asdf
in:
inner_input: first_cat/out_file1
second_cat:
tool_id: cat1
in:
input1: nested_workflow/workflow_output
queries_0|input2: nested_workflow/workflow_output
"""
# WORKFLOW_NESTED_SIMPLE with a nested workflow output marked as an
# output on the outer workflow.
WORKFLOW_NESTED_OUTPUT = """
class: GalaxyWorkflow
inputs:
outer_input: data
outputs:
outer_output:
outputSource: second_cat/out_file1
nested_output:
outputSource: nested_workflow/workflow_output
steps:
first_cat:
tool_id: cat1
in:
input1: outer_input
nested_workflow:
run:
class: GalaxyWorkflow
inputs:
inner_input: data
outputs:
workflow_output:
outputSource: random_lines/out_file1
steps:
random_lines:
tool_id: random_lines1
state:
num_lines: 1
input:
$link: inner_input
seed_source:
seed_source_selector: set_seed
seed: asdf
in:
inner_input: first_cat/out_file1
second_cat:
tool_id: cat1
in:
input1: nested_workflow/workflow_output
queries_0|input2: nested_workflow/workflow_output
"""
# WORKFLOW_NESTED_OUTPUT with two levels of nesting for the workflow
# output
WORKFLOW_NESTED_TWICE_OUTPUT = """
class: GalaxyWorkflow
inputs:
outer_input: data
outputs:
outer_output:
outputSource: second_cat/out_file1
nested_output:
outputSource: nested_workflow/workflow_output
steps:
first_cat:
tool_id: cat1
in:
input1: outer_input
nested_workflow:
run:
class: GalaxyWorkflow
inputs:
inner_input: data
outputs:
workflow_output:
outputSource: inner_nested_workflow/inner_workflow_output
steps:
inner_nested_workflow:
run:
class: GalaxyWorkflow
inputs:
really_inner_input: data
outputs:
inner_workflow_output:
outputSource: random_lines/out_file1
steps:
random_lines:
tool_id: random_lines1
state:
num_lines: 1
input:
$link: really_inner_input
seed_source:
seed_source_selector: set_seed
seed: asdf
in:
really_inner_input: inner_input
in:
inner_input: first_cat/out_file1
second_cat:
tool_id: cat1
in:
input1: nested_workflow/workflow_output
queries_0|input2: nested_workflow/workflow_output
"""
WORKFLOW_NESTED_RUNTIME_PARAMETER = """
class: GalaxyWorkflow
inputs:
outer_input: data
outputs:
outer_output:
outputSource: nested_workflow/workflow_output
steps:
nested_workflow:
run:
class: GalaxyWorkflow
inputs:
inner_input: data
outputs:
workflow_output:
outputSource: random_lines/out_file1
steps:
- tool_id: random_lines1
label: random_lines
runtime_inputs:
- num_lines
state:
input:
$link: inner_input
seed_source:
seed_source_selector: set_seed
seed: asdf
in:
inner_input: outer_input
"""
WORKFLOW_NESTED_WITH_MULTIPLE_VERSIONS_TOOL = """
class: GalaxyWorkflow
inputs:
outer_input: data
outputs:
outer_output:
outputSource: cat/out_file1
steps:
tool_update_step:
tool_id: multiple_versions
tool_version: '0.1'
in:
input1: outer_input
nested_workflow:
run:
class: GalaxyWorkflow
inputs:
inner_input: data
outputs:
workflow_output:
outputSource: random_lines/out_file1
steps:
random_lines:
tool_id: random_lines1
state:
num_lines: 1
input:
$link: inner_input
seed_source:
seed_source_selector: set_seed
seed: asdf
in:
inner_input: tool_update_step/out_file1
cat:
tool_id: cat1
in:
input1: nested_workflow/workflow_output
queries_0|input2: nested_workflow/workflow_output
compose_text_param:
tool_id: compose_text_param
tool_version: 0.1.0
label: compose_text_param
"""
WORKFLOW_WITH_OUTPUT_ACTIONS = """
class: GalaxyWorkflow
inputs:
input1: data
steps:
first_cat:
tool_id: cat1
out:
out_file1:
hide: true
rename: "the new value"
in:
input1: input1
second_cat:
tool_id: cat1
in:
input1: first_cat/out_file1
"""
WORKFLOW_INPUTS_AS_OUTPUTS = """
class: GalaxyWorkflow
inputs:
input1: data
text_input: text
outputs:
wf_output_1:
outputSource: input1
wf_output_param:
outputSource: text_input
steps: []
"""
WORKFLOW_PARAMETER_INPUT_INTEGER_REQUIRED = """
class: GalaxyWorkflow
inputs:
data_input: data
int_input: integer
steps:
random:
tool_id: random_lines1
in:
input: data_input
num_lines: int_input
state:
seed_source:
seed_source_selector: set_seed
seed: asdf
"""
WORKFLOW_PARAMETER_INPUT_INTEGER_OPTIONAL = """
class: GalaxyWorkflow
inputs:
data_input: data
int_input:
type: integer
optional: true
steps:
random:
tool_id: random_lines1
in:
input: data_input
num_lines: int_input
state:
seed_source:
seed_source_selector: set_seed
seed: asdf
"""
WORKFLOW_PARAMETER_INPUT_INTEGER_DEFAULT = """
class: GalaxyWorkflow
inputs:
data_input: data
int_input:
type: integer
default: 3
optional: true
steps:
random:
tool_id: random_lines1
in:
input: data_input
num_lines: int_input
state:
seed_source:
seed_source_selector: set_seed
seed: asdf
"""
WORKFLOW_OPTIONAL_TRUE_INPUT_DATA = """
class: GalaxyWorkflow
inputs:
input1:
type: data
optional: true
outputs:
out1:
outputSource: the_tool/out1
steps:
the_tool:
tool_id: multi_data_optional
in:
input1: input1
out:
out1: out1
"""
# Same workflow but non-optional input
WORKFLOW_OPTIONAL_FALSE_INPUT_DATA = """
class: GalaxyWorkflow
inputs:
input1:
type: data
optional: false
outputs:
out1:
outputSource: the_tool/out1
steps:
the_tool:
tool_id: multi_data_optional
in:
input1: input1
out:
out1: out1
"""
WORKFLOW_OPTIONAL_TRUE_INPUT_COLLECTION = """
class: GalaxyWorkflow
inputs:
input1:
type: collection
collection_type: paired
optional: true
outputs:
out1:
outputSource: the_tool/out1
steps:
the_tool:
tool_id: collection_optional_param
in:
f1: input1
out:
out1: out1
"""
# Same workflow but non-optional input
WORKFLOW_OPTIONAL_FALSE_INPUT_COLLECTION = """
class: GalaxyWorkflow
inputs:
input1:
type: collection
collection_type: paired
optional: false
outputs:
out1:
outputSource: the_tool/out1
steps:
the_tool:
tool_id: collection_optional_param
in:
f1: input1
out:
out1: out1
"""
WORKFLOW_OPTIONAL_INPUT_DELAYED_SCHEDULING = """
class: GalaxyWorkflow
inputs:
required:
type: data
optional:
type: data
optional: true
outputs:
out1:
outputSource: count_multi_file/out_file1
steps:
expression:
tool_id: expression_parse_int
state:
input1: 1
head:
tool_id: head
in:
input: required
state:
lineNum:
$link: expression/out1
count_multi_file:
tool_id: count_multi_file
in:
input1:
- optional
- head/out_file1
out:
out_file1: out_file1
test_data:
required:
value: 1.bed
type: File
"""
WORKFLOW_RUNTIME_PARAMETER_SIMPLE = """
class: GalaxyWorkflow
inputs:
input1: data
steps:
random:
tool_id: random_lines1
runtime_inputs:
- num_lines
state:
input:
$link: input1
seed_source:
seed_source_selector: set_seed
seed: asdf
"""
WORKFLOW_RUNTIME_PARAMETER_AFTER_PAUSE = """
class: GalaxyWorkflow
inputs:
input1: data
steps:
the_pause:
type: pause
in:
input: input1
random:
tool_id: random_lines1
runtime_inputs:
- num_lines
state:
input:
$link: the_pause
seed_source:
seed_source_selector: set_seed
seed: asdf
"""
WORKFLOW_RENAME_ON_INPUT = """
class: GalaxyWorkflow
inputs:
input1: data
steps:
first_cat:
tool_id: cat
state:
input1:
$link: input1
out:
out_file1:
rename: "#{input1 | basename} suffix"
test_data:
input1:
value: 1.fasta
type: File
name: fasta1
"""
WORKFLOW_RENAME_ON_REPLACEMENT_PARAM = """
class: GalaxyWorkflow
inputs:
input1: data
steps:
first_cat:
tool_id: cat
in:
input1: input1
out:
out_file1:
rename: "${replaceme} suffix"
"""
WORKFLOW_NESTED_REPLACEMENT_PARAMETER = """
class: GalaxyWorkflow
inputs:
outer_input: data
outputs:
outer_output:
outputSource: nested_workflow/workflow_output
steps:
nested_workflow:
run:
class: GalaxyWorkflow
inputs:
inner_input: data
outputs:
workflow_output:
outputSource: first_cat/out_file1
steps:
- tool_id: cat
label: first_cat
in:
input1: inner_input
out:
out_file1:
rename: "${replaceme} suffix"
in:
inner_input: outer_input
"""
WORKFLOW_ONE_STEP_DEFAULT = """
class: GalaxyWorkflow
inputs:
input: data
steps:
randomlines:
tool_id: random_lines1
in:
input: input
num_lines:
default: 6
"""
WORKFLOW_LIST_PAIRED_INPUT_TO_TYPE_SOURCE = """
class: GalaxyWorkflow
inputs:
- id: input_header
type: data
- id: input_list
type: collection
collection_type: "list:paired"
steps:
- tool_id: collection_type_source
in:
header: input_header
input_collect: input_list
"""
WORKFLOW_LIST_PAIRED_MAPPED_OVER_PAIRED = """
class: GalaxyWorkflow
inputs:
- id: input_list
type: collection
collection_type: "list:paired"
steps:
- tool_id: collection_paired_test
in:
f1: input_list
"""
WORKFLOW_LIST_PAIRED_OR_UNPAIRED_INPUT = """
class: GalaxyWorkflow
inputs:
- id: input_list
type: collection
collection_type: "list:paired_or_unpaired"
steps:
- tool_id: collection_list_paired_or_unpaired
in:
f1: input_list
"""
WORKFLOW_WITH_OUTPUTS = """
class: GalaxyWorkflow
inputs:
input1: data
outputs:
wf_output_1:
outputSource: first_cat/out_file1
steps:
first_cat:
tool_id: cat1
in:
input1: input1
queries_0|input2: input1
"""
WORKFLOW_WITH_CUSTOM_REPORT_1 = """
class: GalaxyWorkflow
name: My Cool Workflow
inputs:
input_1: data
image_input: data
input_list: collection
outputs:
output_1:
outputSource: first_cat/out_file1
output_image:
outputSource: image_cat/out_file1
steps:
first_cat:
tool_id: cat
in:
input1: input_1
image_cat:
tool_id: cat
in:
input1: image_input
qc_step:
tool_id: qc_stdout
state:
quality: 9
in:
input: input_1
report:
markdown: |
## About This Report
This report is generated from markdown content in the workflow YAML/JSON.
Workflow invocation reports provide a customizable way for workflow authors
to summarize the results of a workflow execution. There is a default markdown
template if a workflow does not define one (right now it just shows the inputs,
outputs, and workflow - but this will evolve).
This report is written in "Galaxy Workflow Flavored Markdown". This workflow
variant of "Galaxy Flavored Markdown" contains workflow-relative references.
Dataset, collections, and jobs are referenced by step labels, input labels, and output
labels - rather than by object IDs. The Galaxy invocation report generator plugin
translates this to "Galaxy Flavored Markdown" at the time the report is viewed and
that format references actual object IDs (by database ID internally, and encoded ID
when exported to the client via the API).
An upshot of translating the workflow markdown to this second neutral format that
has no concept of the workflow invocation is that client side rendering (and much
of the backend processing) is completely general and not tied to workflows or
invocations. The same markdown components could potentially be used to render pages,
history annotations, describe library folders, etc..
The next two sections demonstrate the auto generated inputs and outputs sections
in the default workflow invocation report template.
## Workflow Inputs
```galaxy
invocation_inputs()
```
## Workflow Outputs
```galaxy
invocation_outputs()
```
The auto-generated sections could be hand-crafted from workflow markdown also,
listing out each input and output explicitly. The auto generated sections are merely
a convenience to avoid needing to that by hand and for supplying a default report
for workflows that don't define a custom one report.
## More Custom Content
The rest of this report demonstrates more the directives allowed in the report
markdown. ``invocation_outputs`` and ``invocation_inputs`` are not allow in
"Galaxy Flavored Markdown" (the non-workflow invocation specific format), but
the remainder of these are allowed - they would just need to reference object
IDs instead of inputs, outputs, and steps.
Once can reference an output and embed a display of it as follows:
```galaxy
history_dataset_display(output=output_1)
```
Inputs can be referenced and displayed the same way:
```galaxy
history_dataset_display(input=input_1)
```
---
Images can be embedded directly into the report as follows:
```galaxy
history_dataset_as_image(output=output_image)
```
---
Dataset peek content can be displayed to quickly provided an embedded
summary of an input or output:
```galaxy
history_dataset_peek(output=output_1)
```
---
Dataset "info" content can be displayed as well:
```galaxy
history_dataset_info(input=input_1)
```
---
Collections can be displayed:
```galaxy
history_dataset_collection_display(input=input_list)
```
---
The whole workflow can be embedded to provide some context and display
annotations and steps.
```galaxy
workflow_display()
```
---
Job parameters can be summarized:
```galaxy
job_parameters(step=qc_step)
```
---
Job metrics can be summarized as well:
```galaxy
job_metrics(step=image_cat)
```
---
Tool standard out and error are also available for steps.
```galaxy
tool_stdout(step=qc_step)
```
```galaxy
tool_stderr(step=qc_step)
```
---
*fin*
"""
WORKFLOW_WITH_CUSTOM_REPORT_1_TEST_DATA = """
input_1:
value: 1.bed
type: File
name: my bed file
image_input:
value: 454Score.png
type: File
file_type: png
name: my input image
input_list:
collection_type: list
elements:
- identifier: i1
content: "0"
name: example list
"""
WORKFLOW_WITH_BAD_COLUMN_PARAMETER = """
class: GalaxyWorkflow
inputs:
bed_input: data
steps:
cat1:
tool_id: cat1
in:
input1: bed_input
column_param_list:
tool_id: column_param
in:
input1: cat1/out_file1
state:
col: 9
col_names: notacolumn
"""
WORKFLOW_WITH_BAD_COLUMN_PARAMETER_GOOD_TEST_DATA = """
step_parameters:
'2':
'col': 1
'col_names': 'c1: chr1'
bed_input:
value: 1.bed
file_type: bed
type: File
"""
NESTED_WORKFLOW_WITH_CONDITIONAL_SUBWORKFLOW_AND_DISCONNECTED_MAP_OVER_SOURCE = """
class: GalaxyWorkflow
inputs:
boolean_input_files: collection
steps:
create_list_of_boolean:
tool_id: param_value_from_file
in:
input1: boolean_input_files
state:
param_type: boolean
subworkflow:
run:
class: GalaxyWorkflow
inputs:
boolean_input_file: data
should_run: boolean
steps:
create_more_inputs:
tool_id: collection_creates_dynamic_nested
consume_expression_parameter:
tool_id: cat1
state:
input1:
$link: create_more_inputs/list_output
queries:
- input2:
$link: boolean_input_file
out:
out_file1:
change_datatype: txt
consume_expression_parameter_2:
tool_id: cat1
state:
input1:
$link: consume_expression_parameter/out_file1
outputs:
inner_create_nested:
outputSource: create_more_inputs/list_output
inner_output_1:
outputSource: consume_expression_parameter/out_file1
inner_output_2:
outputSource: consume_expression_parameter_2/out_file1
in:
boolean_input_file: boolean_input_files
should_run: create_list_of_boolean/boolean_param
when: $(inputs.should_run)
outputs:
outer_create_nested:
outputSource: subworkflow/inner_create_nested
outer_output_1:
outputSource: subworkflow/inner_output_1
outer_output_2:
outputSource: subworkflow/inner_output_2
"""
# The location is templated so tests can serve 1.bed from the local test HTTP server.
DEFAULT_FILE_DATASET_INPUT_LOCATION = "https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/1.bed"
WORKFLOW_WITH_DEFAULT_FILE_DATASET_INPUT = """
class: GalaxyWorkflow
inputs:
default_file_input:
default:
class: File
basename: a file
format: txt
location: {location}
steps:
cat1:
tool_id: cat1
in:
input1: default_file_input
"""
WORKFLOW_WITH_STEP_DEFAULT_FILE_DATASET_INPUT = """
class: GalaxyWorkflow
steps:
cat1:
tool_id: cat1
in:
input1:
default:
class: File
basename: a file
format: txt
location: {location}
"""
WORKFLOW_FLAT_CROSS_PRODUCT = """
class: GalaxyWorkflow
inputs:
collection_a: collection
collection_b: collection
steps:
cross_product:
tool_id: __CROSS_PRODUCT_FLAT__
in:
input_a:
collection_a
input_b:
collection_b
outputs:
output_a:
outputSource: cross_product/output_a
output_b:
outputSource: cross_product/output_b
"""
WORKFLOW_WITH_DATA_TAG_FILTER = r"""{
"a_galaxy_workflow": "true",
"annotation": null,
"comments": [],
"format-version": "0.1",
"name": "Export WF4 Assembly HiC (imported from URL) (imported from uploaded file)",
"steps": {
"0": {
"annotation": "With dataset tag : genomescope_model ",
"content_id": null,
"errors": null,
"id": 0,
"input_connections": {},
"inputs": [
{
"description": "With dataset tag : genomescope_model ",
"name": "Genomescope Model"
}
],
"label": "Genomescope Model",
"name": "Input dataset",
"outputs": [],
"position": {
"left": 0,
"top": 0
},
"tool_id": null,
"tool_state": "{\"optional\": false, \"format\": [\"txt\"], \"tag\": \"genomescope_model\"}",
"tool_version": null,
"type": "data_input",
"uuid": "a165c531-371f-4073-9cdd-85ce3506586f",
"when": null,
"workflow_outputs": []
}
},
"tags": [],
"uuid": "03a95ebe-af1e-4628-ac2f-e7553babfb2f",
"version": 3
}"""
WORKFLOW_KEEP_SUCCESSFUL_DATASETS = """
class: GalaxyWorkflow
inputs:
input_c:
type: collection
position: {left: 0, top: 0}
steps:
mixed_collection:
tool_id: exit_code_from_file
position: {left: 230, top: 0}
in:
input: input_c
filtered_collection:
tool_id: "__KEEP_SUCCESS_DATASETS__"
position: {left: 460, top: 0}
in:
input: mixed_collection/out_file1
cat:
tool_id: cat
position: {left: 690, top: 0}
in:
input1: filtered_collection/output
"""
WORKFLOW_KEEP_SUCCESSFUL_DATASETS_TEST_DATA = """
input_c:
collection_type: list
elements:
- identifier: i1
content: "0"
- identifier: i2
content: "1"
"""
WORKFLOW_WITH_IMAGES_IN_REPORT = """
class: GalaxyWorkflow
name: Workflow with Images in Report
inputs:
image_input: data
outputs:
output_image:
outputSource: image_cat/out_file1
steps:
image_cat:
tool_id: cat
in:
input1: image_input
report:
markdown: |
## Images in Report
This report demonstrates embedding images within a markdown workflow report,
including inline images in tables.
### Block-level Image
```galaxy
history_dataset_as_image(output=output_image)
```
### Table with Inline Images
| Description | Image |
|-------------|-------|
| First Image | ${galaxy history_dataset_as_image(output=output_image)} |
| Second Image | ${galaxy history_dataset_as_image(output=output_image)} |
The above table should show two images rendered inline.
"""
WORKFLOW_WITH_IMAGES_IN_REPORT_TEST_DATA = """
image_input_1:
value: 454Score.png
type: File
file_type: png
name: first test image
"""
[docs]
def parameter_input_workflow(label: str, parameter_type: str, validators: list[dict[str, Any]]) -> dict[str, Any]:
"""Native (.ga) workflow with one parameter input declaring ``validators`` (format2 does not carry them)."""
tool_state = {"parameter_type": parameter_type, "optional": False, "validators": validators}
return {
"a_galaxy_workflow": "true",
"format-version": "0.1",
"name": "parameter input validators",
"annotation": "",
"steps": {
"0": {
"id": 0,
"type": "parameter_input",
"label": label,
"tool_state": json.dumps(tool_state),
"input_connections": {},
"position": {"left": 0, "top": 0},
"workflow_outputs": [],
}
},
}