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1b4e6ceff1bbfae058eb986e1baa7475fbf5a0d2
galaxy/test/functional/tools
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mvdbeek 1b4e6ceff1 Fix DataManagerTool.exec_after_process for async API submission 
When a data manager job is submitted via POST /api/jobs (async path), the
Celery task reconstructs the tool from raw XML without a data_manager_id,
causing DataManagerJobAssociation to store the tool XML id instead of the
conf id when those differ. exec_after_process then fails with "Invalid data
manager requested" because DataManagers registry is keyed by conf id.

Fix by preferring self.data_manager_id (always set correctly at toolbox load
time) over job.data_manager_association.data_manager_id in exec_after_process.

Add a regression test using the "data_manager" test tool (tool XML id) which
is registered in sample_data_manager_conf.xml as id="test_data_manager",
replicating the exact id mismatch seen in production (e.g. bowtie2).
2026-06-15 08:56:03 +02:00
..
.claude/commands
claude infrastructure for managing test tools.
2026-02-12 15:58:16 -05:00
data
Tool markdown reports.
2025-05-02 11:25:21 -04:00
deprecated
Disable unqualified parameters in test cases for new tools.
2024-08-23 09:46:44 -04:00
for_tours
Resolve possible symlink before establishing tool file location
2025-10-27 18:12:52 +01:00
for_workflows
Add cat1 (catWrapper) to test tool conf for workflow editor tests
2026-03-22 10:47:00 -04:00
parameters
Merge branch 'release_26.0' into dev
2026-04-28 11:21:45 +02:00
realtime/simple
…
all_output_types.xml
Fix up test cases
2024-06-10 10:34:15 +02:00
bibtex.xml
Switch to only MIT license
2026-03-06 19:05:20 +01:00
boolean_conditional.xml
…
cat_data_and_sleep.xml
…
cat_multiple_user_defined.yml
Modeling and validation of YAML tool test cases.
2026-02-12 10:50:13 -05:00
cat_user_defined.yml
Modeling and validation of YAML tool test cases.
2026-02-12 10:50:13 -05:00
catDocker.xml
Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc
2024-06-21 16:58:21 +02:00
checksum.xml
…
cheetah_casting.xml
Cast None value to ""
2023-02-05 20:06:08 +01:00
cheetah_problem_syntax_error.xml
…
cheetah_problem_unbound_var_input.xml
…
cheetah_problem_unbound_var.xml
…
CLAUDE.md
claude infrastructure for managing test tools.
2026-02-12 15:58:16 -05:00
code_file.py
Apply black formatting.
2022-02-03 07:42:20 -05:00
code_file.xml
…
collection_cat_group_tag_multiple.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
collection_cat_group_tag.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
collection_creates_dynamic_list_of_pairs.xml
Fix collection_creates_dynamic_list_of_pairs test
2022-04-23 12:16:42 +02:00
collection_creates_dynamic_nested_fail.xml
…
collection_creates_dynamic_nested_from_json_elements.xml
…
collection_creates_dynamic_nested_from_json.xml
…
collection_creates_dynamic_nested.xml
Make dataset discovery respect final_job_state
2020-02-20 15:31:49 +01:00
collection_creates_list_2.xml
…
collection_creates_list_fail.xml
…
collection_creates_list_of_pairs.xml
Add testcase
2021-10-02 20:27:03 +02:00
collection_creates_list.xml
…
collection_creates_pair_format.xml
remove test for actions from collection_creates_pair_format
2024-07-30 13:01:51 +02:00
collection_creates_pair_from_type.xml
…
collection_creates_pair_from_work_dir.xml
Lint collection_creates_pair_from_work_dir tool
2021-01-07 16:51:18 +00:00
collection_creates_pair_y.yml
YAML test for collection WIP.
2026-02-12 15:58:16 -05:00
collection_creates_pair.xml
add test tool testing collection default format
2021-03-04 18:37:17 +01:00
collection_list_2x_or_3x_nested.xml
More workflow mapping test cases.
2025-05-03 10:21:17 -04:00
collection_list_or_nested_list_input.xml
Test case for bug where workflow collection mapping interprets collection at wrong rank.
2025-05-03 10:21:17 -04:00
collection_list_paired_or_unpaired.xml
Implement paired_or_unpaired collections, list wizards.
2025-05-09 17:39:38 -04:00
collection_mixed_param.xml
…
collection_nested_default.xml
Implement default locations for data and collection parameters.
2023-11-01 11:52:44 -04:00
collection_nested_test.xml
…
collection_optional_param.xml
…
collection_paired_conditional_structured_like.xml
Always attempt to build tool request for new API endpoint
2026-06-15 08:56:03 +02:00
collection_paired_default.xml
Implement default locations for data and collection parameters.
2023-11-01 11:52:44 -04:00
collection_paired_or_list_paired_input.xml
More workflow mapping test cases.
2025-05-03 10:21:17 -04:00
collection_paired_or_unpaired.xml
Implement paired_or_unpaired collections, list wizards.
2025-05-09 17:39:38 -04:00
collection_paired_structured_like_with_data_input.xml
Rename test tool to describe shape, not test scenario
2026-05-19 19:50:56 +02:00
collection_paired_structured_like.xml
…
collection_paired_test_y.yml
Implement collection input runtimeify for YAML tools.
2026-02-12 15:58:16 -05:00
collection_paired_test.xml
Apply suggestions from code review
2023-09-07 22:02:15 +02:00
collection_record_test_two_files.xml
[WIP] Implement records - heterogenous dataset collections.
2025-05-09 16:38:19 -04:00
collection_split_on_column.xml
Add test that ensures irrelevant outputs are not copied back
2026-01-12 16:08:18 +01:00
collection_two_paired.xml
…
collection_type_source_map_over.xml
…
collection_type_source.xml
…
color_param.xml
…
column_multi_param.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
column_param_configfile.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
column_param_list.xml
Drop test that does not apply to multiple="true" data_column parameters
2021-03-22 09:28:47 +01:00
column_param.xml
column_parameter: use column_names metadata if present
2024-02-15 16:08:46 +01:00
composite_output_tests.xml
Revert "Always create output"
2024-05-21 09:06:22 +02:00
composite_output.xml
Revert "Always create output"
2024-05-21 09:06:22 +02:00
composite_pbed.xml
Fix composite uploads ignoring substitute_name_with_metadata
2026-05-29 18:39:23 +02:00
composite_shapefile.xml
…
composite.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
compressed_bz2_fastq_conversion.xml
…
compressed_bz2_fastq_no_conversion.xml
…
compressed_gz_fastq_conversion.xml
…
compressed_gz_fastq_no_conversion.xml
…
compressed_neostorezip_neostore_conversion.xml
…
compressed_neostorezip_neostore_no_conversion.xml
…
conditional_name_digit_suffix.xml
Fix expand_meta_parameters_async mangling conditional names ending in _N as repeat indices
2026-06-11 20:21:38 +02:00
config_vars.xml
…
configfile_user_defined.yml
Fix test in `configfile_user_defined.yml`
2025-09-08 11:56:34 +01:00
converter_target_datatype.xml
Apply suggestions from code review
2021-06-24 20:39:16 +02:00
create_2.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
create_10.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
create_directory_index.xml
Add `precreate_directory` flag
2025-10-01 09:01:58 +02:00
credentials_test.xml
Add credential integration test tool and configuration
2026-03-16 11:52:56 +01:00
data_manager_add_remove.xml
…
data_manager_add.xml
…
data_manager_select.xml
Fix HDA leak in tool form for data managers (#22674)
2026-05-20 09:01:49 +02:00
data_manager.xml
Fix DataManagerTool.exec_after_process for async API submission
2026-06-15 08:56:03 +02:00
data_optional.xml
add test case for https://github.com/galaxyproject/tools-iuc/issues/5163
2023-03-30 11:18:43 +02:00
data_source.py
…
dbkey_filter_collection.xml
more specific functional tool tests involving fasta_indexes.loc
2021-01-12 13:44:58 +01:00
dbkey_filter_input.xml
Make dbkey_filter_input more realistic, regression test for https://github.com/galaxyproject/galaxy/issues/19975
2025-04-10 16:59:09 +02:00
dbkey_filter_multi_input.xml
more specific functional tool tests involving fasta_indexes.loc
2021-01-12 13:44:58 +01:00
dbkey_output_action.xml
more specific functional tool tests involving fasta_indexes.loc
2021-01-12 13:44:58 +01:00
detect_errors_aggressive.xml
…
detect_errors.xml
Add GalaxyWizard E2E Selenium tests, fix detect_errors stderr redirect
2026-03-18 14:54:16 -04:00
directory_uri_copy_to.py
Apply black formatting.
2022-02-03 07:42:20 -05:00
directory_uri.xml
Add infrastructure for writing to pluggable galaxy file sources.
2020-09-10 09:37:50 -04:00
disambiguate_cond.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
disambiguate_repeats.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
discover_default_ext.xml
Add test tool for default ext handling in discovered collections
2024-06-13 12:53:28 +02:00
discover_long_name.xml
Fail job gracefully when output name exceeds 255 character DB limit
2026-04-03 11:26:38 +02:00
discover_metadata_files.xml
Fix metadata setting for discovered datasets with extended metadata
2022-11-20 16:02:15 +01:00
discover_sort_by_legacy_test.xml
Fix more test case errors caught by parameter validation.
2024-08-09 11:54:19 -04:00
discover_sort_by.xml
extend tests
2025-04-03 10:32:50 +02:00
drill_down.xml
add more doc and test
2022-03-22 18:56:49 +01:00
empty_datasets.xml
…
empty_output.xml
…
empty_select.xml
Cleanup a test tool copy-pasta
2024-08-09 12:47:55 -04:00
environment_variables_inject.xml
…
environment_variables.xml
…
exit_code_from_env.xml
fix test
2025-03-26 18:07:57 +01:00
exit_code_from_file.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
exit_code_oom.xml
fix config file generation
2022-04-21 11:15:07 +02:00
expect_num_outputs.xml
allow only count assertions it test outputs
2025-12-19 13:13:57 +01:00
explicit_container.xml
restructure tests and add tests for explicit container resolvers
2023-06-14 15:28:43 +01:00
explicit_conversion.xml
…
explicit_singularity_container.xml
restructure tests and add tests for explicit container resolvers
2023-06-14 15:28:43 +01:00
export_remote.py
Fix running pytest test/integration/test_remote_files.py::RemoteFilesIntegrationTestCase directly.
2021-12-08 11:33:13 -05:00
export_remote.xml
Fix running pytest test/integration/test_remote_files.py::RemoteFilesIntegrationTestCase directly.
2021-12-08 11:33:13 -05:00
expression_forty_two.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
expression_log_line_count.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
expression_null_handling_boolean.xml
Fix ToolExpressionOutput.to_model() for boolean type.
2026-03-10 08:57:22 -04:00
expression_null_handling_float.xml
Null handling and optional values for integers, floats, and text parameters.
2020-11-12 15:08:35 -05:00
expression_null_handling_integer.xml
Null handling and optional values for integers, floats, and text parameters.
2020-11-12 15:08:35 -05:00
expression_null_handling_text.xml
Null handling and optional values for integers, floats, and text parameters.
2020-11-12 15:08:35 -05:00
expression_parse_int.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
expression_pick_larger_file.xml
Add regression test for https://github.com/galaxyproject/galaxy/issues/19245
2025-01-27 15:35:42 +01:00
expression_text_to_bool.xml
Fix NoReplacement handling in workflow callback_helper
2026-03-06 17:23:32 +01:00
expression_tools
Implement pick_values expression tool...
2020-11-17 11:46:36 +01:00
fail_identifier.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
fail_writing_work_dir_file.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
filter_attribute_value_splitter.xml
attribute value filter
2023-04-12 10:48:33 +00:00
filter_data_table.xml
Update test/functional/tools/filter_data_table.xml
2024-11-21 17:36:36 +01:00
filter_multiple_splitter.xml
tests for multiple value splitter
2021-04-06 18:32:19 +02:00
filter_param_value_ref_attribute.xml
make param_value filter work with multi data inputs
2022-01-11 15:54:42 +01:00
filter_param_value.xml
Skip `param_value` filter if ref value is runtime value
2025-05-04 16:48:33 +02:00
filter_static_regexp.xml
Fix indentation in cheetah
2023-02-07 18:40:33 +01:00
float_default.xml
Add failing test case for #19678
2025-02-25 11:39:58 -05:00
format_source_in_conditional.xml
Test `format_source` with conditional inputs
2023-06-01 17:50:30 +02:00
from_work_dir_glob.xml
Fix and extend extended metadata outputs to working directory tests
2023-09-12 13:07:10 +02:00
galaxy_json_discover_and_sleep.xml
Fix more test case errors caught by parameter validation.
2024-08-09 11:54:19 -04:00
galaxy_slots_and_memory.xml
Add test
2025-05-21 17:09:06 +01:00
gzipped_inputs.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
help_features_markdown.xml
Improvements to help terms & tool help.
2024-08-23 11:03:13 -04:00
help_features_rst.xml
Improvements to help terms & tool help.
2024-08-23 11:03:13 -04:00
hidden_param.xml
…
html_output_with_extra_files.xml
Add trailing slash to dataset display URL and playwright test
2026-03-04 14:35:49 +01:00
html_output.xml
Test sanitization
2025-02-11 14:36:20 +01:00
identifier_all_collection_types.xml
Add more test scenarios
2022-11-08 22:16:20 +01:00
identifier_collection.xml
…
identifier_in_actions.xml
Fix setting metadata elements in conditional tool action
2022-08-25 14:27:44 +02:00
identifier_in_conditional.xml
fix typo
2021-04-07 19:38:25 +02:00
identifier_multiple_in_conditional.xml
Merge branch 'release_21.09' into release_22.01
2022-02-11 13:29:04 +01:00
identifier_multiple_in_repeat.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
identifier_multiple.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
identifier_single_in_repeat.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
identifier_single.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
identifier_source.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
image_diff.xml
Fix for bool images`
2026-01-07 18:11:13 +01:00
implicit_collection_conversion.xml
…
implicit_conversion_format_input.xml
Tighten conversion target input
2024-11-19 17:33:58 +01:00
implicit_conversion_optional_param.xml
Add test tool for triggering implicit bigwig to wig converter
2023-05-24 10:54:31 +02:00
implicit_conversion.xml
…
implicit_default_conds.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
implicit_nested_list_conversion.xml
…
inheritance_simple.xml
…
inputs_as_json_profile.xml
Always attempt to build tool request for new API endpoint
2026-06-15 08:56:03 +02:00
inputs_as_json_with_paths.xml
Always attempt to build tool request for new API endpoint
2026-06-15 08:56:03 +02:00
inputs_as_json_with_staging_path_and_source_path.xml
Fix single data element identifier to be a regular string
2025-06-11 20:02:54 +02:00
inputs_as_json.xml
Always attempt to build tool request for new API endpoint
2026-06-15 08:56:03 +02:00
integer_default.xml
Allow non-optional integer/float params without `value` attribute
2023-11-02 17:19:43 +00:00
interactivetool_simple.xml
Add templating to test IT
2024-02-10 12:15:12 +01:00
interactivetool_two_entry_points.xml
Add testcase and move stop operation into API
2020-12-12 11:26:09 +01:00
is_of_type.xml
Fix is_of_type for datasets in a collection
2021-09-09 11:45:53 +02:00
is_valid_xml.xml
…
job_environment_default_legacy.xml
Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc
2024-06-21 16:58:21 +02:00
job_environment_default.xml
Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc
2024-06-21 16:58:21 +02:00
job_environment_explicit_isolated_home.xml
Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc
2024-06-21 16:58:21 +02:00
job_environment_explicit_shared_home.xml
Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc
2024-06-21 16:58:21 +02:00
job_properties.xml
Fix and extend extended metadata outputs to working directory tests
2023-09-12 13:07:10 +02:00
legacy_interpreter_write_output.py
Implement tool upgrade assistant script.
2024-08-24 11:22:43 -04:00
legacy_interpreter.xml
Implement tool upgrade assistant script.
2024-08-24 11:22:43 -04:00
legacy_r.xml
…
markdown_report_extra_files.xml
Tool markdown reports.
2025-05-02 11:25:21 -04:00
markdown_report_from_script.xml
Tool markdown reports.
2025-05-02 11:25:21 -04:00
markdown_report_simple_script.py
Tool markdown reports.
2025-05-02 11:25:21 -04:00
markdown_report_simple.xml
Tool markdown reports.
2025-05-02 11:25:21 -04:00
maxseconds.xml
…
md5sum.xml
Add file_name property on DatasetFilenameWrapper
2023-12-01 19:57:38 +01:00
metadata_bam.xml
Update test/functional/tools/metadata_bam.xml
2020-07-09 15:21:43 +02:00
metadata_bcf.xml
Merge branch 'release_20.09' into release_21.01
2021-03-12 17:12:04 +00:00
metadata_bed.xml
test case showing failing set_meta
2022-08-25 16:45:26 +02:00
metadata_biom1.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
metadata_check_eq.xml
add value_json
2023-06-06 10:02:30 +02:00
metadata_column_names.xml
Assert column_types
2025-03-25 10:29:01 +01:00
metadata.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
min_repeat.xml
Always attempt to build tool request for new API endpoint
2026-06-15 08:56:03 +02:00
model_attributes.xml
API test case to ensure dataset names get escaped during tool evaluation.
2021-08-18 13:41:06 -04:00
mulled_example_broken_no_requirements_fallback.xml
containers: do not mount /tmp/
2023-06-14 15:28:38 +01:00
mulled_example_broken_no_requirements.xml
containers: do not mount /tmp/
2023-06-14 15:28:38 +01:00
mulled_example_conflict.xml
…
mulled_example_explicit.xml
containers: do not mount /tmp/
2023-06-14 15:28:38 +01:00
mulled_example_invalid_case.xml
containers: do not mount /tmp/
2023-06-14 15:28:38 +01:00
mulled_example_multi_1.xml
Switch to only MIT license
2026-03-06 19:05:20 +01:00
mulled_example_multi_incomplete.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
mulled_example_multi_versionless.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
mulled_example_simple.xml
containers: do not mount /tmp/
2023-06-14 15:28:38 +01:00
multi_data_optional.xml
…
multi_data_param.xml
…
multi_data_repeat.xml
…
multi_output_assign_primary2.xml
add test cases showing bug
2024-01-10 14:34:14 +01:00
multi_output_assign_primary_ext_dbkey.xml
add test tool to integration tests
2020-09-09 10:35:14 +02:00
multi_output_assign_primary.xml
add test cases showing bug
2024-01-10 14:34:14 +01:00
multi_output_configured.xml
…
multi_output_recurse_collection.xml
add test for correct sorting on recursive discovery
2022-04-08 19:38:50 +02:00
multi_output_recurse.xml
fix profile of multi_output_recurse
2022-04-07 12:24:12 +02:00
multi_output.xml
…
multi_repeats.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
multi_select.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
multiple_versions_changes_v01.xml
Bug fixes for tool test case invalidation...
2024-08-05 09:44:43 -04:00
multiple_versions_changes_v02.xml
Bug fixes for tool test case invalidation...
2024-08-05 09:44:43 -04:00
multiple_versions_hidden_v01.xml
hide hidden tools in the tool form for real
2026-03-22 13:49:12 +01:00
multiple_versions_hidden_v02.xml
hide hidden tools in the tool form for real
2026-03-22 13:49:12 +01:00
multiple_versions_sorting_v19.xml
Fixtures for manually ensuring we don't lexiographically sort tool versions.
2025-11-04 11:32:38 -05:00
multiple_versions_sorting_v110.xml
Fixtures for manually ensuring we don't lexiographically sort tool versions.
2025-11-04 11:32:38 -05:00
multiple_versions_v01.xml
Fix more test case errors caught by parameter validation.
2024-08-09 11:54:19 -04:00
multiple_versions_v01galaxy6.xml
Bug fixes for tool test case invalidation...
2024-08-05 09:44:43 -04:00
multiple_versions_v02.xml
Fix more test case errors caught by parameter validation.
2024-08-09 11:54:19 -04:00
options_from_metadata_file.xml
Fix stray xml attribute that does nothing.
2024-08-26 16:55:48 -04:00
output_action_change_format_paired.xml
…
output_action_change_format.xml
Always attempt to build tool request for new API endpoint
2026-06-15 08:56:03 +02:00
output_auto_format.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
output_collection_filter.xml
…
output_empty_work_dir.xml
Lint output_empty_work_dir tool
2021-01-07 16:47:15 +00:00
output_filter_exception_1.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
output_filter_with_input_optional.xml
Failing test case for output problem.
2021-03-14 19:58:31 -04:00
output_filter_with_input.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
output_filter.xml
Add function test for filtering outputs in repeats
2025-12-22 13:51:45 +01:00
output_format_collection.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
output_format_deprecated_when.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
output_format_input.xml
Implement tool upgrade assistant script.
2024-08-24 11:22:43 -04:00
output_format.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
output_order.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
parallelism_optional.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
parallelism.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
param_text_option.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
paths_as_file.xml
…
python_environment_problem.py
Apply black formatting.
2022-02-03 07:42:20 -05:00
python_environment_problem.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
qc_stdout.xml
fix api test
2024-03-01 22:45:38 -05:00
README.txt
Rename samples_tool_conf to sample_tool_conf to match datatypes/data_manager naming convention
2023-01-10 10:03:23 -05:00
remote_test_data_location.xml
Update XSD schema docs
2023-06-28 12:31:42 +02:00
remove_value.xml
more specific functional tool tests involving fasta_indexes.loc
2021-01-12 13:44:58 +01:00
resource_requirements.xml
Add timelimit resource requirement type for Galaxy XML/YAML tools.
2026-02-25 01:59:33 -05:00
sam_to_bam.xml
fix framework test
2023-09-08 13:16:52 +02:00
sam_to_unsorted_bam.xml
fix functional test
2023-09-09 13:19:47 +02:00
sample_data_manager_conf.xml
Fix HDA leak in tool form for data managers (#22674)
2026-05-20 09:01:49 +02:00
sample_datatypes_conf.xml
Add bwa_index format
2026-03-30 15:58:40 -04:00
sample_tool_conf.xml
Fix expand_meta_parameters_async mangling conditional names ending in _N as repeat indices
2026-06-11 20:21:38 +02:00
secret_tool.xml
Add container requirement to secret_tool test fixture
2026-02-11 16:24:41 +01:00
section_24_2.xml
Tool test case parameter models.
2024-08-23 09:46:44 -04:00
section.xml
Always attempt to build tool request for new API endpoint
2026-06-15 08:56:03 +02:00
select_dynamic.xml
make test more precise
2023-10-21 15:31:30 +02:00
select_from_csvdataset.xml
fix test
2022-08-18 14:28:55 +02:00
select_from_data_table_no_name.xml
Add functional test
2026-05-28 18:37:15 +03:00
select_from_dataset_in_conditional.xml
Add test tool w/ dynamic select in conditional
2024-04-02 19:10:20 +02:00
select_from_dataset_optional.xml
Add switch for optional select in workflow editor
2021-06-14 12:49:51 +02:00
select_from_dataset.xml
fix name and value column in select_from_dataset.xml
2021-01-12 19:27:07 +01:00
select_from_url.xml
...
2024-12-19 16:54:03 +01:00
select_optional_legacy.xml
Fix typo
2025-04-15 15:09:32 +02:00
select_optional.xml
Tool Request models.
2024-09-30 13:25:02 -04:00
sim_size_delta.xml
add delta_frac attribute to specify relative size differences
2020-05-05 13:29:47 +02:00
simple_constructs.xml
Fix tool request API for multiple select parameters with defaults.
2025-12-10 09:44:08 -05:00
simple_constructs.yml
Modeling and validation of YAML tool test cases.
2026-02-12 10:50:13 -05:00
special_params.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
strict_shell_default_off.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
strict_shell_profile.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
strict_shell.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
test_data_source.xml
Try to fix API test
2024-02-08 21:14:07 +01:00
text_repeat.xml
add selenium test for reordering repeat blocks
2023-08-14 10:29:45 +02:00
tool_directory_copy.xml
Fix transfer of $_TOOL_DIRECTORY subdirectories
2025-03-13 16:19:10 +01:00
tool_directory_docker.xml
Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc
2024-06-21 16:58:21 +02:00
tool_directory.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
tool_provided_metadata_1.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
tool_provided_metadata_2.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
tool_provided_metadata_3.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
tool_provided_metadata_4.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
tool_provided_metadata_5.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
tool_provided_metadata_6.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
tool_provided_metadata_7.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
tool_provided_metadata_8.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
tool_provided_metadata_9.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
tool_provided_metadata_10.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
tool_provided_metadata_11.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
tool_provided_metadata_12.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
top_level_data.xml
Always attempt to build tool request for new API endpoint
2026-06-15 08:56:03 +02:00
ucsc_tablebrowser.xml
Add selenium test for ucsc table browser data source
2022-06-13 11:03:13 +02:00
unicode_stream.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
upload_tool_conf.xml
…
upload.py
…
upload.xml
…
use_directory_index.xml
Adjust test tool and datatype config to best practices
2025-02-26 13:18:25 +01:00
validation_dataset_metadata_in_file.xml
Use loc file that actually exists in the param validators of test tool
2022-09-30 01:19:43 +01:00
validation_default.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
validation_empty_dataset.xml
fix output assertion in test tool
2021-01-08 12:44:39 +01:00
validation_hdf5.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
validation_image.xml
Add test for content assertions with bool image
2026-01-03 11:59:13 +01:00
validation_metadata_in_datatable.xml
remove TODOs from functional tool tests
2021-08-02 15:02:11 +02:00
validation_metadata_in_range.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
validation_repeat.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
validation_sanitizer.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
validation_tar_gz.xml
tests: check ftype and decompress
2024-02-26 14:08:12 +01:00
validation_tar.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
validation_value_in_datatable.xml
fix value_in_data_table validator for multiple selects
2021-11-17 15:55:01 +01:00
validation_zip.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
vcf_bgzip.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
version_command_interpreter.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
version_command_plain.xml
Progress toward fixing extended metadata with Pulsar
2022-11-02 08:59:12 -04:00
version_command_tool_dir.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
version_command.py
Drop support for retired Python 3.5
2020-10-07 11:52:13 +01:00

README.txt 

This directory contains tools only useful for testing and
demonstrating aspects of the tool syntax. Run the test driver script
'run_tests.sh' with the '-framework' as first argument to run through
these tests. Pass in an '-id' along with one of these tool ids to test
a single tool.

Some API tests use these tools to test various features of the API,
tool, and workflow subsystems. Pass the argument
'-with_framework_test_tools' to 'run_tests.sh' in addition to '-api'
to ensure these tools get loaded during the testing process.

Finally, to play around with these tools interactively - simply
replace the 'galaxy.ini' option 'tool_config_file' with:

tool_config_file = test/functional/tools/sample_tool_conf.xml
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