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galaxy/test/functional/tools
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John ChiltonandClaude Opus 4.6 2a0f9155be Add GalaxyWizard E2E Selenium tests, fix detect_errors stderr redirect 
Add data-description attributes to GalaxyWizard.vue and DatasetError.vue
for test selectors. Add navigation helpers and Selenium test exercising
the inline error analysis widget with the static agent backend.

Fix broken stderr redirect in detect_errors.xml (>2& → >&2).

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
2026-03-18 14:54:16 -04:00
..
.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
Implement default locations for data and collection parameters.
2023-11-01 11:52:44 -04:00
parameters
Add any-collection-type YAML tool with comprehensive job_runtime specs.
2026-02-12 15:58:17 -05:00
realtime/simple
Rebase into intergration testsing..
2019-05-22 08:18:52 -04:00
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
[18.01] Fix structured_like unqualified references + test.
2018-05-17 16:50:40 -04:00
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.xml
[18.01] Fix structured_like unqualified references + test.
2018-05-17 16:50:40 -04:00
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
Add test tool and workflow for mapping over with mapping output
2018-06-20 09:54:40 -04:00
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_shapefile.xml
make tests stricter
2019-04-30 09:47:06 +02:00
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
…
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
data_manager_add_remove.xml
Give test data managers distinct ids and names
2019-11-06 14:33:45 +01:00
data_manager_add.xml
Give test data managers distinct ids and names
2019-11-06 14:33:45 +01:00
data_manager.xml
Give test data managers distinct ids and names
2019-11-06 14:33:45 +01:00
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
Don't unhide mapped-over outputs when job fails
2019-03-30 14:49:59 +01:00
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_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
Separate new inject tests into new tool.
2019-10-30 10:09:34 -04:00
environment_variables.xml
Separate new inject tests into new tool.
2019-10-30 10:09:34 -04:00
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.
2026-03-08 10:54:39 -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
Test that workflows with hidden params can be run
2019-03-04 18:41:51 +01:00
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
Provide element_identifier attribute in DatsetCollectionWrapper
2018-11-20 13:43:08 +01:00
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
Add test tools for implicit coversion of collection input
2019-04-08 18:33:57 +02:00
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
Add double conversion test
2019-04-07 23:15:35 +02:00
implicit_default_conds.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
implicit_nested_list_conversion.xml
Add test tools for implicit coversion of collection input
2019-04-08 18:33:57 +02:00
inheritance_simple.xml
Add test that verifies ftype is being set correctly
2019-04-07 23:15:35 +02:00
inputs_as_json_profile.xml
fix profile logic for configfile generation
2021-02-18 12:33:07 +01:00
inputs_as_json_with_paths.xml
Provide $input.serialize(), allow wrap_json to serialize collections
2021-05-28 22:49:49 +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
fix profile logic for configfile generation
2021-02-18 12:33:07 +01:00
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
…
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
Add a test for not providing an optional input
2018-06-12 18:18:13 +02:00
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
Remove collect_outputs_from option.
2018-12-20 10:45:42 -05:00
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_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
Test case for mapping over inputs with output ftype determined via input extension
2018-06-04 07:00:41 -04:00
output_action_change_format.xml
extend docs and tests for conditional output actions
2022-07-12 14:51:38 +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
…
sample_datatypes_conf.xml
datatype added for lexicmap index
2025-07-14 10:43:36 -04:00
sample_tool_conf.xml
Merge pull request #22020 from mvdbeek/schema-building-changes
2026-03-11 09:30:51 +01:00
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
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
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_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
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
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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