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galaxy/test/functional/tools
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Dannon Baker 5ac7306c91 Merge remote-tracking branch 'upstream/release_22.05' into release_23.0
2023-02-08 11:56:34 -05:00
..
for_tours
…
for_workflows
Test that metadata validators work
2022-06-25 12:55:51 +02:00
realtime/simple
Rebase into intergration testsing..
2019-05-22 08:18:52 -04:00
bibtex.xml
Fix selenium test (bibtex rendering)
2022-01-03 16:18:20 -05:00
boolean_conditional.xml
…
cat_data_and_sleep.xml
Add DELETE /api/jobs/<job_id> as a job cancellation API endpoint.
2017-11-08 15:54:15 -05:00
catDocker.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
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
…
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
Dataset collection state UX test case.
2017-11-30 10:02:03 -05:00
collection_creates_dynamic_nested_from_json_elements.xml
Allow discovering dataset collections in galaxy.json in a nested fashion.
2017-08-17 15:41:11 -04:00
collection_creates_dynamic_nested_from_json.xml
Allow discovering datasets directly from galaxy.json...
2017-08-17 15:41:10 -04:00
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
add indentation to for cycle content
2017-05-16 14:10:53 -04:00
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
add test tool testing collection default format
2021-03-04 18:37:17 +01:00
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
Fix for parsing collection outputs for YAML/dictified tools.
2018-12-26 11:59:06 -05:00
collection_creates_pair.xml
add test tool testing collection default format
2021-03-04 18:37:17 +01:00
collection_mixed_param.xml
…
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_structured_like.xml
[18.01] Fix structured_like unqualified references + test.
2018-05-17 16:50:40 -04:00
collection_paired_test.xml
Provide feedback on why workflow editor nodes won't connect.
2019-04-01 11:34:00 -04:00
collection_split_on_column.xml
MacOS X fix for a test tool.
2017-10-13 19:30:33 -04:00
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
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
composite_output_tests.xml
Quote remaining parametera
2018-12-31 14:32:40 +01:00
composite_output.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
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
added tests
2017-06-13 16:09:00 +02:00
compressed_neostorezip_neostore_no_conversion.xml
added tests
2017-06-13 16:09:00 +02:00
config_vars.xml
Improvements for mule job handler testing. Ensure that the server
2017-08-31 14:30:46 -04:00
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
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_source.py
Simple tests for data source responses.
2017-10-25 14:46:16 -04:00
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
add tests
2021-01-12 13:45:45 +01:00
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
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
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_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
Rework new collection order testing in 20.09.
2020-10-15 15:36:57 -04:00
discover_sort_by.xml
implement expect_test_failure attribute for tests
2021-11-22 12:26:03 +01:00
drill_down.xml
add more doc and test
2022-03-22 18:56:49 +01:00
empty_datasets.xml
Fix to respect galaxy.json supplied metadata for empty outputs.
2017-09-28 11:18:09 -04:00
empty_output.xml
…
empty_select.xml
Add test tool for empty optional select
2018-05-25 18:33:51 +01:00
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
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
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
Apply suggestions from code review
2022-04-22 12:05:56 +02:00
explicit_conversion.xml
…
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
Harden, formalize 'null' handling around booelan tool parameters and between workflow steps.
2020-11-11 19:44:16 -05:00
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
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
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_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
make param_value filter work with multi data inputs
2022-01-11 15:54:42 +01:00
filter_static_regexp.xml
more specific functional tool tests involving fasta_indexes.loc
2021-01-12 13:44:58 +01:00
from_work_dir_glob.xml
Disable created_from_basename test, doesn't work with default setup
2021-10-31 14:19:38 +01:00
galaxy_json_discover_and_sleep.xml
Add test that verifies visible doesn't revert on job finish
2023-02-08 11:56:00 +01:00
gzipped_inputs.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
hidden_param.xml
Test that workflows with hidden params can be run
2019-03-04 18:41:51 +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
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
Fix format="input" with implicit conversions
2021-03-31 22:06:39 +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
Provide $input.serialize(), allow wrap_json to serialize collections
2021-05-28 22:49:49 +02:00
inputs_as_json.xml
fix profile logic for configfile generation
2021-02-18 12:33:07 +01:00
interactivetool_simple.xml
Fix id convention for test interactive tools.
2019-10-30 09:59:55 -04:00
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
Test that tempdir creation is possible
2022-11-21 11:44:24 +01:00
job_environment_default.xml
Test that tempdir creation is possible
2022-11-21 11:44:24 +01:00
job_environment_explicit_isolated_home.xml
Test that tempdir creation is possible
2022-11-21 11:44:24 +01:00
job_environment_explicit_shared_home.xml
Test that tempdir creation is possible
2022-11-21 11:44:24 +01:00
job_properties.xml
Extend kubernetes logs to check that job logs are properly recorded
2022-03-19 12:11:41 +01:00
legacy_r.xml
…
library_data.xml
…
maxseconds.xml
…
md5sum.xml
…
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_column_names.xml
…
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
Support setting per-job-environment container resolvers using the container_resolvers key in the environment config.
2021-08-17 10:28:51 -04:00
mulled_example_broken_no_requirements.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
mulled_example_conflict.xml
…
mulled_example_explicit.xml
Implement bioconductor xref on the frontend.
2022-02-02 14:56:07 -05:00
mulled_example_invalid_case.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
mulled_example_multi_1.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
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
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
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_primary_ext_dbkey.xml
add test tool to integration tests
2020-09-09 10:35:14 +02:00
multi_output_assign_primary.xml
…
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
wf refactor API - add upgrade_tool action
2021-01-03 19:52:28 -05:00
multiple_versions_changes_v02.xml
wf refactor API - add upgrade_tool action
2021-01-03 19:52:28 -05:00
multiple_versions_v01.xml
Merge API GalaxyInteractorTestCase into integration test
2021-09-23 19:05:30 +02:00
multiple_versions_v01galaxy6.xml
breaking test for GalaxyInteractorApi get_tool_tests
2021-04-29 23:50:12 +10:00
multiple_versions_v02.xml
Merge API GalaxyInteractorTestCase into integration test
2021-09-23 19:05:30 +02:00
options_from_metadata_file.xml
fix test output
2022-07-15 10:49:12 +02:00
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
revert changes to test tool
2022-01-30 15:21:34 +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.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
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
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
remove_value.xml
more specific functional tool tests involving fasta_indexes.loc
2021-01-12 13:44:58 +01:00
resource_requirements.xml
adding test extensions for GPU
2022-12-14 11:03:34 +01:00
sam_to_bam.xml
add ftype for sam_to_bam test
2021-05-27 15:17:44 +02:00
sam_to_unsorted_bam.xml
Rename datatype extension 'bam_native' to 'unsorted.bam'.
2018-03-12 12:29:57 -04:00
sample_data_manager_conf.xml
…
sample_datatypes_conf.xml
Fix errors in loading functional test tools
2021-12-08 08:14:13 +00:00
sample_tool_conf.xml
Merge remote-tracking branch 'upstream/release_22.05' into release_23.0
2023-02-08 11:56:34 -05:00
section.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
select_from_csvdataset.xml
fix test
2022-08-18 14:28:55 +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_optional.xml
restructure tests
2021-12-16 09:55:12 +01:00
sim_size_delta.xml
add delta_frac attribute to specify relative size differences
2020-05-05 13:29:47 +02:00
simple_constructs.xml
Lint a bunch of test tools
2021-01-05 12:39:53 +00:00
simple_constructs.yml
Fixup simple_constructs.yml...
2022-04-19 11:23:44 -04:00
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
Remove deprecated `interpreter attribute from tools <command>`
2020-03-05 12:53:09 +01:00
tool_directory_docker.xml
Add test case for https://github.com/galaxyproject/pulsar/issues/249
2021-03-11 16:17:06 +01:00
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
…
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
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validation_metadata_in_datatable.xml
remove TODOs from functional tool tests
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validation_metadata_in_range.xml
Lint a bunch of test tools
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validation_repeat.xml
Lint a bunch of test tools
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validation_sanitizer.xml
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validation_tar_gz.xml
Lint a bunch of test tools
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validation_tar.xml
Lint a bunch of test tools
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validation_value_in_datatable.xml
fix value_in_data_table validator for multiple selects
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validation_zip.xml
Lint a bunch of test tools
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vcf_bgzip.xml
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version_command_interpreter.xml
Lint a bunch of test tools
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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
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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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