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galaxy/test/functional/tools
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Bjoern Gruening e2792994da move default notebook as well 
(cherry picked from commit 6d8848e399)
2019-09-11 10:18:08 +02:00
..
for_tours
Replace CasperJS browser tests with Selenium tests.
2016-11-30 17:44:11 -05:00
for_workflows
Merge pull request #6684 from nsoranzo/deprecate_param_size
2018-12-12 10:51:28 -05:00
realtime/simple
Rebase into intergration testsing..
2019-05-22 08:18:52 -04:00
bibtex.xml
Simple tool test for citations.
2017-11-24 15:25:19 -05:00
boolean_conditional.xml
Fixes for boolean & select handling in test data elements.
2015-05-19 12:43:32 -04:00
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
Allow tools and deployers to specify optional Docker-based dependency resolution.
2014-06-07 01:45:05 -05:00
checksum.xml
Fix output tests for checksum example tools.
2017-02-02 09:31:23 -05:00
cheetah_casting.xml
Fix float to int casting
2019-03-31 17:15:46 +02:00
cheetah_problem_syntax_error.xml
Add another cheetah syntax error example...
2015-11-18 10:45:05 +00:00
cheetah_problem_unbound_var_input.xml
Add example tools demonstrating cheetah problem (unbound variable).
2015-11-18 10:40:57 +00:00
cheetah_problem_unbound_var.xml
Add example tools demonstrating cheetah problem (unbound variable).
2015-11-18 10:40:57 +00:00
code_file.py
Fix all E201 and E202 style errors
2017-08-17 11:35:39 +01:00
code_file.xml
Add code_file example tool from Bjoern.
2014-12-15 14:37:22 -05:00
collection_cat_group_tag_multiple.xml
Flush out collection tag parameters a bit.
2018-07-24 14:31:56 -04:00
collection_cat_group_tag.xml
Flush out collection tag parameters a bit.
2018-07-24 14:31:56 -04:00
collection_creates_dynamic_list_of_pairs.xml
Fix framework tests.
2018-01-31 12:00:38 -05:00
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
Dataset collection state UX test case.
2017-11-30 10:02:03 -05:00
collection_creates_list_2.xml
More configurable format and metadata handling for output collections.
2015-01-15 09:30:00 -05:00
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
Allow tools to explicitly create nested collections with static structure.
2015-07-31 14:10:54 +01:00
collection_creates_list.xml
Allow testing element counts in tool output collections.
2016-03-17 07:39:57 +00:00
collection_creates_pair_from_type.xml
A simpler way to configure output pairs (exploiting static structure).
2015-01-15 09:30:00 -05:00
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
More configurable format and metadata handling for output collections.
2015-01-15 09:30:00 -05:00
collection_mixed_param.xml
Small tweaks to some functional test tools.
2014-09-03 08:43:25 -04:00
collection_nested_test.xml
Bugfix: More left/right -> forward/reverse fixes.
2014-05-27 12:52:41 -05:00
collection_optional_param.xml
Implement optional collection params.
2014-07-25 10:28:50 -05:00
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
Allow using data collection steps via workflow API.
2014-07-28 19:18:40 -04:00
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
Implement type_source on output collections.
2015-11-20 15:32:38 +00:00
color_param.xml
Improved docs and testing for color params.
2016-10-07 09:45:18 -04:00
column_multi_param.xml
XSD discovered tool problems.
2016-09-08 11:40:01 -04:00
column_param_configfile.xml
Test dumping multiple="false" data_column param as json
2018-06-30 09:11:42 -07:00
column_param.xml
Reduced usage of from_work_dir in test tools.
2017-01-20 14:05:28 -05:00
composite_output_tests.xml
Quote remaining parametera
2018-12-31 14:32:40 +01:00
composite_output.xml
Test and clarifications for composite uploads.
2017-08-31 12:47:40 -04:00
composite_shapefile.xml
make tests stricter
2019-04-30 09:47:06 +02:00
composite.xml
Test and clarifications for composite uploads.
2017-08-31 12:47:40 -04:00
compressed_bz2_fastq_conversion.xml
add fastq(*).bz2 datatypes and converters
2016-11-24 15:37:51 +01:00
compressed_bz2_fastq_no_conversion.xml
add fastq(*).bz2 datatypes and converters
2016-11-24 15:37:51 +01:00
compressed_gz_fastq_conversion.xml
add fastq(*).bz2 datatypes and converters
2016-11-24 15:37:51 +01:00
compressed_gz_fastq_no_conversion.xml
add fastq(*).bz2 datatypes and converters
2016-11-24 15:37:51 +01:00
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
create_2.xml
Test renaming multiple different outputs in workflows.
2017-11-15 13:46:01 -05:00
create_10.xml
Improve interaction between job state and purged datasets.
2017-03-20 10:58:23 -04:00
data_manager_add_remove.xml
Add tests for the data manager
2019-06-28 22:18:33 +02:00
data_manager_add.xml
Add tests for the data manager
2019-06-28 22:18:33 +02:00
data_manager.xml
Allow specification of multiple data manager configuration files...
2014-12-15 00:20:35 -05:00
data_source.py
Simple tests for data source responses.
2017-10-25 14:46:16 -04:00
dbkey_filter_input.xml
Add test tool demontrating filtering selections based on dbkey.
2015-07-31 11:09:45 +01:00
dbkey_filter_multi_input.xml
extend test for dbkey filtering
2019-08-16 17:15:44 +02:00
dbkey_output_action.xml
Add a test case to dbkey_output_action.xml.
2016-08-16 14:08:38 -04:00
detect_errors_aggressive.xml
Don't unhide mapped-over outputs when job fails
2019-03-30 14:49:59 +01:00
detect_errors.xml
fixed linting and copy paste errors
2019-03-04 15:38:45 -05:00
disambiguate_cond.xml
Fill in needed state defaults when importing manually curated workflows.
2018-09-24 09:38:34 -04:00
disambiguate_repeats.xml
Improve examples of newer tool functional test features.
2014-02-03 10:11:31 -06:00
empty_datasets.xml
Fix to respect galaxy.json supplied metadata for empty outputs.
2017-09-28 11:18:09 -04:00
empty_output.xml
Implement dataset empty input validator.
2016-02-26 10:39:04 +00:00
empty_select.xml
Add test tool for empty optional select
2018-05-25 18:33:51 +01:00
environment_variables.xml
Add more interesting expression to environment_variables demo tool.
2015-06-24 08:55:44 -04:00
exit_code_from_env.xml
Fix resubmission on tool error detection.
2018-11-23 14:32:04 +01:00
exit_code_from_file.xml
New model tool that filters failed datasets out of a collection.
2016-06-10 13:34:18 -04:00
exit_code_oom.xml
Tool-centric annotation of out of memory errors.
2017-12-22 09:08:18 -05:00
explicit_conversion.xml
Reduced usage of from_work_dir in test tools.
2017-01-20 14:05:28 -05:00
expression_forty_two.xml
Fix expression tool type parsing and docs.
2019-03-20 16:57:38 -04:00
expression_log_line_count.xml
Fix expression tool type parsing and docs.
2019-03-20 16:57:38 -04:00
expression_parse_int.xml
Fix expression tool type parsing and docs.
2019-03-20 16:57:38 -04:00
fail_identifier.xml
Replace collection elements with re-run output
2017-12-31 14:08:26 +02:00
fail_writing_work_dir_file.xml
[18.01] Fix missing job stdout/stderr on Pulsar transfer failures.
2018-02-14 11:30:03 -05:00
filter_static_regexp.xml
add tests for static_value and regexp filter
2019-08-18 16:22:06 +02:00
gzipped_inputs.xml
Fix gz/zip upload of files to test framework.
2014-12-17 09:38:49 -05:00
hidden_param.xml
Test that workflows with hidden params can be run
2019-03-04 18:41:51 +01:00
identifier_collection.xml
Provide element_identifier attribute in DatsetCollectionWrapper
2018-11-20 13:43:08 +01:00
identifier_in_actions.xml
Bug fix - expose proper element_identifier in tool action template expansions. (#5049)
2017-11-20 23:11:00 +01:00
identifier_in_conditional.xml
Add test for single and multi-input identifiers
2018-09-28 19:01:28 +02:00
identifier_multiple_in_conditional.xml
Fix certain aspects of dataset reductions in conditionals/repeats.
2017-04-03 12:19:18 -04:00
identifier_multiple_in_repeat.xml
Fix certain aspects of dataset reductions in conditionals/repeats.
2017-04-03 12:19:18 -04:00
identifier_multiple.xml
XSD discovered tool problems.
2016-09-08 11:40:01 -04:00
identifier_single_in_repeat.xml
Use 4-space indent in identifier_single_in_repeat test tool
2018-06-01 10:56:38 +02:00
identifier_single.xml
XSD discovered tool problems.
2016-09-08 11:40:01 -04:00
identifier_source.xml
Fix the command section (thx @nsoranzo)
2017-08-07 16:42:23 +02:00
implicit_collection_conversion.xml
Add test tools for implicit coversion of collection input
2019-04-08 18:33:57 +02:00
implicit_conversion.xml
Add double conversion test
2019-04-07 23:15:35 +02:00
implicit_default_conds.xml
Fixes related to implicit defaults of param values.
2013-11-21 23:37:22 -06:00
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_with_paths.xml
Allow including paths in inputs json files.
2018-07-05 11:05:15 -04:00
inputs_as_json.xml
XSD discovered tool problems.
2016-09-08 11:40:01 -04:00
interactivetool_simple.xml
standartise naming of IT test tools
2019-08-31 13:32:37 +02:00
interactivetool_two_entry_points.xml
standartise naming of IT test tools
2019-08-31 13:32:37 +02:00
is_valid_xml.xml
added functional test for <is_valid_xml>
2017-02-01 21:17:07 -06:00
job_environment_default_legacy.xml
Fix container integration tests
2019-01-06 15:01:31 +01:00
job_environment_default.xml
Seperate tool and job script standard I/O.
2019-03-04 15:39:07 -05:00
job_environment_explicit_shared_home.xml
Add integration test for remote shell CLI runners
2018-10-10 10:10:51 +02:00
job_properties.xml
Lint job_properties test tool
2018-05-14 19:27:20 +01:00
legacy_r.xml
Samples and defaults for Conda mapping.
2017-01-23 09:47:18 -05:00
library_data.xml
Switch default for library data parameter to multiple entries
2015-04-20 18:31:19 -04:00
maxseconds.xml
Fail maxseconds test tool if sleep is interrupted.
2015-12-05 18:13:07 +00:00
md5sum.xml
Fix output tests for checksum example tools.
2017-02-02 09:31:23 -05:00
metadata_bam.xml
Workaround for metadata_bam.xml failure.
2015-09-19 10:27:09 +01:00
metadata_bcf.xml
Added test for bcf index creation.
2015-04-28 13:45:33 -04:00
metadata_biom1.xml
Allow 4 lines diff to acount for the prefix of python2 unicode strings
2018-08-15 22:30:31 +02:00
metadata_column_names.xml
Implement metadata testing for list metadata.
2016-09-28 11:06:39 -04:00
metadata.xml
Test and clarifications for composite uploads.
2017-08-31 12:47:40 -04:00
min_repeat.xml
Implement failing workflow test case.
2015-09-24 15:40:52 +01:00
mulled_example_conflict.xml
Implement resolve_all on Conda dependency resolver.
2017-01-08 08:24:15 -05:00
mulled_example_explicit.xml
Dockerized job integration testing.
2018-01-09 09:30:15 -05:00
mulled_example_multi_1.xml
Implement beta support for dynamically discovering mulled containers for dependencies.
2016-10-08 10:01:09 -04:00
mulled_example_multi_incomplete.xml
Add a clarification to new test tool.
2017-02-20 11:58:11 -05:00
mulled_example_multi_versionless.xml
Add a test tool for mulled containers with versionless requirements.
2017-06-08 15:42:28 -04:00
mulled_example_simple.xml
Dockerized job integration testing.
2018-01-09 09:30:15 -05:00
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
Implement min/max for multiple data input parameters.
2015-09-21 15:51:58 +01:00
multi_data_repeat.xml
Tests demonstrating multi-data params in repeats are broken.
2016-04-22 10:10:06 -04:00
multi_output_assign_primary.xml
XSD discovered tool problems.
2016-09-08 11:40:01 -04:00
multi_output_configured.xml
XSD discovered tool problems.
2016-09-08 11:40:01 -04:00
multi_output_recurse.xml
Drop optional="true" altogther
2018-03-02 21:33:46 +01:00
multi_output.xml
Remove collect_outputs_from option.
2018-12-20 10:45:42 -05:00
multi_repeats.xml
Clean up tool framework test tools.
2013-11-21 21:17:04 -06:00
multi_select.xml
Merge next-stable.
2014-12-05 20:36:48 -05:00
multiple_versions_v01.xml
Allow multiple tools with the same id in ToolBox.
2014-12-31 18:21:10 -05:00
multiple_versions_v02.xml
Allow multiple tools with the same id in ToolBox.
2014-12-31 18:21:10 -05:00
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
Fix tab problem in test tool.
2016-01-14 06:17:45 +00:00
output_auto_format.xml
Allow setting `auto_format="True" on tool output`s.
2015-04-22 12:45:11 -04:00
output_collection_filter.xml
Implement <filter> tag for output collections.
2015-07-14 10:18:24 +01:00
output_filter_exception_1.xml
Fix typo spotted by @nsoranzo.
2016-07-21 08:55:35 -04:00
output_filter_with_input.xml
Test that switching parameters results in filtered outputs
2019-03-21 20:25:43 +01:00
output_filter.xml
test: added a test check for counting paired collections
2019-02-14 09:25:04 +01:00
output_format_collection.xml
Fix bugs in test and code introduced in PR #1113.
2015-11-23 15:18:57 +00:00
output_format_deprecated_when.xml
Update tool XSD for (hopefully deprecated) change_format syntax.
2017-02-08 14:52:22 -05:00
output_format.xml
Track basename at the time of creation for datasets.
2019-04-20 08:18:39 -04:00
output_order.xml
Allow outputs in tool functional tests to be specified in any order when using API interactor.
2013-11-21 19:17:13 -06:00
parallelism_optional.xml
Use exit code and quote file parameters for paralellism test tools
2018-08-15 22:30:31 +02:00
parallelism.xml
Use exit code and quote file parameters for paralellism test tools
2018-08-15 22:30:31 +02:00
param_text_option.xml
Document using options within a text parameter.
2017-01-09 13:57:57 -05:00
parse_values_from_file.xml
Allow mapping over of expression tool params
2019-05-14 00:14:34 +02:00
paths_as_file.xml
Modify pass_as_file to apply to all Multiple parameters and add test case
2016-02-04 21:11:39 +00:00
python_environment_problem.py
Limit adjusting Galaxy's Python environment to legacy tools.
2017-01-03 13:48:48 -05:00
python_environment_problem.xml
Limit adjusting Galaxy's Python environment to legacy tools.
2017-01-03 13:48:48 -05:00
qc_stdout.xml
Implement workflow invocation reports.
2019-08-30 09:43:01 -04:00
README.txt
Minor typos fixed in test/functional/tools/README.txt
2015-04-10 16:38:34 -04:00
remove_value.xml
Fix tests and name tool more appropriately
2018-10-24 12:11:52 +02:00
sam_to_bam.xml
Add sam-to-bam conversion test tool
2016-11-16 22:01:47 +01:00
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
Allow specification of multiple data manager configuration files...
2014-12-15 00:20:35 -05:00
sample_datatypes_conf.xml
Implement workflow invocation reports.
2019-08-30 09:43:01 -04:00
samples_tool_conf.xml
standartise naming of IT test tools
2019-08-31 13:32:37 +02:00
section.xml
Tool testing sections.
2015-03-23 20:04:49 -04:00
simple_constructs.xml
Fixes for boolean & select handling in test data elements.
2015-05-19 12:43:32 -04:00
simple_constructs.yml
Add EDAM topics to tools and expose in API
2016-05-24 12:17:39 +01:00
special_params.xml
Add functional test tool demonstrating special parameters.
2014-09-03 08:43:25 -04:00
strict_shell_default_off.xml
Introduce strict shell command option.
2016-02-22 09:58:43 +00:00
strict_shell.xml
Introduce strict shell command option.
2016-02-22 09:58:43 +00:00
test_data_source.xml
Simple tests for data source responses.
2017-10-25 14:46:16 -04:00
tool_directory.xml
XSD discovered tool problems.
2016-09-08 11:40:01 -04:00
tool_provided_metadata_1.xml
Overhaul of tool provided job metadata.
2017-08-17 15:41:10 -04:00
tool_provided_metadata_2.xml
Overhaul of tool provided job metadata.
2017-08-17 15:41:10 -04:00
tool_provided_metadata_3.xml
Overhaul of tool provided job metadata.
2017-08-17 15:41:10 -04:00
tool_provided_metadata_4.xml
Overhaul of tool provided job metadata.
2017-08-17 15:41:10 -04:00
tool_provided_metadata_5.xml
Overhaul of tool provided job metadata.
2017-08-17 15:41:10 -04:00
tool_provided_metadata_6.xml
Overhaul of tool provided job metadata.
2017-08-17 15:41:10 -04:00
tool_provided_metadata_7.xml
Allow discovering datasets directly from galaxy.json...
2017-08-17 15:41:10 -04:00
tool_provided_metadata_8.xml
Move determining tool provided metadata style to tool parser.
2017-08-17 15:41:11 -04:00
tool_provided_metadata_9.xml
Track basename at the time of creation for datasets.
2019-04-20 08:18:39 -04:00
tool_provided_metadata_10.xml
Test for 'metadata' in newer style discovered primary datasets.
2018-12-18 15:47:25 -05:00
tool_provided_metadata_11.xml
Tests for tool provided metadata specifing extra files.
2018-12-18 15:54:43 -05:00
tool_provided_metadata_12.xml
Tests for tool provided metadata specifing extra files.
2018-12-18 15:54:43 -05:00
top_level_data.xml
Test tool fixes.
2015-03-15 09:53:05 -04:00
unicode_stream.xml
Change unicode test tool
2019-06-15 20:04:17 +02:00
upload_tool_conf.xml
Rename shed_conf attribute to is_shed_conf.
2016-04-01 10:01:54 -04:00
upload.py
Remove the galaxy-app package for now, and PEP 8 fixes
2016-07-07 13:49:27 -04:00
upload.xml
Remove the galaxy-app package for now, and PEP 8 fixes
2016-07-07 13:49:27 -04:00
validation_default.xml
Add assert for n_lines. This can be used in tool and workflow testing.
2019-08-09 22:00:17 +02:00
validation_empty_dataset.xml
Implement dataset empty input validator.
2016-02-26 10:39:04 +00:00
validation_hdf5.xml
Removed testing using 'containsh5keys' attribute
2019-05-17 10:02:43 -04:00
validation_metadata_in_range.xml
Fix test tool label and tool xsd
2019-03-05 16:00:10 +01:00
validation_repeat.xml
XSD discovered tool problems.
2016-09-08 11:40:01 -04:00
validation_sanitizer.xml
More tool functional tests for validation stuff.
2014-09-16 21:29:10 -04:00
validation_tar_gz.xml
SQUASH: Adding in other archive containers
2019-02-26 16:43:23 -07:00
validation_tar.xml
SQUASH: Adding in other archive containers
2019-02-26 16:43:23 -07:00
validation_zip.xml
SQUASH ME: rename suggestion from @bgruening
2019-02-26 08:36:30 -07:00
vcf_bgzip.xml
Simplify vcf_bgzip.xml test wrapper and fix index file access
2017-07-07 18:29:29 +03:00
version_command_interpreter.xml
Revise and improve `version_command` tag.
2016-09-23 13:31:07 -04:00
version_command_plain.xml
Revise and improve `version_command` tag.
2016-09-23 13:31:07 -04:00
version_command_tool_dir.xml
Revise and improve `version_command` tag.
2016-09-23 13:31:07 -04:00
version_command.py
Revise and improve `version_command` tag.
2016-09-23 13:31:07 -04:00

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/samples_tool_conf.xml
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