galaxy

mirror of https://github.com/galaxyproject/galaxy.git synced 2026-10-30 18:13:23 +08:00

Files

T

mvdbeek 7d15049c48 Fix bam conversion test tool

Starting with 16344a6 we attempt to set metadata also for files that have no
content. BAM files need to contain at least a header. To avoid failing tests we
only create the appropriate output based on the input.

2018-01-19 20:16:26 +01:00

for_tours

Replace CasperJS browser tests with Selenium tests.

2016-11-30 17:44:11 -05:00

for_workflows

Allow mapping over empty collections.

2017-11-30 10:02:02 -05:00

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

Improved Cheetah type casting for int/float types.

2015-04-16 09:34:08 -04:00

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_creates_dynamic_list_of_pairs.xml

Add some docs to more complicated nested collection creation examples.

2015-07-31 15:13:00 +01:00

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.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_test.xml

Small tweaks to some functional test tools.

2014-09-03 08:43:25 -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.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.xml

Reduced usage of from_work_dir in test tools.

2017-01-20 14:05:28 -05:00

composite_output_tests.xml

Test and clarifications for composite uploads.

2017-08-31 12:47:40 -04:00

composite_output.xml

Test and clarifications for composite uploads.

2017-08-31 12:47:40 -04:00

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.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

Allow dbkey filtering of multiple input targets.

2015-07-31 11:09:45 +01:00

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

Implement detect_errors attribute on XML.

2015-04-15 12:38:35 -04:00

disambiguate_cond.xml

Fix errors when starting "./run_tests.sh -with_framework_test_tools -api"

2015-09-25 17:51:21 +01:00

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

environment_variables.xml

Add more interesting expression to environment_variables demo tool.

2015-06-24 08:55:44 -04:00

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

fail_identifier.xml

Replace collection elements with re-run output

2017-12-31 14:08:26 +02:00

gzipped_inputs.xml

Fix gz/zip upload of files to test framework.

2014-12-17 09:38:49 -05:00

identifier_collection.xml

XSD discovered tool problems.

2016-09-08 11:40:01 -04:00

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_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.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_conversion.xml

Reduced usage of from_work_dir in test tools.

2017-01-20 14:05:28 -05:00

implicit_default_conds.xml

Fixes related to implicit defaults of param values.

2013-11-21 23:37:22 -06:00

inheritance_simple.xml

Add test tool demonstrating/testing type inheritance.

2015-04-09 09:41:43 -04:00

inputs_as_json.xml

XSD discovered tool problems.

2016-09-08 11:40:01 -04:00

is_valid_xml.xml

added functional test for <is_valid_xml>

2017-02-01 21:17:07 -06:00

job_environment_default_legacy.xml

Improved home and temp directory handling.

2018-01-09 09:30:16 -05:00

job_environment_default.xml

Improved home and temp directory handling.

2018-01-09 09:30:16 -05:00

job_environment_explicit_shared_home.xml

Improved home and temp directory handling.

2018-01-09 09:30:16 -05:00

job_properties.xml

Add job resume test with HDCA input to paused dataset

2017-12-31 14:08:26 +02:00

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

Add test for failing handling of BIOM1 metadata.

2016-06-07 12:02:09 -04:00

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 documentation on optional `multiple="true"` data parameters.

2016-10-10 10:51:36 -04:00

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

Added support for recursively discovering output datasets

2017-12-21 22:59:50 +05:30

multi_output.xml

XSD discovered tool problems.

2016-09-08 11:40:01 -04:00

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.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 cases for mapping for outputs with filter statements.

2017-11-30 10:02:01 -05:00

output_filter.xml

Add functional test tool demonstrating output filters.

2014-09-03 08:43:25 -04:00

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

format_source in workflow editor is too restrictive.

2016-02-23 17:16:27 +00:00

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

paired_collection_map_over_structured_like.xml

Fix test tool -- functional test framework appears to not support mapping over test-data

2016-11-22 20:17:13 +01:00

parallelism_optional.xml

Add tool functional test for parallelism with optional inputs.

2014-03-16 20:41:42 -05:00

parallelism.xml

Add example tool with task splitting to tool functional framework tests.

2014-01-28 14:34:26 -06:00

param_text_option.xml

Document using options within a text parameter.

2017-01-09 13:57:57 -05:00

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

README.txt

Minor typos fixed in test/functional/tools/README.txt

2015-04-10 16:38:34 -04:00

sam_to_bam_native.xml

Fix bam conversion test tool

2018-01-19 20:16:26 +01:00

sam_to_bam.xml

Add sam-to-bam conversion test tool

2016-11-16 22:01:47 +01:00

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

Fix datatype order

2018-01-17 18:11:31 +01:00

samples_tool_conf.xml

Merge pull request #5193 from jmchilton/structured_job_environment_1

2018-01-19 11:33:26 -05:00

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

Allow override of provided metadata location.

2017-08-17 15:41:11 -04:00

top_level_data.xml

Test tool fixes.

2015-03-15 09:53:05 -04:00

unicode_stream.xml

Improved unicode handling stdout/stderr/command_line.

2015-11-10 12:59:22 +00:00

upload_tool_conf.xml

Rename shed_conf attribute to is_shed_conf.

2016-04-01 10:01:54 -04:00

upload.py

Add new option, tools, and data to functional test framework to test/demonstrate tool framework itself.

2013-11-21 19:17:12 -06:00

upload.xml

Add new option, tools, and data to functional test framework to test/demonstrate tool framework itself.

2013-11-21 19:17:12 -06:00

validation_default.xml

Synchronize validation of workflows between web and API controllers.

2014-09-10 11:51:10 -04:00

validation_empty_dataset.xml

Implement dataset empty input validator.

2016-02-26 10:39:04 +00:00

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

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