galaxy

mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-24 16:30:27 +08:00

Files

T

John Chilton 652bd0fc30 Support selections in interface dict rep of tools.

Expose and test through experimental YAML representation of tools. This doesn't represent official support of (vastly superior) YAML tools, this representation continues to serve as an easy way to exercise the abstract tool parsing interface.

Brings simple_constructs.yml and simple_constructs.xml further in line also.

Test:

    ./run_tests.sh -framework -id simple_constructs_y

2015-10-20 13:49:24 +01:00

for_workflows

Workflow scaling test infrastructure.

2015-03-25 14:54:48 -04:00

bibtex.xml

Add github citation example.

2015-03-16 11:14:01 -04:00

boolean_conditional.xml

Fixes for boolean & select handling in test data elements.

2015-05-19 12:43:32 -04:00

catDocker.xml

Allow tools and deployers to specify optional Docker-based dependency resolution.

2014-06-07 01:45:05 -05:00

cheetah_casting.xml

Improved Cheetah type casting for int/float types.

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

code_file.py

PEP-8 and pylint fixes.

2015-06-16 16:53:49 +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.xml

Add some docs to more complicated nested collection creation examples.

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

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_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

More configurable format and metadata handling for output collections.

2015-01-15 09:30:00 -05:00

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

Allow tools to output collections with a dynamic number of datasets.

2015-01-15 09:30:00 -05:00

collection_two_paired.xml

Allow using data collection steps via workflow API.

2014-07-28 19:18:40 -04:00

column_multi_param.xml

Fix data column parameters pointed at multiple data parameters.

2014-09-26 10:49:43 -04:00

column_param.xml

Fix data column parameters pointed at multiple data parameters.

2014-09-26 10:49:43 -04:00

composite_output.xml

Add more sample tools for tool testing framework.

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

composite.xml

Test tool fixes.

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

data_manager.xml

Allow specification of multiple data manager configuration files...

2014-12-15 00:20:35 -05:00

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

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

environment_variables.xml

Add more interesting expression to environment_variables demo tool.

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

gzipped_inputs.xml

Fix gz/zip upload of files to test framework.

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

identifier_multiple.xml

Expose improved sample tracking to tools for implicit map/reduce ops.

2015-02-02 16:29:42 -05:00

identifier_single.xml

Expose improved sample tracking to tools for implicit map/reduce ops.

2015-02-02 16:29:42 -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

job_properties.xml

Fix apparent typo for tool failure testing

2015-03-11 11:24:14 +00:00

library_data.xml

Switch default for library data parameter to multiple entries

2015-04-20 18:31:19 -04:00

md5sum.xml

Allow testing tool outputs based on MD5 hashes.

2015-04-16 14:19:36 -04:00

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.xml

Check ftype attribute (if defined) on test output datasets.

2014-03-14 10:12:41 -05:00

min_repeat.xml

Implement failing workflow test case.

2015-09-24 15:40:52 +01:00

multi_data_param.xml

Implement min/max for multiple data input parameters.

2015-09-21 15:51:58 +01:00

multi_output_assign_primary.xml

Implement tool test demonstrating pull request 569.

2014-11-25 22:13:17 -05:00

multi_output_configured.xml

Allow discover_datasets tag to use format attribute (instead of ext).

2015-09-21 14:24:24 +01:00

multi_output.xml

Allow tools to test runtime discovered datasets.

2014-03-29 17:11:17 -05:00

multi_page.xml

Fix multi-page tool help parsing.

2014-08-12 08:19:04 -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

More functional tests of output actions.

2015-04-06 09:08:01 -04:00

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.xml

Add functional test tool demonstrating output filters.

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

output_format.xml

Fix output_format framework test.

2015-09-18 17:48:59 +01:00

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

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

README.txt

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

2015-04-10 16:38:34 -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

Added test for bcf index creation.

2015-04-28 13:45:33 -04:00

samples_tool_conf.xml

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

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

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

Support selections in interface dict rep of tools.

2015-10-20 13:49:24 +01:00

special_params.xml

Add functional test tool demonstrating special parameters.

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

tool_directory.xml

Expose $__tool_directory__ to tools.

2015-02-03 10:29:34 -05:00

top_level_data.xml

Test tool fixes.

2015-03-15 09:53:05 -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_repeat.xml

Add regression test for issue in #798 .

2015-09-25 14:29:05 +01:00

validation_sanitizer.xml

More tool functional tests for validation stuff.

2014-09-16 21:29:10 -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