mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
mvdbeek
26680e0ca1
Unfortunately you can select an invalid value (in the API, not the UI) and Galaxy will replace the invalid value with the first valid value.
205 lines
8.6 KiB
XML
205 lines
8.6 KiB
XML
<?xml version="1.0"?>
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<toolbox tool_path="${tool_conf_dir}" is_shed_conf="false">
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<tool file="upload.xml"/>
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<tool file="test_data_source.xml"/>
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<tool file="simple_constructs.xml" />
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<tool file="color_param.xml" />
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<tool file="inheritance_simple.xml" />
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<tool file="boolean_conditional.xml" />
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<tool file="composite.xml" />
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<tool file="environment_variables.xml" />
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<tool file="code_file.xml" />
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<tool file="disambiguate_cond.xml" />
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<tool file="multi_repeats.xml"/>
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<tool file="library_data.xml"/>
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<tool file="remove_value.xml"/>
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<tool file="bibtex.xml"/>
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<tool file="multi_select.xml" />
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<tool file="multi_output.xml" />
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<tool file="multi_output_configured.xml" />
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<tool file="multi_output_assign_primary.xml" />
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<tool file="multi_output_recurse.xml" />
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<tool file="tool_provided_metadata_1.xml" />
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<tool file="tool_provided_metadata_2.xml" />
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<tool file="tool_provided_metadata_3.xml" />
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<tool file="tool_provided_metadata_4.xml" />
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<tool file="tool_provided_metadata_5.xml" />
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<tool file="tool_provided_metadata_6.xml" />
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<tool file="tool_provided_metadata_7.xml" />
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<tool file="tool_provided_metadata_8.xml" />
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<tool file="tool_provided_metadata_9.xml" />
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<tool file="empty_datasets.xml" />
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<tool file="inputs_as_json.xml" />
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<tool file="inputs_as_json_with_paths.xml" />
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<tool file="dbkey_filter_input.xml" />
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<tool file="dbkey_filter_multi_input.xml" />
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<tool file="dbkey_output_action.xml" />
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<tool file="composite_output.xml" />
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<tool file="composite_output_tests.xml" />
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<tool file="unicode_stream.xml" />
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<tool file="vcf_bgzip.xml" />
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<tool file="metadata.xml" />
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<tool file="metadata_bam.xml" />
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<tool file="metadata_bcf.xml" />
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<tool file="metadata_biom1.xml" />
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<tool file="metadata_column_names.xml" />
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<tool file="strict_shell.xml" />
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<tool file="strict_shell_default_off.xml" />
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<tool file="detect_errors_aggressive.xml" />
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<tool file="md5sum.xml" />
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<tool file="checksum.xml" />
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<tool file="is_valid_xml.xml" />
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<!--
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TODO: Figure out why this transiently fails on Jenkins.
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<tool file="maxseconds.xml" />
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-->
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<tool file="job_properties.xml" />
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<tool file="job_environment_default.xml" />
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<tool file="job_environment_default_legacy.xml" />
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<tool file="job_environment_explicit_shared_home.xml" />
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<tool file="version_command_plain.xml" />
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<tool file="version_command_interpreter.xml" />
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<tool file="version_command_tool_dir.xml" />
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<tool file="exit_code_oom.xml" />
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<tool file="exit_code_from_file.xml" />
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<tool file="gzipped_inputs.xml" />
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<tool file="output_order.xml" />
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<tool file="output_format.xml" />
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<tool file="output_format_deprecated_when.xml" />
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<tool file="output_format_collection.xml" />
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<tool file="output_filter.xml" />
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<tool file="output_filter_with_input.xml" />
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<tool file="output_filter_exception_1.xml" />
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<tool file="output_collection_filter.xml" />
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<tool file="output_auto_format.xml" />
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<tool file="create_2.xml" />
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<tool file="create_10.xml" />
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<tool file="disambiguate_repeats.xml" />
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<tool file="min_repeat.xml" />
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<tool file="parallelism.xml" />
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<tool file="parallelism_optional.xml" />
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<tool file="implicit_default_conds.xml" />
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<tool file="multi_data_param.xml" />
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<tool file="multi_data_repeat.xml" />
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<tool file="multi_data_optional.xml" />
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<tool file="paths_as_file.xml" />
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<tool file="param_text_option.xml" />
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<tool file="column_param.xml" />
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<tool file="column_param_configfile.xml" />
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<tool file="column_multi_param.xml" />
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<tool file="special_params.xml" />
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<tool file="section.xml" />
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<tool file="sam_to_unsorted_bam.xml" />
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<tool file="top_level_data.xml" />
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<tool file="validation_default.xml" />
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<tool file="validation_sanitizer.xml" />
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<tool file="validation_repeat.xml" />
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<tool file="empty_output.xml" />
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<tool file="validation_empty_dataset.xml" />
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<tool file="implicit_conversion.xml" />
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<tool file="explicit_conversion.xml" />
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<tool file="identifier_source.xml" />
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<tool file="identifier_single.xml" />
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<tool file="identifier_single_in_repeat.xml" />
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<tool file="identifier_in_conditional.xml" />
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<tool file="identifier_multiple.xml" />
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<tool file="identifier_multiple_in_conditional.xml" />
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<tool file="identifier_multiple_in_repeat.xml" />
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<tool file="identifier_collection.xml" />
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<tool file="identifier_in_actions.xml" />
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<tool file="fail_identifier.xml" />
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<tool file="fail_writing_work_dir_file.xml" />
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<tool file="tool_directory.xml" />
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<tool file="output_action_change_format.xml" />
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<tool file="output_action_change_format_paired.xml" />
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<tool file="collection_paired_test.xml" />
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<tool file="collection_paired_structured_like.xml" />
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<tool file="collection_paired_conditional_structured_like.xml" />
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<tool file="collection_nested_test.xml" />
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<tool file="collection_mixed_param.xml" />
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<tool file="collection_two_paired.xml" />
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<tool file="collection_creates_pair.xml" />
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<tool file="collection_creates_pair_from_type.xml" />
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<tool file="collection_creates_list.xml" />
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<tool file="collection_creates_list_2.xml" />
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<tool file="collection_creates_list_of_pairs.xml" />
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<tool file="collection_optional_param.xml" />
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<tool file="collection_split_on_column.xml" />
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<tool file="collection_creates_dynamic_nested.xml" />
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<tool file="collection_creates_dynamic_nested_from_json.xml" />
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<tool file="collection_creates_dynamic_nested_from_json_elements.xml" />
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<tool file="collection_creates_dynamic_list_of_pairs.xml" />
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<tool file="collection_type_source.xml" />
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<tool file="collection_type_source_map_over.xml" />
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<tool file="collection_creates_list_fail.xml" />
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<tool file="collection_creates_dynamic_nested_fail.xml" />
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<tool file="collection_cat_group_tag.xml" />
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<tool file="collection_cat_group_tag_multiple.xml" />
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<tool file="cheetah_casting.xml" />
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<tool file="cheetah_problem_unbound_var.xml" />
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<tool file="cheetah_problem_unbound_var_input.xml" />
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<tool file="cheetah_problem_syntax_error.xml" />
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<tool file="python_environment_problem.xml" />
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<tool file="config_vars.xml" />
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<tool file="multiple_versions_v01.xml" />
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<tool file="multiple_versions_v02.xml" />
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<!-- Tools interesting only for building up test workflows. -->
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<!-- Next three tools demonstrate concatenating multiple datasets
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with a repeat, multiple datasets with a multiple input data
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parameter, and multiple datasets from a collection. -->
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<tool file="for_workflows/cat.xml" />
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<tool file="for_workflows/cat_list.xml" />
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<tool file="for_workflows/cat_collection.xml" />
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<tool file="for_workflows/head.xml" />
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<tool file="for_workflows/cat_interleave.xml" />
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<tool file="for_workflows/pileup.xml" />
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<tool file="for_workflows/mapper.xml" />
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<tool file="for_workflows/mapper2.xml" />
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<tool file="for_workflows/mapper_two.xml" />
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<tool file="for_workflows/split.xml" />
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<tool file="for_workflows/empty_list.xml" />
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<tool file="for_workflows/count_list.xml" />
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<tool file="for_workflows/count_multi_file.xml" />
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<tool file="for_workflows/create_input_collection.xml" />
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<section id="filter" name="For Tours">
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<tool file="for_tours/filtering.xml" />
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</section>
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<!-- Tools for dependency and container testing. -->
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<tool file="legacy_r.xml" />
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<tool file="mulled_example_multi_1.xml" />
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<tool file="mulled_example_multi_versionless.xml" />
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<tool file="mulled_example_multi_incomplete.xml" />
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<tool file="mulled_example_conflict.xml" />
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<tool file="mulled_example_simple.xml" />
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<tool file="mulled_example_explicit.xml" />
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<tool file="simple_constructs.yml" />
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<!-- Tools without tool test but useful for hand-crafted, artisanal test cases. -->
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<tool file="cat_data_and_sleep.xml" />
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<!-- Load collection operation tools - I consider these part of the
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"framework" and they are used to in API tests to test the underlying
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ToolActions. -->
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<tool file="${model_tools_path}/unzip_collection.xml" />
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<tool file="${model_tools_path}/zip_collection.xml" />
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<tool file="${model_tools_path}/filter_failed_collection.xml" />
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<tool file="${model_tools_path}/filter_empty_collection.xml" />
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<tool file="${model_tools_path}/flatten_collection.xml" />
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<tool file="${model_tools_path}/sort_collection_list.xml" />
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<tool file="${model_tools_path}/merge_collection.xml" />
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<tool file="${model_tools_path}/relabel_from_file.xml" />
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<tool file="${model_tools_path}/filter_from_file.xml" />
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<tool file="${model_tools_path}/tag_collection_from_file.xml" />
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<tool file="${model_tools_path}/apply_rules.xml" />
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<tool file="${model_tools_path}/build_list.xml" />
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<tool file="${model_tools_path}/extract_dataset.xml" />
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</toolbox>
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