mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-11-03 21:34:30 +08:00
mvdbeek
b7341edae9
split_inputs_nested flattened the already-nested input state to |‑separated flat keys via visit_input_values, then called expand_flat_parameters_to_nested to rebuild the dict. That rebuild uses process_key / looks_like_flattened_repeat_key, which treats any path component ending in _<digit> (e.g. "column_selector_options_1") as a repeat-item index rather than a literal conditional name. The result was a spurious "column_selector_options" list instead of the expected "column_selector_options_1" / "column_selector_options_2" dicts, which then caused Pydantic to report extra_forbidden on the fake list and list_type (None) on col1 once fill_static_defaults initialised the now-missing conditional to an empty dict. The flat→nested round-trip was never needed for the nested-input path: the dict coming in is already correctly structured. Fix by returning nested_dict directly from split_inputs_nested as single_inputs, only extracting batch (matched / multiplied) inputs as flat-key entries as before. Strip internal state keys starting with __ that visit_input_values stamps so they don't appear as extra fields when the state reaches Pydantic validation. Also remove stray print() debug calls left in visitor.py.
380 lines
17 KiB
XML
380 lines
17 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="export_remote.xml" />
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<section id="test" name="Test Section">
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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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</section>
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<tool file="image_diff.xml" />
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<tool file="output_format_input.xml" />
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<tool file="ucsc_tablebrowser.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="composite_pbed.xml" />
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<tool file="environment_variables.xml" />
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<tool file="environment_variables_inject.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="remove_value.xml" />
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<tool file="bibtex.xml" />
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<tool file="help_features_rst.xml" />
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<tool file="help_features_markdown.xml" />
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<tool file="select_from_url.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_assign_primary_ext_dbkey.xml" />
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<tool file="multi_output_recurse.xml" />
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<tool file="multi_output_recurse_collection.xml" />
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<tool file="galaxy_json_discover_and_sleep.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="tool_provided_metadata_10.xml" />
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<tool file="tool_provided_metadata_11.xml" />
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<tool file="tool_provided_metadata_12.xml" />
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<tool file="empty_datasets.xml" />
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<tool file="is_of_type.xml" />
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<tool file="data_optional.xml" />
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<tool file="inputs_as_json.xml" />
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<tool file="inputs_as_json_profile.xml" />
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<tool file="inputs_as_json_with_paths.xml" />
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<tool file="inputs_as_json_with_staging_path_and_source_path.xml" />
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<tool file="filter_multiple_splitter.xml" />
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<tool file="filter_param_value.xml" />
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<tool file="filter_param_value_ref_attribute.xml" />
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<tool file="filter_static_regexp.xml" />
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<tool file="select_from_dataset.xml" />
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<tool file="select_from_dataset_in_conditional.xml" />
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<tool file="conditional_name_digit_suffix.xml" />
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<tool file="select_from_csvdataset.xml" />
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<tool file="select_from_dataset_optional.xml" />
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<tool file="drill_down.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_filter_collection.xml" />
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<tool file="filter_data_table.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="discover_metadata_files.xml" />
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<tool file="metadata_bcf.xml" />
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<tool file="metadata_bed.xml" />
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<tool file="metadata_biom1.xml" />
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<tool file="metadata_check_eq.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="strict_shell_profile.xml" />
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<tool file="detect_errors.xml" />
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<tool file="detect_errors_aggressive.xml" />
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<tool file="qc_stdout.xml" />
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<tool file="directory_uri.xml" />
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<tool file="md5sum.xml" />
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<tool file="checksum.xml" />
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<tool file="sim_size_delta.xml" />
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<tool file="composite_shapefile.xml" />
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<tool file="is_valid_xml.xml" />
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<tool file="expression_tools/parse_values_from_file.xml" />
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<tool file="expression_tools/pick_value.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="job_environment_explicit_isolated_home.xml" />
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<tool file="galaxy_slots_and_memory.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="exit_code_from_env.xml" />
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<tool file="gzipped_inputs.xml" />
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<tool file="options_from_metadata_file.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="format_source_in_conditional.xml" />
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<tool file="output_filter.xml" />
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<tool file="output_empty_work_dir.xml" />
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<tool file="output_filter_with_input.xml" />
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<tool file="output_filter_with_input_optional.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_param_list.xml" />
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<tool file="column_multi_param.xml" />
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<tool file="select_optional_legacy.xml" />
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<tool file="select_optional.xml" />
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<tool file="select_dynamic.xml" />
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<tool file="select_from_data_table_no_name.xml" />
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<tool file="hidden_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_hdf5.xml" />
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<tool file="validation_image.xml" />
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<tool file="validation_zip.xml" />
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<tool file="validation_tar.xml" />
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<tool file="validation_tar_gz.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="validation_metadata_in_range.xml" />
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<tool file="validation_metadata_in_datatable.xml" />
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<tool file="validation_dataset_metadata_in_file.xml" />
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<tool file="validation_value_in_datatable.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="implicit_conversion_format_input.xml" />
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<tool file="implicit_conversion_optional_param.xml" />
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<tool file="implicit_collection_conversion.xml" />
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<tool file="implicit_nested_list_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_all_collection_types.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="legacy_interpreter.xml" />
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<tool file="tool_directory.xml" />
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<tool file="tool_directory_docker.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_test_y.yml" />
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<tool file="collection_paired_default.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_paired_structured_like_with_data_input.xml" />
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<tool file="collection_nested_test.xml" />
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<tool file="collection_nested_default.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_y.yml" />
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<tool file="collection_creates_pair_format.xml" />
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<tool file="collection_creates_pair_from_type.xml" />
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<tool file="collection_creates_pair_from_work_dir.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_list_or_nested_list_input.xml" />
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<tool file="collection_list_2x_or_3x_nested.xml" />
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<tool file="collection_paired_or_list_paired_input.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="collection_record_test_two_files.xml" />
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<tool file="collection_paired_or_unpaired.xml" />
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<tool file="collection_list_paired_or_unpaired.xml" />
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<tool file="discover_sort_by.xml" />
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<tool file="discover_long_name.xml" />
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<tool file="discover_default_ext.xml" />
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<tool file="expression_forty_two.xml" />
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<tool file="expression_pick_larger_file.xml" />
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<tool file="expression_parse_int.xml" />
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<tool file="expression_log_line_count.xml" />
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<tool file="expression_null_handling_boolean.xml" />
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<tool file="expression_null_handling_integer.xml" />
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<tool file="expression_null_handling_float.xml" />
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<tool file="expression_null_handling_text.xml" />
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<tool file="expression_text_to_bool.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="model_attributes.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="expect_num_outputs.xml" />
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<tool file="text_repeat.xml" />
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<tool file="integer_default.xml" />
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<tool file="float_default.xml" />
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<tool file="all_output_types.xml" />
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<tool file="markdown_report_simple.xml" />
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<tool file="markdown_report_extra_files.xml" />
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<tool file="markdown_report_from_script.xml" />
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<tool file="multiple_versions_v01.xml" />
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<tool file="multiple_versions_v01galaxy6.xml" />
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<tool file="multiple_versions_v02.xml" />
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<tool file="multiple_versions_hidden_v01.xml" hidden="true" />
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<tool file="multiple_versions_hidden_v02.xml" />
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<section id="test_section_multi" name="Test Section with Multiple Versions">
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<tool file="multiple_versions_v01.xml" />
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<tool file="multiple_versions_v01galaxy6.xml" />
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<tool file="multiple_versions_v02.xml" />
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</section>
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<tool file="multiple_versions_sorting_v19.xml" />
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<tool file="multiple_versions_sorting_v110.xml" />
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<tool file="multiple_versions_changes_v01.xml" />
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<tool file="multiple_versions_changes_v02.xml" />
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<tool file="html_output.xml" />
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<tool file="html_output_with_extra_files.xml" />
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<tool file="interactivetool_simple.xml" />
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<tool file="interactivetool_two_entry_points.xml" />
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<tool file="converter_target_datatype.xml" />
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<tool file="tool_directory_copy.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_default.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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<tool file="for_workflows/randomlines.xml" />
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<tool file="for_workflows/catWrapper.xml" />
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<tool file="create_directory_index.xml" />
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<tool file="use_directory_index.xml" />
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<tool_dir dir="parameters/" />
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<!-- YAML tools not picked up automatically yet - arguably for the
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best until they are out of beta. -->
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<tool file="parameters/gx_boolean_user.yml" />
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<tool file="parameters/gx_data_user.yml" />
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<tool file="parameters/gx_data_multiple_user.yml" />
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<tool file="parameters/gx_select_multiple_one_default_user.yml" />
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<tool file="parameters/gx_data_collection_list_or_paired.yml" />
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<tool file="parameters/gx_data_collection_record.yml" />
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<tool file="parameters/gx_data_collection_sample_sheet.yml" />
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<tool file="parameters/gx_data_collection_paired_or_unpaired.yml" />
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<tool file="parameters/gx_data_collection_list_paired.yml" />
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<tool file="parameters/gx_data_collection_list_list.yml" />
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<tool file="parameters/gx_data_collection_list_list_paired.yml" />
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<tool file="parameters/gx_data_collection_list_or_record.yml" />
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<tool file="parameters/gx_data_collection_list_paired_or_list_list.yml" />
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<tool file="parameters/gx_data_collection_list_or_list_paired.yml" />
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<tool file="parameters/gx_data_collection_paired_or_pou.yml" />
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<tool file="parameters/gx_data_collection_any.yml" />
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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="mulled_example_invalid_case.xml" />
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<tool file="mulled_example_broken_no_requirements.xml" />
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<tool file="mulled_example_broken_no_requirements_fallback.xml" />
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<tool file="explicit_container.xml" />
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<tool file="explicit_singularity_container.xml"/>
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<tool file="simple_constructs.yml" />
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<tool file="cat_user_defined.yml" />
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<tool file="cat_multiple_user_defined.yml" />
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<tool file="configfile_user_defined.yml" />
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<tool file="from_work_dir_glob.xml" />
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<tool file="secret_tool.xml" />
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<tool file="credentials_test.xml" />
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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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<tool file="parameters/gx_int_min_max.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="${model_tools_path}/keep_success_collection.xml" />
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<tool file="${model_tools_path}/filter_empty_collection.xml" />
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<tool file="${model_tools_path}/filter_null.xml" />
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<tool file="${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}/harmonize_two_collections_list.xml" />
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<tool file="${model_tools_path}/harmonize_two_collections_list_1.0.0.xml" />
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<tool file="${model_tools_path}/nest_collection.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}/cross_product_flat.xml" />
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<tool file="${model_tools_path}/cross_product_nested.xml" />
|
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<tool file="${model_tools_path}/tag_collection_from_file.xml" />
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|
<tool file="${model_tools_path}/apply_rules.xml" />
|
|
<tool file="${model_tools_path}/build_list.xml" />
|
|
<tool file="${model_tools_path}/build_list_1.2.0.xml" />
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|
<tool file="${model_tools_path}/sample_sheet_to_tabular.xml" />
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|
<tool file="${model_tools_path}/convert_sample_sheet.xml" />
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|
<tool file="${model_tools_path}/extract_dataset.xml" />
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|
<tool file="${model_tools_path}/duplicate_file_to_collection.xml" />
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|
<tool file="${model_tools_path}/split_paired_and_unpaired.xml" />
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</toolbox>
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