mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
mvdbeek
90ccfefe9a
If the `Set value for this optional select field ? `switch is set to no we serialize the value as `null` instead of `""`, which is especially important in optional select fields, where `""` may correspond to an option that is distinct from not setting a value. I have only enabled this for select parameters that are cast to text parameters, but I think this discrimination between set and unset would also be great for optional text parameters. There might be a better way to do it in the UI (maybe some icon that indicates that the value is set, that can be toggled with an backspace when the field is empty?), but I think this will do for the relatively rare case of optional select parameters that are cast to text fields. Fixes https://github.com/galaxyproject/galaxy/issues/12081
267 lines
11 KiB
XML
267 lines
11 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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<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="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="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="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_assign_primary_ext_dbkey.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="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="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="filter_multiple_splitter.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_optional.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="dbkey_filter_paired_collection.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="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="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="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_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="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_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_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="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_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_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_cat_group_tag.xml" />
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<tool file="collection_cat_group_tag_multiple.xml" />
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<tool file="discover_sort_by.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="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_v01galaxy6.xml" />
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<tool file="multiple_versions_v02.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="interactivetool_simple.xml" />
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<tool file="interactivetool_two_entry_points.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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<tool file="for_workflows/randomlines.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="mulled_example_invalid_case.xml" />
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<tool file="mulled_example_broken_no_requirements.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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