mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-11-02 19:52:14 +08:00
Marius van den Beek
f820d570be
When discovered dataset designations are very long (e.g., taxonomic names),
the job output association name (__new_primary_file_{name}|{designation}__)
can exceed the VARCHAR(255) column limit, causing StringDataRightTruncation
which corrupts the SQLAlchemy session and triggers PendingRollbackError.
Add name length validation in Job.add_output_dataset and related methods
that raises ValueError before the DB INSERT. Catch the error in both the
normal and extended metadata code paths to fail the job with a clear error
message instead of crashing the transaction session.
Fixes https://github.com/galaxyproject/galaxy/issues/22045
351 lines
15 KiB
XML
351 lines
15 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="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="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="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_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_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_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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<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="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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<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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<!-- 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="${model_tools_path}/keep_success_collection.xml" />
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<tool file="${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="${model_tools_path}/apply_rules.xml" />
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<tool file="${model_tools_path}/build_list.xml" />
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<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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