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samples_tool_conf.xml
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samples_tool_conf.xml
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<?xml version="1.0"?>
<toolbox tool_path="${tool_conf_dir}" is_shed_conf="false">
<tool file="upload.xml"/>
<tool file="simple_constructs.xml" />
<tool file="color_param.xml" />
<tool file="inheritance_simple.xml" />
<tool file="boolean_conditional.xml" />
<tool file="composite.xml" />
<tool file="environment_variables.xml" />
<tool file="code_file.xml" />
<tool file="disambiguate_cond.xml" />
<tool file="multi_repeats.xml"/>
<tool file="library_data.xml"/>
<tool file="multi_select.xml" />
<tool file="multi_output.xml" />
<tool file="multi_output_configured.xml" />
<tool file="multi_output_assign_primary.xml" />
<tool file="tool_provided_metadata_1.xml" />
<tool file="tool_provided_metadata_2.xml" />
<tool file="tool_provided_metadata_3.xml" />
<tool file="inputs_as_json.xml" />
<tool file="dbkey_filter_input.xml" />
<tool file="dbkey_filter_multi_input.xml" />
<tool file="dbkey_output_action.xml" />
<tool file="composite_output.xml" />
<tool file="composite_output_tests.xml" />
<tool file="unicode_stream.xml" />
<tool file="metadata.xml" />
<tool file="metadata_bam.xml" />
<tool file="metadata_bcf.xml" />
<tool file="metadata_biom1.xml" />
<tool file="metadata_column_names.xml" />
<tool file="strict_shell.xml" />
<tool file="strict_shell_default_off.xml" />
<tool file="detect_errors_aggressive.xml" />
<tool file="md5sum.xml" />
<tool file="checksum.xml" />
<tool file="is_valid_xml.xml" />
<!--
TODO: Figure out why this transiently fails on Jenkins.
<tool file="maxseconds.xml" />
-->
<tool file="job_properties.xml" />
<tool file="version_command_plain.xml" />
<tool file="version_command_interpreter.xml" />
<tool file="version_command_tool_dir.xml" />
<tool file="exit_code_from_file.xml" />
<tool file="gzipped_inputs.xml" />
<tool file="output_order.xml" />
<tool file="output_format.xml" />
<tool file="output_format_deprecated_when.xml" />
<tool file="output_format_collection.xml" />
<tool file="output_filter.xml" />
<tool file="output_filter_exception_1.xml" />
<tool file="output_collection_filter.xml" />
<tool file="output_auto_format.xml" />
<tool file="create_2.xml" />
<tool file="create_10.xml" />
<tool file="disambiguate_repeats.xml" />
<tool file="min_repeat.xml" />
<tool file="parallelism.xml" />
<tool file="parallelism_optional.xml" />
<tool file="implicit_default_conds.xml" />
<tool file="multi_data_param.xml" />
<tool file="multi_data_repeat.xml" />
<tool file="multi_data_optional.xml" />
<tool file="paths_as_file.xml" />
<tool file="param_text_option.xml" />
<tool file="column_param.xml" />
<tool file="column_multi_param.xml" />
<tool file="special_params.xml" />
<tool file="section.xml" />
<tool file="top_level_data.xml" />
<tool file="validation_default.xml" />
<tool file="validation_sanitizer.xml" />
<tool file="validation_repeat.xml" />
<tool file="empty_output.xml" />
<tool file="validation_empty_dataset.xml" />
<tool file="implicit_conversion.xml" />
<tool file="explicit_conversion.xml" />
<tool file="identifier_single.xml" />
<tool file="identifier_multiple.xml" />
<tool file="identifier_multiple_in_conditional.xml" />
<tool file="identifier_multiple_in_repeat.xml" />
<tool file="identifier_collection.xml" />
<tool file="tool_directory.xml" />
<tool file="output_action_change_format.xml" />
<tool file="collection_paired_test.xml" />
<tool file="paired_collection_map_over_structured_like.xml" />
<tool file="collection_nested_test.xml" />
<tool file="collection_mixed_param.xml" />
<tool file="collection_two_paired.xml" />
<tool file="collection_creates_pair.xml" />
<tool file="collection_creates_pair_from_type.xml" />
<tool file="collection_creates_list.xml" />
<tool file="collection_creates_list_2.xml" />
<tool file="collection_creates_list_of_pairs.xml" />
<tool file="collection_optional_param.xml" />
<tool file="collection_split_on_column.xml" />
<tool file="collection_creates_dynamic_nested.xml" />
<tool file="collection_creates_dynamic_list_of_pairs.xml" />
<tool file="collection_type_source.xml" />
<tool file="cheetah_casting.xml" />
<tool file="cheetah_problem_unbound_var.xml" />
<tool file="cheetah_problem_unbound_var_input.xml" />
<tool file="cheetah_problem_syntax_error.xml" />
<tool file="python_environment_problem.xml" />
<tool file="multiple_versions_v01.xml" />
<tool file="multiple_versions_v02.xml" />
<!-- Tools interesting only for building up test workflows. -->
<!-- Next three tools demonstrate concatenating multiple datasets
with a repeat, multiple datasets with a multiple input data
parameter, and multiple datasets from a collection. -->
<tool file="for_workflows/cat.xml" />
<tool file="for_workflows/cat_list.xml" />
<tool file="for_workflows/cat_collection.xml" />
<tool file="for_workflows/head.xml" />
<tool file="for_workflows/cat_interleave.xml" />
<tool file="for_workflows/pileup.xml" />
<tool file="for_workflows/mapper.xml" />
<tool file="for_workflows/mapper2.xml" />
<tool file="for_workflows/split.xml" />
<tool file="for_workflows/create_input_collection.xml" />
<section id="filter" name="For Tours">
<tool file="for_tours/filtering.xml" />
</section>
<!-- Tools for dependency and container testing. -->
<tool file="legacy_r.xml" />
<tool file="mulled_example_multi_1.xml" />
<tool file="mulled_example_multi_incomplete.xml" />
<tool file="mulled_example_conflict.xml" />
<tool file="simple_constructs.yml" />
<!-- Load collection operation tools - I consider these part of the
"framework" and they are used to in API tests to test the underlying
ToolActions. -->
<tool file="${model_tools_path}/unzip_collection.xml" />
<tool file="${model_tools_path}/zip_collection.xml" />
<tool file="${model_tools_path}/filter_failed_collection.xml" />
<tool file="${model_tools_path}/flatten_collection.xml" />
<tool file="${model_tools_path}/merge_collection.xml" />
<tool file="${model_tools_path}/relabel_from_file.xml" />
<tool file="${model_tools_path}/filter_from_file.xml" />
</toolbox>