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https://github.com/galaxyproject/galaxy.git
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John Chilton
d5d404c912
```
<configfiles>
<inputs name="inputs" format="json" version="1" />
</configfiles>
```
Version is specified as 1, because the Galaxy tool plumbing doesn't really distinguish between parameter is '', parameter was explicitly supplied as None, parameter was absent, etc... - everything is a just a string in some ways. This distinction may be more important with JSON and for instance the CWL will require more percision, so we may want to revise Galaxy's tool handling in a backward compatible way someday.
96 lines
3.6 KiB
XML
96 lines
3.6 KiB
XML
<?xml version="1.0"?>
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<toolbox tool_path="${tool_conf_dir}">
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<tool file="upload.xml"/>
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<tool file="simple_constructs.xml" />
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<tool file="inheritance_simple.xml" />
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<tool file="boolean_conditional.xml" />
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<tool file="composite.xml" />
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<tool file="environment_variables.xml" />
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<tool file="code_file.xml" />
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<tool file="disambiguate_cond.xml" />
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<tool file="multi_repeats.xml"/>
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<tool file="multi_page.xml"/>
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<tool file="library_data.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="inputs_as_json.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="composite_output.xml" />
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<tool file="unicode_stream.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="detect_errors_aggressive.xml" />
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<tool file="md5sum.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="gzipped_inputs.xml" />
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<tool file="output_order.xml" />
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<tool file="output_format.xml" />
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<tool file="output_format_collection.xml" />
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<tool file="output_filter.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_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="column_param.xml" />
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<tool file="column_multi_param.xml" />
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<tool file="special_params.xml" />
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<tool file="section.xml" />
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<tool file="top_level_data.xml" />
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<tool file="validation_default.xml" />
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<tool file="validation_sanitizer.xml" />
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<tool file="validation_repeat.xml" />
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<tool file="identifier_single.xml" />
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<tool file="identifier_multiple.xml" />
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<tool file="tool_directory.xml" />
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<tool file="output_action_change_format.xml" />
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<tool file="collection_paired_test.xml" />
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<tool file="collection_nested_test.xml" />
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<tool file="collection_mixed_param.xml" />
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<tool file="collection_two_paired.xml" />
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<tool file="collection_creates_pair.xml" />
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<tool file="collection_creates_pair_from_type.xml" />
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<tool file="collection_creates_list.xml" />
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<tool file="collection_creates_list_2.xml" />
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<tool file="collection_creates_list_of_pairs.xml" />
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<tool file="collection_optional_param.xml" />
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<tool file="collection_split_on_column.xml" />
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<tool file="collection_creates_dynamic_nested.xml" />
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<tool file="collection_creates_dynamic_list_of_pairs.xml" />
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<tool file="collection_type_source.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="multiple_versions_v01.xml" />
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<tool file="multiple_versions_v02.xml" />
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<!-- Tools interesting only for building up test workflows. -->
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<!-- Next three tools demonstrate concatenating multiple datasets
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with a repeat, multiple datasets with a multiple input data
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parameter, and multiple datasets from a collection. -->
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<tool file="for_workflows/cat.xml" />
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<tool file="for_workflows/cat_list.xml" />
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<tool file="for_workflows/cat_collection.xml" />
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<tool file="for_workflows/head.xml" />
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<tool file="for_workflows/cat_interleave.xml" />
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<tool file="simple_constructs.yml" />
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</toolbox>
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