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John Chilton
3784fece91
An ``<environment_variables>`` top-level XML block can be used to define these.
```
<environment_variables>
<environment_variable name="FOO">$bar</environment_variable>
<environment_variable name="FOO2">$bar2</environment_variable
</environment_variables>
```
The expressions are contained in the text of the block.
Implementation Detials:
In order to avoid odd shell expression stuff - the evaluated expressions are written to files and environment variables are read from these files at runtime.
Testing:
A demo tool ``test/functional/tools/environment_variables.xml`` with a test case that can be executed with the following expression.
```
./run_tests.sh -framework -id environment_variables
```
79 lines
2.9 KiB
XML
79 lines
2.9 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="compare_bam_as_sam.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="composite_output.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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<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_filter.xml" />
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<tool file="output_auto_format.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_optional_param.xml" />
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<tool file="collection_split_on_column.xml" />
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<tool file="cheetah_casting.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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