Index
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A
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C
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D
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E
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F
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G
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I
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M
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N
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O
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P
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R
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S
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T
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U
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V
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W
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Y
_
__init__() (wic.wic_types.GraphData method)
A
add_graph_edge() (in module wic.utils_graphs)
add_subgraphs() (in module wic.utils_graphs)
add_yamldict_keyval_in() (in module wic.utils_cwl)
add_yamldict_keyval_out() (in module wic.utils_cwl)
apply_args() (in module wic.inlineing)
C
canonicalize_type() (in module wic.utils_cwl)
check_args_match_inputs() (in module wic.python_cwl_adapter)
compile_workflow() (in module wic.compiler)
compile_workflow_generate_schema() (in module wic.schemas.wic_schema)
compile_workflow_once() (in module wic.compiler)
compiled_cwl (wic.wic_types.NodeData attribute)
CompilerInfo (class in wic.wic_types)
copy_cwl_input_output_dict() (in module wic.utils_cwl)
cwl (wic.wic_types.Tool attribute)
cwl_schema() (in module wic.schemas.wic_schema)
cwl_type_to_jsonschema_type() (in module wic.schemas.wic_schema)
cwl_type_to_jsonschema_type_schema() (in module wic.schemas.wic_schema)
D
data (wic.wic_types.RoseTree attribute)
default_schema() (in module wic.schemas.wic_schema)
delete_previously_uploaded() (in module wic.labshare)
E
env (wic.wic_types.CompilerInfo attribute)
EnvData (class in wic.wic_types)
explicit_edge_calls (wic.wic_types.EnvData attribute)
(wic.wic_types.NodeData attribute)
explicit_edge_defs (wic.wic_types.EnvData attribute)
(wic.wic_types.NodeData attribute)
extract_implementation() (in module wic.utils)
F
flatten() (in module wic.utils)
flatten_forest() (in module wic.utils)
flatten_graphdata() (in module wic.utils_graphs)
flatten_rose_tree() (in module wic.utils)
G
generate_CWL_CommandLineTool() (in module wic.python_cwl_adapter)
get_absolute_paths() (in module wic.input_output)
get_args() (in module wic.cli)
get_config() (in module wic.input_output)
get_default_config() (in module wic.input_output)
get_graph_reps() (in module wic.utils_graphs)
get_inference_rules() (in module wic.inference)
get_inlineable_subworkflows() (in module wic.inlineing)
get_input_mappings() (in module wic.utils)
get_inputs_workflow() (in module wic.python_cwl_adapter)
get_main_args() (in module wic.python_cwl_adapter)
get_module() (in module wic.python_cwl_adapter)
get_output_mapping() (in module wic.utils)
get_step_name_1() (in module wic.utils)
get_steps_keys() (in module wic.utils)
get_subkeys() (in module wic.utils)
get_validator() (in module wic.schemas.wic_schema)
get_workflow_outputs() (in module wic.utils_cwl)
graph (wic.wic_types.NodeData attribute)
GraphData (class in wic.wic_types)
graphdata (wic.wic_types.GraphReps attribute)
graphdata_to_cytoscape() (in module wic.utils_graphs)
GraphReps (class in wic.wic_types)
graphviz (wic.wic_types.GraphReps attribute)
I
ignore_aliases() (wic.input_output.NoAliasDumper method)
import_python_file() (in module wic.python_cwl_adapter)
inline_subworkflow() (in module wic.inlineing)
inline_subworkflow_cwl() (in module wic.inlineing)
inline_subworkflow_wic_tag() (in module wic.inlineing)
input_mapping (wic.wic_types.EnvData attribute)
inputs_file_workflow (wic.wic_types.EnvData attribute)
inputs_workflow (wic.wic_types.NodeData attribute)
insert_step_into_workflow() (in module wic.compiler)
M
make_plugins_dag() (in module wic.utils_graphs)
make_tool_dag() (in module wic.utils_graphs)
maybe_add_requirements() (in module wic.utils_cwl)
merge_yml_trees() (in module wic.ast)
module
wic.ast
wic.cli
wic.compiler
wic.inference
wic.inlineing
wic.input_output
wic.labshare
wic.python_cwl_adapter
wic.schemas.wic_schema
wic.utils
wic.utils_cwl
wic.utils_graphs
wic.wic_types
move_slash_last() (in module wic.inlineing)
N
name (wic.wic_types.NodeData attribute)
named_empty_schema() (in module wic.schemas.wic_schema)
named_null_schema() (in module wic.schemas.wic_schema)
namespaces (wic.wic_types.NodeData attribute)
networkx (wic.wic_types.GraphReps attribute)
NoAliasDumper (class in wic.input_output)
NodeData (class in wic.wic_types)
O
output_mapping (wic.wic_types.EnvData attribute)
P
parse_int_string_tuple() (in module wic.utils)
parse_provenance_output_files() (in module wic.utils)
parse_provenance_output_files_() (in module wic.utils)
parse_step_name_str() (in module wic.utils)
partition_by_lowest_common_ancestor() (in module wic.utils)
perform_edge_inference() (in module wic.inference)
plugin_ns (wic.wic_types.StepId attribute)
pretty_print_forest() (in module wic.utils)
pretty_print_request() (in module wic.labshare)
print_plugins() (in module wic.labshare)
python_script_generate_cwl() (in module wic.ast)
R
read_ast_from_disk() (in module wic.ast)
read_config_from_disk() (in module wic.input_output)
read_lines_pairs() (in module wic.input_output)
recursively_contains_dict_key() (in module wic.utils)
recursively_delete_dict_key() (in module wic.utils)
reindex_wic_steps() (in module wic.utils)
remove_dot_dollar() (in module wic.labshare)
restore_namespaced_output_name() (in module wic.utils)
rose (wic.wic_types.CompilerInfo attribute)
RoseTree (class in wic.wic_types)
run_path (wic.wic_types.Tool attribute)
S
shorten_namespaced_output_name() (in module wic.utils)
stem (wic.wic_types.StepId attribute)
step_id (wic.wic_types.YamlTree attribute)
step_name_1 (wic.wic_types.NodeData attribute)
step_name_str() (in module wic.utils)
StepId (class in wic.wic_types)
sub_forests (wic.wic_types.YamlForest attribute)
sub_trees (wic.wic_types.RoseTree attribute)
T
Tool (class in wic.wic_types)
tool (wic.wic_types.NodeData attribute)
tree_to_forest() (in module wic.ast)
U
upload_all() (in module wic.labshare)
upload_plugin() (in module wic.labshare)
V
vars_workflow_output_internal (wic.wic_types.EnvData attribute)
W
wic.ast
module
wic.cli
module
wic.compiler
module
wic.inference
module
wic.inlineing
module
wic.input_output
module
wic.labshare
module
wic.python_cwl_adapter
module
wic.schemas.wic_schema
module
wic.utils
module
wic.utils_cwl
module
wic.utils_graphs
module
wic.wic_types
module
wic_main_schema() (in module wic.schemas.wic_schema)
wic_tag_schema() (in module wic.schemas.wic_schema)
workflow_inputs_file (wic.wic_types.NodeData attribute)
write_absolute_yaml_tags() (in module wic.input_output)
write_config_to_disk() (in module wic.input_output)
write_to_disk() (in module wic.input_output)
Y
yaml_tree (wic.wic_types.YamlForest attribute)
YamlForest (class in wic.wic_types)
YamlTree (class in wic.wic_types)
yml (wic.wic_types.NodeData attribute)
(wic.wic_types.YamlTree attribute)
Workflow Inference Compiler
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