pulsar.tools package¶
Submodules¶
pulsar.tools.toolbox module¶
- class pulsar.tools.toolbox.InputsValidator(command_validator, config_validators)[source]¶
Bases:
object
- class pulsar.tools.toolbox.SimpleToolConfig(tool_el, tool_path)[source]¶
Bases:
ToolConfig
Abstract description of a Galaxy tool loaded from a toolbox with the tool tag not containing a guid, i.e. one not from the toolshed.
- class pulsar.tools.toolbox.ToolBox(path_string)[source]¶
Bases:
object
Abstraction over a tool config file largely modelled after Galaxy’s shed_tool_conf.xml. Hopefully over time this toolbox schema will be a direct superset of Galaxy’s with extensions to support simple, non-toolshed based tool setups.
- class pulsar.tools.toolbox.ToolConfig[source]¶
Bases:
object
Abstract description of a Galaxy tool.
- property inputs_validator¶
- class pulsar.tools.toolbox.ToolShedToolConfig(tool_el, tool_path)[source]¶
Bases:
SimpleToolConfig
Abstract description of a Galaxy tool loaded from a toolbox with the tool tag, i.e. one from the toolshed.
<tool file="../shed_tools/gvk.bx.psu.edu/repos/test/column_maker/f06aa1bf1e8a/column_maker/column_maker.xml" guid ="gvk.bx.psu.edu:9009/repos/test/column_maker/Add_a_column1/1.1.0"> <tool_shed>gvk.bx.psu.edu:9009</tool_shed> <repository_name>column_maker</repository_name> <repository_owner>test</repository_owner> <installed_changeset_revision>f06aa1bf1e8a</installed_changeset_revision <id>gvk.bx.psu.edu:9009/repos/test/column_maker/Add_a_column1/1.1.0</id> <version>1.1.0</version> </tool>
pulsar.tools.validator module¶
Module contents¶
Tools