pulsar.tools package

Submodules

pulsar.tools.authorization module

pulsar.tools.authorization.get_authorizer(toolbox)[source]

pulsar.tools.toolbox module

class pulsar.tools.toolbox.InputsValidator(command_validator, config_validators)[source]

Bases: object

validate_command(job_directory, command)[source]
validate_config(job_directory, name, path)[source]
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.

get_tool(id)[source]
class pulsar.tools.toolbox.ToolConfig[source]

Bases: object

Abstract description of a Galaxy tool.

get_tool_dir()[source]
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

class pulsar.tools.validator.ExpressionValidator(xml_el)[source]

Bases: object

validate(job_directory, string)[source]

Module contents

Tools

class pulsar.tools.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.

get_tool(id)[source]