Expanded Galaxy configuration parsing
- Added the GalaxyWorkflowEngineMetadata class as the access point for Galaxy workflow and tool metadata.
- Add tool metadata to the workflow steps (in the GalaxyWorkflowMetadata.addToolsMetadata and GalaxyWorkflowStep.addToolsMetadata methods).
- Moved the parse package to the galaxy.metadata package and renamed it to parsers.
- Renamed the ToolDefinitionParser class to GalaxyToolMetadataParser.
- Pass the toolsDirectory parameter to the ToolDefinitionParser.parseToolsConfiguration method.
- Renamed the ToolMetadata class to GalaxyToolMetadata and added fields to store the metadata.
- Added the GalaxyToolParameterMetadata class to store data about tool parameters.
- Moved the tool_conf.xml file to the tools subdirectory.