How to use ToolDog ?

ToolDog can either generates a template from a bio.tools entry for Galaxy or CWL but also annotates exiting tool descriptors with missing metadata. ToolDog supports generation of XML files for Galaxy (-g/–galaxy) or CWL tool (-c/–cwl). It works in two main steps: (1) Analysis of the source code when possible (for the moment, only support Python code using argparse), (2) Addition of metadata to the tool description.

Note

If you find a bug, have any questions or suggestions, please create an issue on GitHub or contact us on Gitter.

Import from https://bio.tools entry

You can generate a XML for Galaxy from an online https://bio.tools description from the identifier using the following command:

tooldog -g/--galaxy id > outfile.xml

Import from JSON local file

To generate XML from a local file downloaded from http://bio.tools, use the following command:

tooldog -g/--galaxy file.json > outfile.xml

Annotation of existing files

You can also use ToolDog to add missing metadata from your tool descriptor if the tool is registered on https://bio.tools:

tooldog -g/--galaxy id --existing_desc your_xml.xml > annotated_xml.xml

Note

For the moment, only annotation of Galaxy XML is supported.

Advanced options

Please refer to the help section (tooldog -h) of ToolDog to see the full list of options.

Run parts independently

You can decide to run both parts of ToolDog in an independant manner using tooldog -g id --analyse and tooldog -g id --annotate options.

Use your own settings and local files

ToolDog offers the possibility to use your own settings for most of the step of the generation.

Options for source code analysis

  • --source_language: specify the language of your source code.
  • --source_code: specify the path to your source code directory.

Warning

For the moment, only analysis of Python code is available

Options for tool description annotation

  • --inout_biotools: select this option to also add inputs and outputs found on the https://bio.tools description to your Galaxy XML or CWL tool description.

Options specific to Galaxy XML generation

The options below are used for the mapping between EDAM formats and data to Galaxy datatypes. As some Galaxy instances sometimes have their own defined datatypes, you can here specify the url:

  • --galaxy_url: URL of the Galaxy instance (default is https://usegalaxy.org)
  • --edam_url: URL or local path to EDAM.owl (default is http://edamontology.org/EDAM.owl)
  • --mapping_file: this is a JSON file generated by ToolDog that you can keep once you have performed your own mapping.