How to add a new tool?#

On which platform should you develop your new tool?#

Create a Virtual Machine (IaaS)#

If you are working in Norway and at the University of Oslo, Tromso or Bergen, see documentation at IaaS.

Then install planemo.

Use Planemo OVA image#

See Planemo Virtual Appliance documentation.

Develop a tool#

Best practices for developing new tools are https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_xml.html.

Always use quotes for tool directory (python3 ‘$tool_directory/psymap_simple.py’) and tool parameters (–cmap ‘$adv.colormap’)
When wrapping an existing underlying tool, use the same version than the underlying tool
from_work_dir will tell Galaxy to pick this file, this saves you the cp/mv command in the command section:

<data name="ofilename" format="png" from_work_dir="image.png"/>

If the output format depends on the type of output file, try to avoid auto_format and use change_format instead:

<data name="ofilename" format="json">
                <change_format>
                    <when input="format" value="csv" format="csv" />

Add EDAM ontology in your tool, for both topics and operations. Most climate tools will have:

<edam_topics>
  <edam_topic>topic_3855</edam_topic>
  <edam_topic>topic_3318</edam_topic>
</edam_topics>

Environmental science (topic 3855)
Physics (topic_3318)
If you are using firefox, you can install EDAM Popovers plugin to get the detailed information to EDAM terms.

EDAM popovers

We may need to update all the tools later when additional topics will be added for geosciences.

Do not forget to follow Galaxy IUC coding style.

Test a tool with planemo#

planemo t --galaxy_root=/opt/uio/packages/galaxy --conda_prefix=/opt/uio/packages/miniconda3 mean-per-zone/mean-per-zone.xml --conda_dependency_resolution --conda_auto_install --conda_channels conda-forge,bioconda,defaults,iuc

Serve galaxy-tools with planemo#

planemo s --galaxy_root=/opt/uio/packages/galaxy --conda_prefix=/opt/uio/packages/miniconda3 mean-per-zone/mean-per-zone.xml --conda_dependency_resolution --conda_auto_install --conda_channels conda-forge,bioconda,defaults,iuc