Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

add checkm2 #6542

Draft
wants to merge 7 commits into
base: main
Choose a base branch
from
Draft

add checkm2 #6542

wants to merge 7 commits into from

Conversation

astrovsky01
Copy link
Contributor

FOR CONTRIBUTOR:

  • I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
  • License permits unrestricted use (educational + commercial)
  • This PR adds a new tool or tool collection
  • This PR updates an existing tool or tool collection
  • This PR does something else (explain below)

bgruening
bgruening reviewed Nov 9, 2024
View reviewed changes
tools/checkm2/.shed.yml
description: Rapid assessment of genome bin quality using machine learning
long_description: Enhanced version of checkm, using machine learning models for greater speed and accuracy
homepage_url: https://github.com/chklovski/CheckM2
remote_repository_url: https://github.com/galaxyproject/tools-iuc/
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This could be more precise pointing to the folder.

tools/checkm2/checkm2.xml
<command detect_errors="exit_code"><![CDATA[
mkdir input_dir &&
#for $i, $file in enumerate($input):
cp $file input_dir/${file.element_identifier}.dat &&
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

single-quotes

tools/checkm2/checkm2.xml
<when value="no"/>
<when value="yes">
<!-- It's not all numbers and there's a check internally if it's in a specific list, so it had to be spelled out -->
<param argument="ttable" type="select" label="Prodigal table">
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

It would be useful for the user to tell what those numbers mean.

tools/checkm2/checkm2.xml Outdated
#end if
-x .dat
--threads "\${GALAXY_SLOTS:-1}"
--database_path "\${CHECKM2_DB_PATH:-$__tool_directory__/tool-data/CheckM2_database/uniref100.KO.1.dmnd}"
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Is this database stable forever and will not change? If those databases update over time, we need a location file.

@astrovsky01 astrovsky01 marked this pull request as draft November 13, 2024 00:12
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@bgruening bgruening bgruening left review comments

At least 1 approving review is required to merge this pull request.

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@astrovsky01 @bgruening