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

New Galaxy tool wrapper for CELESTA #87

Merged
merged 23 commits into from
Aug 28, 2024
Merged

New Galaxy tool wrapper for CELESTA #87

merged 23 commits into from
Aug 28, 2024

Conversation

CameronFRWatson
Copy link
Contributor

Tool wrapper for CELESTA, a cell phenotyping tool for MTI data that uses both marker expression and spatial information. See #58

This PR is related to

  • Adding a new tool
  • Updating an existing tool to a newer version
  • Fixing a bug or updating just the Galaxy wrapper of an existing tool
  • Making a change to the tools-mti repo, CI, or other misc. change

If updating an existing tool to a newer major version

  • I have updated the TOOL_VERSION token in the tool's macros file
  • I have reset the VERSION_SUFFIX to 0 in the tool's macros file

Provide details here

  • Tool has 2 run-modes. One that plots the expression of markers for all cells in the image. Second that allows the user to assign cell types, and plot any combination of those assigned cell types
  • Created a new Docker container for CELESTA on quay

@CameronFRWatson
CELESTA initial commit
fdbf0e1
@CameronFRWatson
add r-anndata, r-optparse, r-janitor to docker dependencies
321fd77
@CameronFRWatson
Building up XML logic for CELESTA tool run modes
4c17fe2
@CameronFRWatson
add repeat plot param to assign_cells mode, and other small param cha…
f563c85 
…nges
@CameronFRWatson
Changes to overall R code organization
3827e22
@CameronFRWatson
finalize celesta test data
aeea03d
@CameronFRWatson
change r-anndata to anndataR in celesta deps
5a07150
@CameronFRWatson
CELESTA tool wrapper development
ace7c90
@CameronFRWatson
add expression threshold test data files
7d83003
@CameronFRWatson
add advanced params to CELESTA assign_cells runmode
5def150
@CameronFRWatson
finalize CELESTA plot_expression run mode
4cec7a5
@CameronFRWatson
Add CELESTA help and rm unused rep param
557b2ec
@CameronFRWatson
Merge branch 'main' into celesta
df69523
@CameronFRWatson
small fixes
e19a02c
@CameronFRWatson
move requirements to dockerfile
b0410b7
@CameronFRWatson
Final changes to celesta wrapper, test-data, docker container
70c00ed
@CameronFRWatson
Merge branch 'main' into celesta
cec7348
bgruening
bgruening reviewed Aug 27, 2024
View reviewed changes
tools/celesta/celesta.xml Outdated Show resolved Hide resolved
tools/celesta/celesta.xml Outdated Show resolved Hide resolved
tools/celesta/celesta.xml Outdated Show resolved Hide resolved
@CameronFRWatson CameronFRWatson marked this pull request as ready for review August 27, 2024 21:07
bgruening
bgruening approved these changes Aug 28, 2024
View reviewed changes
Copy link
Collaborator

@bgruening bgruening left a comment

Choose a reason for hiding this comment

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

Great! Very nice, thanks @CameronFRWatson

@alliecreason alliecreason merged commit 0ec4671 into main Aug 28, 2024
10 checks passed
@CameronFRWatson CameronFRWatson mentioned this pull request Aug 28, 2024
Closed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@bgruening bgruening bgruening approved these changes

@alliecreason alliecreason alliecreason approved these changes

@luke-c-sargent luke-c-sargent Awaiting requested review from luke-c-sargent

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

Successfully merging this pull request may close these issues.
3 participants
@CameronFRWatson @bgruening @alliecreason