add anndata2seurat conversion #265
Open
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
# Description Based on the code from https://github.com/cellgeni/sceasy/blob/master/R/functions.R I tried to adapt it to SCEasy in order to allow Galaxy users to convert AnnData to Seurat files. I find it more useful to expand the SCEasy tool rather than create a new one. It might be also possible to incorporate AnnData to CDS object conversion within SCEasy, once my pull request fixing the bug in the source code is approved. Fixes # (issue) If the changed code works, it will fix the issue ebi-gene-expression-group#225 (SCEasy - AnnData-->Seurat) ## Type of change - [ ] Bug fix (non-breaking change which fixes an issue) - [x] New feature (non-breaking change which adds functionality) - [ ] Breaking change (fix or feature that would cause existing functionality to not work as expected) - [x] This change requires a documentation update ## Checklist - [ ] I have made any required changes to upstream dependencies for a tool wrapper, and they are available in distribution channels (e.g. Pip, Conda). - [ ] If I have updated the underlying software for a tool wrapper (e.g. scanpy-scripts by changing the value of `@TOOL_VERSION@`), then I have reset all 'build' values to 0 (e.g. `@TOOL_VERSION@+galaxy0`) - [ ] If I have updated a tool wrapper without a software change, then I have bumped the associated 'build' values (e.g. `@TOOL_VERSION@+galaxy0` `@TOOL_VERSION@+galaxy1`)
|
Thanks for this @wee-snufkin ! I suspect that for this to work we might need a release from sceasy, right @nh3 ? Could you guys at cellgeni do a release for sceasy so that it is picked up by bioconda please? Thanks! I guess it might need some dependency updates on the bioconda side. Then this could be used here I think. |
pcm32
reviewed
Aug 9, 2022
| @@ -74,6 +78,14 @@ | |||
| <option value="scale.data">scale.data</option> | |||
| </param> | |||
| </when> | |||
| <when value="anndata2seurat"> | |||
There was a problem hiding this comment.
I think that you also need to add an option in the conditional.param block (lines 42 to 46) for anndata2seurat.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Description
Based on the code from https://github.com/cellgeni/sceasy/blob/master/R/functions.R I tried to adapt it to SCEasy in order to allow Galaxy users to convert AnnData to Seurat files. I find it more useful to expand the SCEasy tool rather than to create a new one. It might be also possible to incorporate AnnData to CDS object conversion within SCEasy, once my pull request fixing the bug in the source code is approved.
Fixes # (issue)
If the changed code works, it will fix the issue #225 (SCEasy - AnnData-->Seurat)
Type of change
Checklist
@TOOL_VERSION@), then I have reset all 'build' values to 0 (e.g.@TOOL_VERSION@+galaxy0)@TOOL_VERSION@+galaxy0@TOOL_VERSION@+galaxy1)