[WIP] ProteoRE topGO enrichment analysis 20210412 #598
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
bgruening
reviewed
May 22, 2021
| <option value="parentchild" >ParentChild</option> | ||
| </param> | ||
| <param name="threshold" type="text" label="p-value threshold (e.g : 1e-3)" value="1e-3"/> | ||
| <param name="correction" label="Multiple testing procedure (p-value adjustment)" type="select"> |
There was a problem hiding this comment.
indentation ... I recommend using https://github.com/galaxyproject/galaxy-language-server it will format your files nicely and will point you to a few limiting issues.
| <param name="genelist" value="ID_Converter_FKW_Lacombe_et_al_2017_OK.txt"/> | ||
| <param name="column" value="c8"/> | ||
| <param name="header" value="TRUE"/> | ||
| </conditional> |
There was a problem hiding this comment.
please add a test for at least every conditional. The Galaxy language server has a feature to bootstrap the test cases.
|
|
||
| **Galaxy integration** | ||
|
|
||
| Lisa Perus, Lien Nguyen, Florence Combes, Yves Vandenbrouck - CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR |
There was a problem hiding this comment.
can you add this as proper citation? maybe in bibtex?
bgruening
reviewed
May 22, 2021
|
@combesf can I help here in some way? |
combesf
changed the title
bgruening
reviewed
May 31, 2021
| @@ -0,0 +1,10 @@ | |||
| library("topGO") | |||
There was a problem hiding this comment.
that file should go and should probably be added to the .gitignore file
|
@combesf thanks for the adjustments. There are a few open questions. |
yvandenb
changed the title
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Outdated suggestions cannot be applied.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.
Another ProteoRE tool for review.
Thanks !