add spacexr #6212
Draft
add spacexr #6212
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
Aug 25, 2024
Co-authored-by: Björn Grüning <[email protected]>
|
Is there another way other than "compare=sim_size" to check ".pdf" and ".rds" outputs? |
bgruening
reviewed
Oct 19, 2024
tools/spacexr/macros.xml
Outdated
| <param argument="doublet_mode" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Use RCTD doublet mode weights?" help="Otherwise, uses RCTD full mode weights." /> | ||
| <param argument="weight_threshold" type="float" min="0" value="" optional="true" label="Weight threshold" help="The threshold of total normalized weights across all cell types in 'cell types' per pixel to be included in the model."/> | ||
| <param argument="sigma_gene" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Fit gene specific overdispersion parameter?" help="If FALSE, overdispersion parameter is same across all genes." /> | ||
| <param argument="PRECISION_THRESHOLD" type="float" min="0" value="0.05" label="Precision threshold" help="For checking for convergence, the maximum parameter change per algorithm step."/> |
There was a problem hiding this comment.
Just because it is all caps in the function :)
I'll change it.
tools/spacexr/macros.xml
Outdated
| test_genes_sig = $type.test_genes_sig, | ||
| logs = $type.logs | ||
| </token> | ||
| <token name="CSIDE_SINGLE_RUN"> |
There was a problem hiding this comment.
You can use CDATA here and than avoid $lt;
tools/spacexr/spacexr_cside.xml
Outdated
| #end if | ||
| ]]></command> | ||
| <configfiles> | ||
| <configfile name="cside_script"> |
tools/spacexr/spacexr_cside.xml
Outdated
| myRCTD <- readRDS('inputs/rctd.rds') | ||
|
|
||
| # set core | ||
| myRCTD@config$max_cores <- \${GALAXY_SLOTS:-2} |
There was a problem hiding this comment.
GALAXY_SLOTS will only work in bash. Here you are in R you need to access the environment variable GALAXY_SLOTS via an R function.
The tests should fail here, if they are not - why are they not failing :)
There was a problem hiding this comment.
There is a Cheetah syntax error before starting the job. I am trying to find it.
I'm offending it somehow :)
tools/spacexr/spacexr_cside.xml
Outdated
| <expand macro="cside_common_input"/> | ||
| </when> | ||
| <when value="point_density"> | ||
| <param argument="pathologic_barcode" type="text" optional="false" label="Barcodes" help="Comma separated barcodes of the pathological region."/> |
tools/spacexr/spacexr_cside.xml
Outdated
| <expand macro="cside_single_input"/> | ||
| </when> | ||
| <when value="custom"> | ||
| <param argument="pathologic_barcode" type="text" optional="false" label="Barcodes" help="Comma separated barcodes of the pathological region."/> |
There was a problem hiding this comment.
should this be a macro? its used a lot
tools/spacexr/spacexr_cside.xml
Outdated
| <param argument="log_FC_thresh" type="float" min="0" value="0.4" label="LogFC threshold" help="The natural log fold change cutoff for differential expression."/> | ||
| </when> | ||
| </conditional> | ||
| <section name="output" title="Output options"> |
There was a problem hiding this comment.
you can simply use a select box here with multiple=true
tools/spacexr/spacexr_rctd.xml
Outdated
| <param name="UMI_max" type="integer" min="0" value="20000000" label="UMI_max" help="Maximum UMI per pixel included in the analysis" /> | ||
| <param name="counts_MIN" type="integer" min="0" value="10" label="counts_MIN" help="Minimum total counts per pixel of genes used in the analysis." /> | ||
| <param name="UMI_min_sigma" type="integer" min="0" value="300" label="UMI_min_sigma" help="Minimum UMI per pixel for the choose_sigma_c function" /> | ||
| <param name="CELL_MIN_INSTANCE" type="integer" min="0" value="25" label="CELL_MIN_INSTANCE" help="Minimum number of cells required per cell type." /> |
There was a problem hiding this comment.
Its only a recommendation, but to stay consistent I would name all variables small letters.
tools/spacexr/spacexr_rctd.xml
Outdated
| <param name="DOUBLET_THRESHOLD" type="integer" min="0" value="20" label="DOUBLET_THRESHOLD" help="The penalty weight of predicting a doublet instead of a singlet for a pixel." /> | ||
| </section> | ||
| </section> | ||
| <section name="output" title="Output options"> |
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.
FOR CONTRIBUTOR:
This PR adds spacexr to Galaxy. This tool is used for cell-type deconvolution and cell type-specific differential expression in spatial transcriptomics.