add spacexr #6212
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add spacexr #6212
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bgruening
reviewed
Aug 25, 2024
Co-authored-by: Björn Grüning <[email protected]>
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Is there another way other than "compare=sim_size" to check ".pdf" and ".rds" outputs? |
bgruening
reviewed
Oct 19, 2024
| <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."/> |
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Just because it is all caps in the function :)
I'll change it.
| test_genes_sig = $type.test_genes_sig, | ||
| logs = $type.logs | ||
| </token> | ||
| <token name="CSIDE_SINGLE_RUN"> |
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You can use CDATA here and than avoid $lt;
| #end if | ||
| ]]></command> | ||
| <configfiles> | ||
| <configfile name="cside_script"> |
| myRCTD <- readRDS('inputs/rctd.rds') | ||
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| # set core | ||
| myRCTD@config$max_cores <- \${GALAXY_SLOTS:-2} |
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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 :)
| <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."/> |
| <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."/> |
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should this be a macro? its used a lot
| <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"> |
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you can simply use a select box here with multiple=true
| <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." /> |
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Its only a recommendation, but to stay consistent I would name all variables small letters.
| <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"> |
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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.