# HG changeset patch
# User iuc
# Date 1738057447 0
# Node ID 2b1797b4cbb168a3c8efe597afd9c7df347232ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca
diff -r 000000000000 -r 2b1797b4cbb1 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Tue Jan 28 09:44:07 2025 +0000
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+
+ 2.2.1
+ 0
+ 23.0
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+ r-spacexr
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+ topic_3308
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+ operation_3223
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+ 10.1038/s41587-021-00830-w
+ 10.1038/s41592-022-01575-3
+ @Manual{github,
+ title = {SpatialeXpressionR: Cell type identification and cell type-specific differential expression in spatial transcriptomics.},
+ author = {Dylan Cable},
+ url = {https://github.com/dmcable/spacexr}}
+
+
+
+
\ No newline at end of file
diff -r 000000000000 -r 2b1797b4cbb1 spacexr_cside.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/spacexr_cside.xml Tue Jan 28 09:44:07 2025 +0000
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+
+ Cell type-specific differential expression with C-SIDE
+
+ macros.xml
+
+
+
+ r-ggplot2
+
+ 'results/cside_script.R' &&
+ Rscript 'results/cside_script.R'
+ ]]>
+
+ $type.lim)
+names(explanatory.variable) <- rownames(myRCTD@spatialRNA@coords)
+
+ #else
+explanatory.variable <- as.integer(myRCTD@spatialRNA@coords[['y']] > $type.lim)
+names(explanatory.variable) <- rownames(myRCTD@spatialRNA@coords)
+ #end if
+CSIDE_SINGLE_RUN
+
+#else:
+barcodes_df <- read.delim('inputs/barcodes.tabular', header = FALSE, sep = '\t', check.names = FALSE)
+region_list <- list()
+for (i in 1:ncol(barcodes_df)) {
+ region <- barcodes_df[, i]
+ region <- region[region != "" & !is.na(region)]
+ region_list[[i]] <- region
+}
+
+myRCTD <- run.CSIDE.regions(myRCTD,
+ region_list,
+ log_fc_thresh = $type.log_FC_thresh,
+ CSIDE_COMMON_RUN
+ )
+#end if
+
+
+# save the results
+
+# save significant genes in each cell type
+cell_types <- names(myRCTD@de_results[["sig_gene_list"]])
+for (cell_type in cell_types) {
+ df <- myRCTD@de_results[["sig_gene_list"]][[cell_type]]
+ assign(cell_type, df)
+ write.table(df, file = paste0("results/", cell_type, "_sig.tabular"), sep = "\t", quote = FALSE)
+}
+# save all genes in each cell type
+cell_types <- names(myRCTD@de_results[["all_gene_list"]])
+for (cell_type in cell_types) {
+ df <- myRCTD@de_results[["all_gene_list"]][[cell_type]]
+ assign(cell_type, df)
+ write.table(df, file = paste0("results/", cell_type, ".tabular"), sep = "\t", quote = FALSE)
+}
+
+#if 'plots' in $output_selector:
+# create plots
+library('ggplot2')
+make_all_de_plots(myRCTD, "figures")
+#end if
+
+#if 'rds' in $output_selector:
+# save rds file
+saveRDS(myRCTD, file = 'results/cside_results.rds')
+#end if
+ ]]>
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+ output['output_selector'] and 'plots' in output['output_selector']
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+ output['output_selector'] and 'plots' in output['output_selector']
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+ output['output_selector'] and 'plots' in output['output_selector']
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+ output['output_selector'] and 'rds' in output['output_selector']
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+ output['output_selector'] and 'rscript' in output['output_selector']
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+ output['output_selector'] and 'log' in output['output_selector']
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\ No newline at end of file