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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 9961b5acbf9081f10e14bc272406b36854fa2924"
author iuc
date Mon, 08 Nov 2021 12:03:34 +0000
parents 7a365ec81b52
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1 #!/usr/bin/env Rscript
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2 #Filters a SingleCellExperiment object, using PCA on the following metrics:
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3 # "pct_counts_top_100_features"
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4 # "total_features"
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5 # "pct_counts_feature_control"
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6 # "total_features_feature_control"
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7 # "log10_total_counts_endogenous"
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8 # "log10_total_counts_feature_control"
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10 # Load optparse we need to check inputs
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11 library(optparse)
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12 library(workflowscriptscommon)
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13 library(LoomExperiment)
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14 library(scater)
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15 library(robustbase)
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17 # parse options
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18 option_list <- list(
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19 make_option(
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20 c("-i", "--input-loom"),
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21 action = "store",
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22 default = NA,
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23 type = "character",
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24 help = "A SingleCellExperiment object file in Loom format."
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25 ),
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26 make_option(
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27 c("-o", "--output-loom"),
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28 action = "store",
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29 default = NA,
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30 type = "character",
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31 help = "File name in which to store the SingleCellExperiment object in Loom format."
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32 )
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33 )
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34
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35 opt <- wsc_parse_args(option_list, mandatory = c("input_loom", "output_loom"))
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37 # Check parameter values
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38
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39 if (! file.exists(opt$input_loom)) {
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40 stop((paste("File", opt$input_loom, "does not exist")))
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41 }
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42
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43 # Filter out unexpressed features
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45 sce <- import(opt$input_loom, format = "loom", type = "SingleCellLoomExperiment")
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47 print(paste("Starting with", ncol(sce), "cells"))
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48
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49 sce <- runColDataPCA(sce, outliers = TRUE, variables = list("sum", "detected", "subsets_Mito_percent"))
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50 sce$use <- !sce$outlier
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51 sce <- sce[, colData(sce)$use]
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52 print(paste("Ending with", ncol(sce), "cells"))
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54
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55 # Output to a Loom file
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56 if (file.exists(opt$output_loom)) {
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57 file.remove(opt$output_loom)
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58 }
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59 export(sce, opt$output_loom, format = "loom")