Mercurial > repos > iuc > scater_plot_tsne

annotate scater-create-qcmetric-ready-sce.R @ 2:99f912d5af9f draft default tip

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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 12:03:09 +0000
parents 2b09ca1c5e41
children
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0
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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1 #!/usr/bin/env Rscript
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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2 #Creates a SingleCellExperiment object, which scater's calculateQCMetrics already applied
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3
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4 library(optparse)
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5 library(workflowscriptscommon)
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6 library(scater)
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7 library(LoomExperiment)
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8
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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9 # parse options
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10 #SCE-specific options
1
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11 option_list <- list(
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12 make_option(
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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13 c("-a", "--counts"),
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14 action = "store",
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15 default = NA,
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16 type = "character",
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17 help = "A tab-delimited expression matrix. The first column of all files is assumed to be feature names and the first row is assumed to be sample names."
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18 ),
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19 make_option(
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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20 c("-r", "--row-data"),
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21 action = "store",
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22 default = NULL,
1
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23 type = "character",
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24 help = "Path to TSV (tab-delimited) format file describing the features. Row names from the expression matrix (-a), if present, become the row names of the SingleCellExperiment."
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25 ),
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26 make_option(
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27 c("-c", "--col-data"),
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28 action = "store",
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29 default = NULL,
1
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30 type = "character",
0
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31 help = "Path to TSV format file describing the samples (annotation). The number of rows (samples) must equal the number of columns in the expression matrix."
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32 ),
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33 #The scater-specific options
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34 make_option(
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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35 c("-f", "--mt-controls"),
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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36 action = "store",
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37 default = NULL,
1
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38 type = "character",
0
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39 help = "Path to file containing a list of the mitochondrial control genes"
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40 ),
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41 make_option(
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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42 c("-p", "--ercc-controls"),
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43 action = "store",
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44 default = NULL,
1
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45 type = "character",
0
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46 help = "Path to file containing a list of the ERCC controls"
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47 ),
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48 make_option(
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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49 c("-l", "--cell-controls"),
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50 action = "store",
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51 default = NULL,
1
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52 type = "character",
0
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53 help = "Path to file (one cell per line) to be used to derive a vector of cell (sample) names used to identify cell controls (for example, blank wells or bulk controls)."
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54 ),
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55 make_option(
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56 c("-o", "--output-loom"),
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57 action = "store",
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58 default = NA,
1
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59 type = "character",
0
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60 help = "File name in which to store the SingleCellExperiment object in Loom format."
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61 )
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62 )
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63
1
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64 opt <- wsc_parse_args(option_list, mandatory = c("counts", "output_loom"))
0
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65
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66 # Read the expression matrix
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67
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68 counts <- wsc_split_string(opt$counts)
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69 reads <- read.table(counts)
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70
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71 # Read row and column annotations
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72
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73 rowdata <- opt$row_data
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74
1
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75 if (! is.null(opt$row_data)) {
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76 rowdata <- read.delim(opt$row_data)
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77 }
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78
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79 coldata <- opt$col_data
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80
1
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81 if (! is.null(opt$col_data)) {
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82 coldata <- read.delim(opt$col_data)
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83 }
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84
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85 # Now build the object
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86
1
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87 sce <- SingleCellLoomExperiment(assays = list(counts = as.matrix(reads)), colData = coldata)
0
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88 #Scater options
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89
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90 # Check feature_controls (only mitochondrial and ERCC used for now)
1
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91
2b09ca1c5e41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
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92 if (! is.null(opt$mt_controls)) {
2b09ca1c5e41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
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93 if (! file.exists(opt$mt_controls)) {
2b09ca1c5e41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
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94 stop((paste("Supplied feature_controls file", opt$mt_controls, "does not exist")))
0
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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95 } else {
1
2b09ca1c5e41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
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96 mts <- readLines(opt$mt_controls)
0
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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97 }
1
2b09ca1c5e41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
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98 } else {
2b09ca1c5e41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
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99 mts <- NULL
0
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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100 }
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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101
1
2b09ca1c5e41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
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102 if (! is.null(opt$ercc_controls)) {
2b09ca1c5e41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
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103 if (! file.exists(opt$ercc_controls)) {
2b09ca1c5e41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
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104 stop((paste("Supplied feature_controls file", opt$ercc_controls, "does not exist")))
0
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
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105 } else {
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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106 ercc_controls <- readLines(opt$ercc_controls)
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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107 }
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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108 } else {
1
2b09ca1c5e41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
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109 ercc_controls <- NULL
0
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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110 }
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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111
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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112 # Check cell_controls
1
2b09ca1c5e41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
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113
2b09ca1c5e41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
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114 if (! is.null(opt$cell_controls)) {
2b09ca1c5e41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
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115 if (! file.exists(opt$cell_controls)) {
2b09ca1c5e41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
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116 stop((paste("Supplied feature_controls file", opt$cell_controls, "does not exist")))
0
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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117 } else {
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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118 cell_controls <- readLines(opt$cell_controls)
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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119 }
1
2b09ca1c5e41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
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120 } else {
2b09ca1c5e41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
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121 cell_controls <- NULL
0
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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122 }
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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123
1
2b09ca1c5e41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
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124 # calculate QCMs
0
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125
1
2b09ca1c5e41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
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126 sce <- addPerCellQC(sce, subsets = list(Mito = mts, ERCC = ercc_controls, cell_controls = cell_controls))
0
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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127
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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128 # Output to a Loom file
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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129 if (file.exists(opt$output_loom)) {
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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130 file.remove(opt$output_loom)
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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131 }
1
2b09ca1c5e41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
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132 export(sce, opt$output_loom, format = "loom")