Mercurial > repos > gaelcge > r_signac_galaxy

annotate signac-createAssayObject.R @ 0:6e0b320d8b6a draft default tip

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"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
author gaelcge
date Tue, 02 Aug 2022 19:11:27 +0000
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1 #!/usr/bin/env Rscript
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2
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3 # Load optparse we need to check inputs
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4
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5 suppressPackageStartupMessages(require(optparse))
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6
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7 # Load common functions
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8
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9 suppressPackageStartupMessages(require(workflowscriptscommon))
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10
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11 # parse options
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12 option_list = list(
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13 make_option(
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14 c("--signac-object"),
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15 action = "store",
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16 default = NA,
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17 type = 'character',
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18 help = "A Seurat object."
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19 ),
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20 make_option(
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21 c("--counts"),
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22 action = "store",
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23 default = NA,
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24 type = 'character',
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25 help = "Counts Matrix."
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26 ),
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27 make_option(
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28 c("--name"),
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29 action = "store",
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30 default = NA,
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31 type = 'character',
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32 help = "Assay Name."
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33 ),
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34 make_option(
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35 c("--min-cells"),
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36 action = "store",
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37 default = NA,
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38 type = 'numeric',
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39 help = "Min Cells."
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40 ),
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41 make_option(
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42 c("--min-features"),
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43 action = "store",
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44 default = NA,
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45 type = 'numeric',
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46 help = "Min Features."
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47 ),
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48 make_option(
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49 c("--method"),
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50 action = "store",
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51 default = NA,
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52 type = 'character',
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53 help = "Method for normalization."
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54 ),
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55 make_option(
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56 c("--scale-factor"),
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57 action = "store",
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58 default = 10000,
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59 type = 'numeric',
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60 help = "Sets the scale factor for cell-level normalization."
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61 ),
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62 make_option(
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63 c("--margin"),
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64 action = "store",
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65 default = NA,
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66 type = 'character',
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67 help = "If performing CLR normalization, normalize across features (1) or cells (2)."
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68 ),
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69 make_option(
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70 c("--output-object-file"),
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71 action = "store",
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72 default = NA,
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73 type = 'numeric',
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74 help = "File name in which to store serialized R matrix object."
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75 )
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76 )
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77 opt <- wsc_parse_args(option_list)
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78
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79 suppressPackageStartupMessages(require(Seurat))
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80 suppressPackageStartupMessages(require(Signac))
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81
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82 set.seed(1234)
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83
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84 if (! file.exists(opt$signac_object)){
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85 stop((paste('File', opt$signac_object, 'does not exist')))
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86 }
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87 if (! file.exists(opt$counts)){
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88 stop((paste('File', opt$counts, 'does not exist')))
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89 }
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90
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91 signac_object <- readRDS(file = opt$signac_object)
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92 counts <- readRDS(opt$counts)
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93
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94 signac_object[[opt$name]] <- CreateAssayObject(counts = counts)#, min.cells = opt$min_cells, min.features = opt$min_features)
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95
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96 signac_object <- NormalizeData(object = signac_object, normalization.method = opt$method, scale.factor = opt$scale_factor, margin = opt$margin, assay = opt$name)
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97
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98 saveRDS(signac_object, file = opt$output_object_file)