Mercurial > repos > gaelcge > r_signac_galaxy

annotate signac-geneactivity.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("--fragment-file"),
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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 = "Fragments file."
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26 ),
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27 make_option(
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28 c("--assay"),
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29 action = "store",
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30 default = NULL,
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31 type = 'character',
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32 help = "Assay."
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33 ),
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34 make_option(
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35 c("--features"),
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36 action = "store",
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37 default = NA,
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38 type = 'character',
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39 help = "Features."
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40 ),
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41 make_option(
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42 c("--extend-upstream"),
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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 = "Number of bases to extend upstream of the TSS."
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47 ),
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48 make_option(
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49 c("--extend-downstream"),
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50 action = "store",
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51 default = NA,
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52 type = 'numeric',
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53 help = "Number of bases to extend downstream of the TSS."
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54 ),
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55 make_option(
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56 c("--biotypes"),
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57 action = "store",
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58 default = NA,
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59 type = 'character',
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60 help = "Gene biotypes to include. If NULL, use all biotypes in the gene annotation."
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61 ),
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62 make_option(
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63 c("--max-width"),
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64 action = "store",
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65 default = NA,
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66 type = 'numeric',
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67 help = "Maximum allowed gene width for a gene to be quantified."
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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 = 'character',
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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
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78 opt <- wsc_parse_args(option_list)
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79
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80 suppressPackageStartupMessages(require(Seurat))
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81 suppressPackageStartupMessages(require(Signac))
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82
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83 set.seed(1234)
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84
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85 if (! file.exists(opt$signac_object)){
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86 stop((paste('File', opt$signac_object, 'does not exist')))
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87 }
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88
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89 signac_object <- readRDS(file = opt$signac_object)
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90
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91 signac_object@assays$peaks@fragments[[1]]@path <- opt$fragment_file
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92
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93 # Check features
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94 features <- NULL
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95 if (! is.null(opt$features) && opt$features != 'NULL'){
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96 if (file.exists(opt$features)){
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97 features <- readLines(opt$features)
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98 }
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99 }
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100
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101 # Check assay
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102 assay <- NULL
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103 if (! is.null(opt$assay) && opt$assay != 'NULL'){
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104 assay <- opt$assay
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105 }
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106
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107 saveRDS(GeneActivity(object = signac_object, assay = assay, features = features, extend.upstream = opt$extend_upstream, extend.downstream = opt$extend_downstream, biotypes = opt$biotypes, max.width = opt$max_width), file = opt$output_object_file)