Mercurial > repos > iuc > lineagespot

annotate lineagespot_verbose.R @ 1:99494998688a draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 6a6a37f2574954dae65f9ec407fe38594ed37659
author iuc
date Sun, 25 Feb 2024 09:49:20 +0000
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1 ## How to execute this tool
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3 # A command-line interface to lineagespot for use with Galaxy
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4 #
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5 # The following arguments are required:
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6 #
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7 # 'in_vcf' a character vector of paths to VCF files object from Galaxy lineagespot/test-data
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8 # 'in_gff3' a character vector of path to GFF3 file containing SARS-CoV-2 gene coordinates object from Galaxy lineagespot/test-data
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9 # 'in_ref' a character vector of path to a folder containing lineage reports object from Galaxy lineagespot/test-data
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10 # 'in_voc' a character vector containing the names of the lineages of interest
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11 # 'in_threshold' a parameter indicating the AF threshold for identifying variants per sample
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12 #
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13 # Rscript ${__tool_directory__}/lineagespot_verbose.R --in_vcf ${__tool_directory__}/test-data/extdata/vcf-files --in_gff3 ${__tool_directory__}/test-data/extdata/NC_045512.2_annot.gff3 --in_ref ${__tool_directory__}/test-data/extdata/ref --in_voc "B.1.617.2, B.1.1.7, B.1.351, P.1" --in_threshold 0.8
6ddf5a9ce4a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
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14 # Set up R error handling to go to stderr
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15 options(show.error.messages = FALSE, error = function() {
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16 cat(geterrmessage(), file = stderr())
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17 q("no", 1, FALSE)
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18 })
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20 # Import required libraries
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22 library_path <- .libPaths()
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24 suppressPackageStartupMessages({
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25 library("getopt", lib.loc = library_path)
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26 library("data.table", lib.loc = library_path)
99494998688a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 6a6a37f2574954dae65f9ec407fe38594ed37659
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27 library("lineagespot", lib.loc = library_path)
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28 })
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31 options(stringAsfactors = FALSE, useFancyQuotes = FALSE)
6ddf5a9ce4a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
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33 # Take in trailing command line arguments
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34 args <- commandArgs(trailingOnly = TRUE)
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36 # Get options using the spec as defined by the enclosed list
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37 # Read the options from the default: commandArgs(TRUE)
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38 option_specification <- matrix(c(
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39 "in_vcf", "vcf", 1, "character",
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40 "in_gff3", "gff3", 1, "character",
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41 "in_ref", "ref", 1, "character",
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42 "in_voc", "voc", 2, "character",
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43 "in_threshold", "thr", 2, "double"
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44 ), byrow = TRUE, ncol = 4)
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46 options <- getopt(option_specification)
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48 if (!is.null(options$in_voc) && is.character(options$in_voc)) {
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49 options$in_voc <- unlist(strsplit(options$in_voc, split = ","))
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50 }
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51
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52 result <- lineagespot(
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53 vcf_folder = options$in_vcf,
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54 ref_folder = options$in_ref,
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55 gff3_path = options$in_gff3,
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56 voc = options$in_voc,
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57 AF_threshold = options$in_threshold
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58 )
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61 # Write output to new file which will be recognized by Galaxy
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62 fwrite(result$variants.table, sep = "\t", file = "variants_table.txt", row.names = FALSE)
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63 fwrite(result$lineage.hits, sep = "\t", file = "lineage_hits.txt", row.names = FALSE)
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64 fwrite(result$lineage.report, sep = "\t", file = "lineage_report.txt", row.names = FALSE)
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66 cat("\n Process has been completed !\n")