Mercurial > repos > ecology > ab1_fastq_converter
view ab1_fastq.R @ 0:307518fb51af draft default tip
"planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
author | ecology |
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date | Wed, 12 Jan 2022 15:12:58 +0000 |
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#Rscript ############################################ ## Convert ab1 files into fastq ## ############################################ #####Packages library(CrispRVariants, quietly = TRUE) library(sangerseqR, quietly = TRUE) #####Load arguments args <- commandArgs(trailingOnly = TRUE) if (length(args) == 0) { stop("This tool needs at least one argument") } else { file <- args[1] filename <- args[2] tr <- as.logical(args[3]) co <- as.numeric(args[4]) min_seq <- as.integer(args[5]) os <- as.numeric(args[6]) } ##### Conversion if (grepl("^.+\\.[aA][bB][1i]$", filename)) { nfile <- sub("^(.+)\\.[aA][bB][1i]$", "\\1", filename) } else { nfile <- filename } CrispRVariants::abifToFastq(nfile, file, "output.fastq", trim = tr, cutoff = co, min_seq_len = min_seq, offset = os)