Mercurial > repos > ecology > ab1_fastq_converter
comparison 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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-1:000000000000 | 0:307518fb51af |
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1 #Rscript | |
2 | |
3 ############################################ | |
4 ## Convert ab1 files into fastq ## | |
5 ############################################ | |
6 | |
7 #####Packages | |
8 | |
9 library(CrispRVariants, quietly = TRUE) | |
10 library(sangerseqR, quietly = TRUE) | |
11 | |
12 #####Load arguments | |
13 | |
14 args <- commandArgs(trailingOnly = TRUE) | |
15 | |
16 if (length(args) == 0) { | |
17 stop("This tool needs at least one argument") | |
18 } else { | |
19 file <- args[1] | |
20 filename <- args[2] | |
21 tr <- as.logical(args[3]) | |
22 co <- as.numeric(args[4]) | |
23 min_seq <- as.integer(args[5]) | |
24 os <- as.numeric(args[6]) | |
25 } | |
26 | |
27 ##### Conversion | |
28 | |
29 if (grepl("^.+\\.[aA][bB][1i]$", filename)) { | |
30 nfile <- sub("^(.+)\\.[aA][bB][1i]$", "\\1", filename) | |
31 } else { | |
32 nfile <- filename | |
33 } | |
34 | |
35 CrispRVariants::abifToFastq(nfile, file, "output.fastq", trim = tr, cutoff = co, min_seq_len = min_seq, offset = os) |