Mercurial > repos > ecology > ab1_fastq_converter

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"planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
author ecology
date Wed, 12 Jan 2022 15:12:58 +0000
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307518fb51af "planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
ecology
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1 #Rscript
307518fb51af "planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
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307518fb51af "planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
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3 ############################################
307518fb51af "planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
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4 ## Convert ab1 files into fastq ##
307518fb51af "planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
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5 ############################################
307518fb51af "planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
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307518fb51af "planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
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7 #####Packages
307518fb51af "planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
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307518fb51af "planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
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9 library(CrispRVariants, quietly = TRUE)
307518fb51af "planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
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10 library(sangerseqR, quietly = TRUE)
307518fb51af "planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
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307518fb51af "planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
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12 #####Load arguments
307518fb51af "planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
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307518fb51af "planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
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14 args <- commandArgs(trailingOnly = TRUE)
307518fb51af "planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
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307518fb51af "planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
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16 if (length(args) == 0) {
307518fb51af "planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
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17 stop("This tool needs at least one argument")
307518fb51af "planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
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18 } else {
307518fb51af "planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
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19 file <- args[1]
307518fb51af "planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
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20 filename <- args[2]
307518fb51af "planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
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21 tr <- as.logical(args[3])
307518fb51af "planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
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22 co <- as.numeric(args[4])
307518fb51af "planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
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23 min_seq <- as.integer(args[5])
307518fb51af "planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
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24 os <- as.numeric(args[6])
307518fb51af "planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
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25 }
307518fb51af "planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
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307518fb51af "planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
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27 ##### Conversion
307518fb51af "planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
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307518fb51af "planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
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29 if (grepl("^.+\\.[aA][bB][1i]$", filename)) {
307518fb51af "planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
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30 nfile <- sub("^(.+)\\.[aA][bB][1i]$", "\\1", filename)
307518fb51af "planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
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31 } else {
307518fb51af "planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
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32 nfile <- filename
307518fb51af "planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
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33 }
307518fb51af "planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
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307518fb51af "planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
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35 CrispRVariants::abifToFastq(nfile, file, "output.fastq", trim = tr, cutoff = co, min_seq_len = min_seq, offset = os)