Mercurial > repos > ecology > ab1_fastq_converter
annotate 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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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"
ecology
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2 |
307518fb51af
"planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
ecology
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3 ############################################ |
307518fb51af
"planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
ecology
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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"
ecology
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5 ############################################ |
307518fb51af
"planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
ecology
parents:
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6 |
307518fb51af
"planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
ecology
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7 #####Packages |
307518fb51af
"planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
ecology
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8 |
307518fb51af
"planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
ecology
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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"
ecology
parents:
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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"
ecology
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11 |
307518fb51af
"planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
ecology
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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"
ecology
parents:
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13 |
307518fb51af
"planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
ecology
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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"
ecology
parents:
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15 |
307518fb51af
"planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
ecology
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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"
ecology
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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"
ecology
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18 } else { |
307518fb51af
"planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
ecology
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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"
ecology
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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"
ecology
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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"
ecology
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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"
ecology
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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"
ecology
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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"
ecology
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25 } |
307518fb51af
"planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
ecology
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26 |
307518fb51af
"planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
ecology
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27 ##### Conversion |
307518fb51af
"planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
ecology
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28 |
307518fb51af
"planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
ecology
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29 if (grepl("^.+\\.[aA][bB][1i]$", filename)) { |
307518fb51af
"planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
ecology
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30 nfile <- sub("^(.+)\\.[aA][bB][1i]$", "\\1", filename) |
307518fb51af
"planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
ecology
parents:
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31 } else { |
307518fb51af
"planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
ecology
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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"
ecology
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33 } |
307518fb51af
"planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
ecology
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34 |
307518fb51af
"planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
ecology
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35 CrispRVariants::abifToFastq(nfile, file, "output.fastq", trim = tr, cutoff = co, min_seq_len = min_seq, offset = os) |