Mercurial > repos > iuc > tximport
annotate tximport.R @ 0:206a71a69161 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
author | iuc |
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date | Wed, 04 Dec 2019 05:57:26 -0500 |
parents | |
children | 2c338211927c |
rev | line source |
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0
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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1 # setup R error handling to go to stderr |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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2 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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3 |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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4 # we need that to not crash galaxy with an UTF8 error on German LC settings. |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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5 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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6 |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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7 library("getopt") |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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8 options(stringAsFactors = FALSE, useFancyQuotes = FALSE) |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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9 args <- commandArgs(trailingOnly = TRUE) |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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10 |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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11 # get options, using the spec as defined by the enclosed list. |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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12 # we read the options from the default: commandArgs(TRUE). |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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13 spec <- matrix(c( |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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14 "help", "h", 0, "logical", |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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15 "out_file", "o", 1, "character", |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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16 "countsFiles", "n", 1, "character", |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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17 "countsFromAbundance", "r", 1, "character", |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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18 "format", "v", 1, "character", |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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19 "gff_file", "H", 0, "character", |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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20 "tx2gene", "f", 0, "character", |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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21 "geneIdCol", "l", 0, "character", |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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22 "txIdCol" , "p", 1, "character", |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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23 "abundanceCol", "i", 0, "character", |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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24 "countsCol", "y", 1, "character", |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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25 "lengthCol", "x", 1, "character"), |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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26 byrow=TRUE, ncol=4) |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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27 |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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28 opt <- getopt(spec) |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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29 |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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30 # if help was asked for print a friendly message |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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31 # and exit with a non-zero error code |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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32 if (!is.null(opt$help)) { |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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33 cat(getopt(spec, usage=TRUE)) |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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34 q(status=1) |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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35 } |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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36 |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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37 if (is.null(opt$gff_file) & is.null(opt$tx2gene)) { |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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38 cat("A GFF/GTF file or a tx2gene table is required\n") |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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39 q(status=1) |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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40 } |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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41 |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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42 if (opt$format == 'none'){ #custom format |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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43 if (is.null(opt$txIdCol) | is.null(opt$abundanceCol) | is.null(opt$countsCol) | is.null(opt$lengthCol)) { |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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44 cat("If you select a custom format for the input files you need to specify the column names\n") |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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45 q(status=1) |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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46 } |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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47 } |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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48 |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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49 if (is.null(opt$countsFiles)) { |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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50 cat("'countsFiles' is required\n") |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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51 q(status=1) |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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52 } |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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53 |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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54 |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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55 # load samples from tab file |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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56 samples_df <- read.table(opt$countsFiles, sep="\t", header=TRUE) |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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57 colnames(samples_df) <- c("id","path") |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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58 rownames(samples_df) <- NULL |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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59 # Prepare char vector with files and sample names |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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60 files <- file.path(samples_df[,"path"]) |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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61 names(files) <- samples_df[,"id"] |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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62 |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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63 |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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64 |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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65 library(tximport) |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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66 |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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67 ### if the input is a gff/gtf file first need to create the tx2gene table |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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68 if (!is.null(opt$gff_file)) { |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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69 suppressPackageStartupMessages({ |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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70 library("GenomicFeatures") |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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71 }) |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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72 txdb <- makeTxDbFromGFF(opt$gff_file) |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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73 k <- keys(txdb, keytype = "TXNAME") |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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74 tx2gene <- select(txdb, keys=k, columns="GENEID", keytype="TXNAME") |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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75 # Remove 'transcript:' from transcript IDs (when gffFile is a GFF3 from Ensembl and the transcript does not have a Name) |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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76 tx2gene$TXNAME <- sub('^transcript:', '', tx2gene$TXNAME) |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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77 |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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78 } else { |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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79 tx2gene <- read.table(opt$tx2gene,header=FALSE) |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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80 } |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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81 |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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82 |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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83 |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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84 ## |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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85 if (is.null(opt$geneIdCol)) { ## there is a tx2gene table |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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86 if (opt$format == 'none'){ #predefined format |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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87 txi_out <- tximport(files, type="none",txIdCol=opt$txIdCol,abundanceCol=opt$abundanceCol,countsCol=opt$countsCol,lengthCol=opt$lengthCol,tx2gene=tx2gene,countsFromAbundance=opt$countsFromAbundance) |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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88 } else { |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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89 txi_out <- tximport(files, type=opt$format, tx2gene=tx2gene,countsFromAbundance=opt$countsFromAbundance) |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff
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90 } |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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91 } else { # the gene_ID is a column in the counts table |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff
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92 if (opt$format == 'none'){ #predefined format |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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93 txi_out <- tximport(files, type="none",geneIdCol=opt$geneIdCol,txIdCol=opt$txIdCol,abundanceCol=opt$abundanceCol,countsCol=opt$countsCol,lengthCol=opt$lengthCol,tx2gene=tx2gene,countsFromAbundance=opt$countsFromAbundance) |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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94 } else { |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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95 txi_out <- tximport(files, type=opt$format, geneIdCol=opt$geneIdCol,countsFromAbundance=opt$countsFromAbundance) |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff
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96 } |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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97 |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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98 } |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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99 # write count as table |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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100 write.table(txi_out$counts, file=opt$out_file, row.names = TRUE, col.names = TRUE, quote = FALSE, sep = "\t") |