Mercurial > repos > mingchen0919 > rmarkdown_fastq_dump

annotate fastq_dump_pe_render.R @ 11:d4a9c31d0046 draft

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
author mingchen0919
date Wed, 27 Sep 2017 16:43:52 -0400
parents 7ec600e7dba7
children 66bc1016ec2a
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11
d4a9c31d0046 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
mingchen0919
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1 ##======= Handle arguments from command line ========
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mingchen0919
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2 # setup R error handline to go to stderr
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mingchen0919
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3 options(show.error.messages=FALSE,
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mingchen0919
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4 error=function(){
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mingchen0919
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5 cat(geterrmessage(), file=stderr())
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mingchen0919
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6 quit("no", 1, F)
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mingchen0919
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7 })
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mingchen0919
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8
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mingchen0919
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9 # we need that to not crash galaxy with an UTF8 error on German LC settings.
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mingchen0919
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10 loc = Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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mingchen0919
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11
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mingchen0919
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12 # suppress warning
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mingchen0919
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13 options(warn = -1)
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14
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mingchen0919
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15 options(stringsAsFactors=FALSE, useFancyQuotes=FALSE)
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mingchen0919
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16 args = commandArgs(trailingOnly=TRUE)
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17
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18 suppressPackageStartupMessages({
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mingchen0919
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19 library(getopt)
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20 library(tools)
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21 })
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22
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mingchen0919
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23 #/////////////////////// SINK WARNINGS AND ERRORS TO A FILE FOR DEBUGGING ///////////
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24 zz = file('warnings_and_errors.txt')
d4a9c31d0046 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
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25 sink(zz)
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26 sink(zz, type = 'message')
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27
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mingchen0919
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28 # column 1: the long flag name
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29 # column 2: the short flag alias. A SINGLE character string
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mingchen0919
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30 # column 3: argument mask
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31 # 0: no argument
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32 # 1: argument required
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33 # 2: argument is optional
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34 # column 4: date type to which the flag's argument shall be cast.
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35 # possible values: logical, integer, double, complex, character.
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mingchen0919
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36 ##------- 1. input data ---------------------
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37 spec_list=list()
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38 spec_list$SRA_ACCESSION = c('sra_accession', 'i', '1', 'character')
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39 spec_list$FORMAT = c('format', 'f', '1', 'character')
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40 spec_list$ECHO = c('echo', 'e', '1', 'character')
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41 spec_list$SPLIT_FILES = c('split_files', 'p', '1', 'character')
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42 ##--------2. output report and outputs --------------
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43 spec_list$REPORT_HTML = c('report_html', 'r', '1', 'character')
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44 spec_list$OUTPUT_DIR = c('output_dir', 'd', '1', 'character')
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45 spec_list$SINK_OUTPUT = c('sink_output', 's', '1', 'character')
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46 ##--------3. Rmd templates in the tool directory ----------
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47 spec_list$FASTQ_DUMP_SE_RMD = c('fastq_dump_pe_rmd', 't', '1', 'character')
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48
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49 spec = t(as.data.frame(spec_list))
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50 opt = getopt(spec)
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51
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52 #------ Load libraries ---------
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53 library(rmarkdown)
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54 library(htmltools)
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55 library(dplyr)
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56
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57 #----- 1. create the report directory ------------------------
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58 system(paste0('mkdir -p ', opt$output_dir))
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59
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60 #----- 2. generate Rmd files with Rmd templates --------------
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61 # a. templates without placeholder variables:
d4a9c31d0046 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
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62 # copy templates from tool directory to the working directory.
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63 # b. templates with placeholder variables:
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64 # substitute variables with user input values and place them in the working directory.
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65
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66 #----- 01 fastq_dump_pe.Rmd -----------------------
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67 readLines(opt$fastq_dump_pe_rmd) %>%
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68 (function(x) {
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69 gsub('SRA_ACCESSION', opt$sra_accession, x)
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70 }) %>%
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71 (function(x) {
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72 gsub('FORMAT', opt$format, x)
d4a9c31d0046 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
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73 }) %>%
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74 (function(x) {
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75 gsub('ECHO', opt$echo, x)
d4a9c31d0046 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
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76 }) %>%
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77 (function(x) {
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78 gsub('SPLIT_FILES', opt$split_files, x)
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79 }) %>%
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80 (function(x) {
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81 gsub('OUTPUT_DIR', opt$output_dir, x)
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82 }) %>%
d4a9c31d0046 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
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83 (function(x) {
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84 fileConn = file('fastq_dump_pe.Rmd')
d4a9c31d0046 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
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85 writeLines(x, con=fileConn)
d4a9c31d0046 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
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86 close(fileConn)
d4a9c31d0046 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
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87 })
d4a9c31d0046 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
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88
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89 #------ 3. render all Rmd files --------
d4a9c31d0046 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
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90 render('fastq_dump_pe.Rmd', output_file = opt$report_html)
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91
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92
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93 #-------4. manipulate outputs -----------------------------
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94
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95
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96
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97
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98
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99 sink()
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100 #/////////// END OF SINK OUTPUT ///////////////////////////