Mercurial > repos > mingchen0919 > rmarkdown_mirdeep2

annotate mirdeep2_mapper_render.R @ 4:543ee6fdadeb draft default tip

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit a23e23222252167ef7c3338a4872e84706df8f83-dirty
author mingchen0919
date Tue, 08 Aug 2017 15:06:46 -0400
parents 963905bcb754
children
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963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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1 ##======= Handle arguments from command line ========
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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2 # setup R error handline to go to stderr
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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3 options(show.error.messages=FALSE,
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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4 error=function(){
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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5 cat(geterrmessage(), file=stderr())
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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6 quit("no", 1, F)
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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7 })
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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9 # we need that to not crash galaxy with an UTF8 error on German LC settings.
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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10 loc = Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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12 # suppress warning
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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13 options(warn = -1)
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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15 options(stringsAsFactors=FALSE, useFancyQuotes=FALSE)
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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16 args = commandArgs(trailingOnly=TRUE)
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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18 suppressPackageStartupMessages({
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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19 library(getopt)
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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20 library(tools)
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21 })
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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23 # column 1: the long flag name
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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24 # column 2: the short flag alias. A SINGLE character string
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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25 # column 3: argument mask
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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26 # 0: no argument
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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27 # 1: argument required
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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28 # 2: argument is optional
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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29 # column 4: date type to which the flag's argument shall be cast.
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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30 # possible values: logical, integer, double, complex, character.
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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31 spec_list=list()
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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32
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33 ##------- 1. input data ---------------------
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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34 spec_list$FASTQ_READS = c('reads', 'r', '1', 'character')
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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35 spec_list$REFERENCE_GENOME = c('reference_genome', 'g', 1, 'character')
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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36 spec_list$ECHO = c('echo', 'e', '1', 'character')
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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37
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38 ##--------2. output report and report site directory --------------
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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39 spec_list$OUTPUT_HTML = c('mirdeep2_mapper', 'o', '1', 'character')
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40 spec_list$OUTPUT_DIR = c('mirdeep2_mapper_dir', 'd', '1', 'character')
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41 spec_list$READS_COLLAPSED = c('reads_collapsed', 'm', '1', 'character')
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42 spec_list$READ_X_COLLAPSED_VS_GENOME = c('reads_collapsed_vs_genome', 'n', '1', 'character')
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43 spec_list$REPORT_LOG = c("report_log", 't', '1', 'character')
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44
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45 ##---------other parameters---------------
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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46 spec_list$PARSE_TO_FASTA = c('parse_to_fasta', 'b', '1', 'character')
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47 spec_list$CLEAN_ENTRIES = c('clean_entries', 'c', '1', 'character')
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48 spec_list$CLIP_3_ADAPTER = c('clip_3_adapter', 'f', '2', 'character')
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49 spec_list$DISCARD_SHORTER_READS = c('discard_shorter_reads', 'h', '1', 'character')
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50 spec_list$COLLAPSE_READS_OR_NOT = c('collapse_reads_or_not', 'j', '1', 'character')
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51 spec_list$MAP_WITH_ONE_MISMATCH = c('map_with_one_mismatch', 'k', '1', 'character')
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52 spec_list$MAP_UP_TO_POSITION = c('map_up_to_position', 'l', '1', 'character')
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53
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54 ##--------3. Rmd templates sitting in the tool directory ----------
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56 ## _site.yml and index.Rmd files
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57 spec_list$SITE_YML = c('site_yml', 's', 1, 'character')
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58 spec_list$INDEX_Rmd = c('index_rmd', 'i', 1, 'character')
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60 ## other Rmd body template files
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61 spec_list$MIRDEEP2_MAPPER_RMD = c('mirdeep2_mapper_rmd', 'p', '1', 'character')
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65 ##------------------------------------------------------------------
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66
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67 spec = t(as.data.frame(spec_list))
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68 opt = getopt(spec)
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69 # arguments are accessed by long flag name (the first column in the spec matrix)
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70 # NOT by element name in the spec_list
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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71 # example: opt$help, opt$expression_file
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72 ##====== End of arguments handling ==========
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73
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74 #------ Load libraries ---------
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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75 library(rmarkdown)
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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76 library(plyr)
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77 # library(stringr)
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78 library(dplyr)
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79 # library(highcharter)
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80 # library(DT)
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81 # library(reshape2)
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82 # library(plotly)
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83 # library(formattable)
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84 library(htmltools)
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85
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86
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87 #----- 1. create the report directory ------------------------
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88 paste0('mkdir -p ', opt$mirdeep2_mapper_dir) %>%
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89 system()
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90
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91 #----- 2. generate Rmd files with Rmd templates --------------
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92 # a. templates without placeholder variables:
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93 # copy templates from tool directory to the working directory.
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94 # b. templates with placeholder variables:
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95 # substitute variables with user input values and place them in the working directory.
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96
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97
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98 #----- mirdeep2_mapper.Rmd -----------------------
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99 readLines(opt$mirdeep2_mapper_rmd) %>%
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100 (function(x) {
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101 gsub('ECHO', opt$echo, x)
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102 }) %>%
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103 (function(x) {
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104 gsub('FASTQ_READS', opt$reads, x)
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105 }) %>%
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106 (function(x) {
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107 gsub('REFERENCE_GENOME', opt$reference_genome, x)
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108 }) %>%
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109 (function(x) {
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110 gsub('PARSE_TO_FASTA', opt$parse_to_fasta, x)
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111 }) %>%
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112 (function(x) {
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113 gsub('CLEAN_ENTRIES', opt$clean_entries, x)
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114 }) %>%
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115 (function(x) {
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116 gsub('CLIP_3_ADAPTER', opt$clip_3_adapter, x)
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117 }) %>%
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118 (function(x) {
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119 gsub('DISCARD_SHORTER_READS', opt$discard_shorter_reads, x)
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120 }) %>%
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121 (function(x) {
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122 gsub('COLLAPSE_READS', opt$collapse_reads, x)
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123 }) %>%
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124 (function(x) {
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125 gsub('MAP_WITH_ONE_MISMATCH', opt$map_with_one_mismatch, x)
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126 }) %>%
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127 (function(x) {
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128 gsub('MAP_UP_TO_POSITION', opt$map_up_to_position, x)
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129 }) %>%
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130 (function(x) {
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131 gsub('OUTPUT_DIR', opt$mirdeep2_mapper_dir, x)
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132 }) %>%
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133 (function(x) {
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134 fileConn = file('mirdeep2_mapper.Rmd')
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135 writeLines(x, con=fileConn)
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136 close(fileConn)
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137 })
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138
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139
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140 #------ 3. render all Rmd files with render() --------
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141 render('mirdeep2_mapper.Rmd', output_file = opt$mirdeep2_mapper)
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142
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143
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144 #-------4. manipulate outputs -----------------------------
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145 # a. copy non-site files
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146 file.copy('reads_collapsed.fa', opt$reads_collapsed, recursive=TRUE)
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147 file.copy('reads_collapsed_vs_genome.arf', opt$reads_collapsed_vs_genome, recursive=TRUE)
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148 file.copy('report.log', opt$report_log, recursive=TRUE)
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149
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150
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151
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152
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153