Mercurial > repos > mingchen0919 > rmarkdown_i_adhore

annotate i_adhore_configure_render.R @ 1:fd719a0a6b26 draft

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
author mingchen0919
date Tue, 08 Aug 2017 12:59:51 -0400
parents 9755ce6ac4d5
children f8bedb407e5c
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1
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2 ##======= Handle arguments from command line ========
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3 # setup R error handline to go to stderr
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4 options(show.error.messages=FALSE,
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5 error=function(){
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6 cat(geterrmessage(), file=stderr())
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7 quit("no", 1, F)
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8 })
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10 # we need that to not crash galaxy with an UTF8 error on German LC settings.
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
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11 loc = Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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13 # suppress warning
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14 options(warn = -1)
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16 options(stringsAsFactors=FALSE, useFancyQuotes=FALSE)
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17 args = commandArgs(trailingOnly=TRUE)
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19 suppressPackageStartupMessages({
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20 library(getopt)
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21 library(tools)
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22 })
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24 # column 1: the long flag name
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25 # column 2: the short flag alias. A SINGLE character string
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26 # column 3: argument mask
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27 # 0: no argument
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28 # 1: argument required
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29 # 2: argument is optional
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30 # column 4: date type to which the flag's argument shall be cast.
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31 # possible values: logical, integer, double, complex, character.
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32 spec_list=list()
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35 ##------- 1. input data ---------------------
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36 spec_list$ECHO = c('echo', 'e', '1', 'character')
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37 spec_list$G_ANALYSIS_FILES = c('g_analysis_files', 'G', '1', 'character')
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38 spec_list$BLAST_TABLE = c('blast_table', 'b', '1', 'character')
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39 spec_list$GAP_SIZE = c('gap_size', 'g', '1', 'character')
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40 spec_list$CLUSTER_GAP = c('cluster_gap', 'c', '1', 'character')
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41 spec_list$Q_VALUE = c('q_value', 'q', '1', 'character')
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42 spec_list$PROB_CUTOFF = c('prob_cutoff', 'p', '1', 'character')
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43 spec_list$ANCHOR_POINTS = c('anchor_points', 'a', '1', 'character')
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44 spec_list$ALIGNMENT_METHOD = c('alignment_method', 'm', '1', 'character')
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45 spec_list$LEVEL2ONLY = c('level2only', 'l', '1', 'character')
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46 spec_list$TABLE_TYPE = c('table_type', 'T', '1', 'character')
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47 spec_list$MULTI_HYPOTHESIS_CORRECTION = c('multi_hypothesis_correction', 'h', '1', 'character')
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50 ##--------2. output report and report site directory --------------
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51 spec_list$I_ADHORE_CONFIGURE_TXT = c('i_adhore_configure_txt', 'x', '1', 'character')
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52 spec_list$OUTPUT_HTML = c('i_adhore_configure_html', 'o', '1', 'character')
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53 spec_list$OUTPUT_DIR = c('i_adhore_configure_dir', 'd', '1', 'character')
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56 ##--------3. Rmd templates sitting in the tool directory ----------
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57 spec_list$I_ADHORE_CONFIGURE_RMD = c('i_adhore_configure_rmd', '-t', '1', 'character')
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60 spec = t(as.data.frame(spec_list))
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61 opt = getopt(spec)
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62 # arguments are accessed by long flag name (the first column in the spec matrix)
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63 # NOT by element name in the spec_list
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64 # example: opt$help, opt$expression_file
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65 ##====== End of arguments handling ==========
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66
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67 #------ Load libraries ---------
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68 library(rmarkdown)
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69 library(plyr)
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70 library(dplyr)
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73 #----- 1. create the report directory ------------------------
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74 system(paste0('mkdir -p ', opt$i_adhore_configure_dir))
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75 # set working directory to output files directory
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76 setwd(opt$i_adhore_configure_dir)
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77
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78
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79 #----- 2. generate Rmd files with Rmd templates --------------
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
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80 # a. templates without placeholder variables:
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
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81 # copy templates from tool directory to the working directory.
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
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82 # b. templates with placeholder variables:
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
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83 # substitute variables with user input values and place them in the working directory.
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
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84
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85
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86 #----- 01 i_adhore_configure.Rmd -----------------------
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
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87 readLines(opt$i_adhore_configure_rmd) %>%
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
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88 (function(x) {
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
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89 gsub('ECHO', opt$echo, x)
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
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90 }) %>%
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
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91 (function(x) {
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
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92 gsub('I_ADHORE_CONFIGURE_TXT', opt$i_adhore_configure_txt, x)
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
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93 }) %>%
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
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94 (function(x) {
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
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95 fileConn = file('i_adhore_configure.Rmd')
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
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96 writeLines(x, con=fileConn)
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
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97 close(fileConn)
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98 })
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
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99
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100
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101 #------ 3. render all Rmd files --------
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
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102 render('i_adhore_configure.Rmd', output_file = opt$i_adhore_configure_html)