Mercurial > repos > mingchen0919 > rmarkdown_i_adhore

comparison i_adhore_configure_render.R @ 0:9755ce6ac4d5 draft

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
author mingchen0919
date Tue, 08 Aug 2017 12:53:57 -0400
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children f8bedb407e5c
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-1:000000000000 0:9755ce6ac4d5
1
2 ##======= Handle arguments from command line ========
3 # setup R error handline to go to stderr
4 options(show.error.messages=FALSE,
5 error=function(){
6 cat(geterrmessage(), file=stderr())
7 quit("no", 1, F)
8 })
9
10 # we need that to not crash galaxy with an UTF8 error on German LC settings.
11 loc = Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
12
13 # suppress warning
14 options(warn = -1)
15
16 options(stringsAsFactors=FALSE, useFancyQuotes=FALSE)
17 args = commandArgs(trailingOnly=TRUE)
18
19 suppressPackageStartupMessages({
20 library(getopt)
21 library(tools)
22 })
23
24 # column 1: the long flag name
25 # column 2: the short flag alias. A SINGLE character string
26 # column 3: argument mask
27 # 0: no argument
28 # 1: argument required
29 # 2: argument is optional
30 # column 4: date type to which the flag's argument shall be cast.
31 # possible values: logical, integer, double, complex, character.
32 spec_list=list()
33
34
35 ##------- 1. input data ---------------------
36 spec_list$ECHO = c('echo', 'e', '1', 'character')
37 spec_list$G_ANALYSIS_FILES = c('g_analysis_files', 'G', '1', 'character')
38 spec_list$BLAST_TABLE = c('blast_table', 'b', '1', 'character')
39 spec_list$GAP_SIZE = c('gap_size', 'g', '1', 'character')
40 spec_list$CLUSTER_GAP = c('cluster_gap', 'c', '1', 'character')
41 spec_list$Q_VALUE = c('q_value', 'q', '1', 'character')
42 spec_list$PROB_CUTOFF = c('prob_cutoff', 'p', '1', 'character')
43 spec_list$ANCHOR_POINTS = c('anchor_points', 'a', '1', 'character')
44 spec_list$ALIGNMENT_METHOD = c('alignment_method', 'm', '1', 'character')
45 spec_list$LEVEL2ONLY = c('level2only', 'l', '1', 'character')
46 spec_list$TABLE_TYPE = c('table_type', 'T', '1', 'character')
47 spec_list$MULTI_HYPOTHESIS_CORRECTION = c('multi_hypothesis_correction', 'h', '1', 'character')
48
49
50 ##--------2. output report and report site directory --------------
51 spec_list$I_ADHORE_CONFIGURE_TXT = c('i_adhore_configure_txt', 'x', '1', 'character')
52 spec_list$OUTPUT_HTML = c('i_adhore_configure_html', 'o', '1', 'character')
53 spec_list$OUTPUT_DIR = c('i_adhore_configure_dir', 'd', '1', 'character')
54
55
56 ##--------3. Rmd templates sitting in the tool directory ----------
57 spec_list$I_ADHORE_CONFIGURE_RMD = c('i_adhore_configure_rmd', '-t', '1', 'character')
58
59
60 spec = t(as.data.frame(spec_list))
61 opt = getopt(spec)
62 # arguments are accessed by long flag name (the first column in the spec matrix)
63 # NOT by element name in the spec_list
64 # example: opt$help, opt$expression_file
65 ##====== End of arguments handling ==========
66
67 #------ Load libraries ---------
68 library(rmarkdown)
69 library(plyr)
70 library(dplyr)
71
72
73 #----- 1. create the report directory ------------------------
74 system(paste0('mkdir -p ', opt$i_adhore_configure_dir))
75 # set working directory to output files directory
76 setwd(opt$i_adhore_configure_dir)
77
78
79 #----- 2. generate Rmd files with Rmd templates --------------
80 # a. templates without placeholder variables:
81 # copy templates from tool directory to the working directory.
82 # b. templates with placeholder variables:
83 # substitute variables with user input values and place them in the working directory.
84
85
86 #----- 01 i_adhore_configure.Rmd -----------------------
87 readLines(opt$i_adhore_configure_rmd) %>%
88 (function(x) {
89 gsub('ECHO', opt$echo, x)
90 }) %>%
91 (function(x) {
92 gsub('I_ADHORE_CONFIGURE_TXT', opt$i_adhore_configure_txt, x)
93 }) %>%
94 (function(x) {
95 fileConn = file('i_adhore_configure.Rmd')
96 writeLines(x, con=fileConn)
97 close(fileConn)
98 })
99
100
101 #------ 3. render all Rmd files --------
102 render('i_adhore_configure.Rmd', output_file = opt$i_adhore_configure_html)