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comparison rmarkdown_feature_counts_render.R @ 0:5af86972b408 draft

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planemo upload
author mingchen0919
date Fri, 29 Dec 2017 15:03:18 -0500
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-1:000000000000 0:5af86972b408
1 ##============ Sink warnings and errors to a file ==============
2 ## use the sink() function to wrap all code within it.
3 ##==============================================================
4 zz = file('warnings_and_errors.txt')
5 sink(zz)
6 sink(zz, type = 'message')
7
8 ##============== load packages ===============================
9 library(getopt)
10 library(rmarkdown)
11 library(htmltools)
12 library(dplyr)
13 library(Rsubread)
14 library(DT)
15 ##============================================================
16
17 ##---------below is the code for rendering .Rmd templates-----
18
19 ##=============STEP 1: handle command line arguments==========
20 ##
21 ##============================================================
22 # column 1: the long flag name
23 # column 2: the short flag alias. A SINGLE character string
24 # column 3: argument mask
25 # 0: no argument
26 # 1: argument required
27 # 2: argument is optional
28 # column 4: date type to which the flag's argument shall be cast.
29 # possible values: logical, integer, double, complex, character.
30 #-------------------------------------------------------------
31 #++++++++++++++++++++ Best practice ++++++++++++++++++++++++++
32 # 1. short flag alias should match the flag in the command section in the XML file.
33 # 2. long flag name can be any legal R variable names
34 # 3. two names in args_list can have common string but one name should not be a part of another name.
35 # for example, one name is "ECHO", if another name is "ECHO_XXX", it will cause problems.
36 #+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
37 args_list=list()
38 ##------- 1. input data ---------------------
39 args_list$e = c('echo', 'e', '1', 'logical')
40 args_list$a = c('input_bam_paths', 'a', '1', 'character')
41 args_list$N = c('input_bam_names', 'N', '1', 'character')
42 args_list$b = c('annot_inbuilt', 'b', '1', 'character')
43 args_list$c = c('annot_ext', 'c', '1', 'character')
44 args_list$f = c('isGTFAnnotationFile', 'f', '1', 'logical')
45 args_list$g = c('gtf_feature_type', 'g', '1', 'character')
46 args_list$h = c('gtf_attr_type', 'h', '1', 'character')
47 args_list$i = c('chr_aliases', 'i', '2', 'character')
48 args_list$j = c('use_meta_features', 'j', '1', 'logical')
49 args_list$k = c('allow_multi_overlap', 'k', '1', 'logical')
50 args_list$l = c('min_overlap', 'l', '1', 'integer')
51 args_list$m = c('largest_overlap', 'm', '1', 'logical')
52 args_list$n = c('read_extension_5', 'n', '1', 'integer')
53 args_list$o = c('read_extension_3', 'o', '1', 'integer')
54 args_list$p = c('read_2_pos', 'p', '1', 'character')
55 args_list$q = c('count_multi_mapping_reads', 'q', '1', 'logical')
56 args_list$u = c('fraction', 'u', '1', 'logical')
57 args_list$v= c('min_mqs', 'v', '1', 'integer')
58 args_list$w= c('split_only', 'w', '1', 'logical')
59 args_list$x= c('non_split_only', 'x', '1', 'logical')
60 args_list$y= c('primary_only', 'y', '1', 'logical')
61 args_list$z= c('ignore_dup', 'z', '1', 'logical')
62 args_list$A= c('strand_specific', 'A', '1', 'integer')
63 args_list$B= c('junc_counts', 'B', '1', 'logical')
64 args_list$C= c('genome', 'C', '1', 'character')
65 args_list$D= c('is_paired_end', 'D', '1', 'logical')
66 args_list$E= c('require_both_ends_mapped', 'E', '1', 'logical')
67 args_list$F= c('check_frag_length', 'F', '1', 'logical')
68 args_list$G= c('min_frag_length', 'G', '1', 'integer')
69 args_list$H= c('max_frag_length', 'H', '1', 'integer')
70 args_list$I= c('count_chimeric_fragments', 'I', '1', 'logical')
71 args_list$J= c('auto_sort', 'J', '1', 'logical')
72 args_list$K= c('n_threads', 'K', '1', 'integer')
73 args_list$L= c('max_mop', 'L', '1', 'integer')
74 args_list$M= c('report_reads', 'M', '1', 'logical')
75
76 ##--------2. output report and outputs --------------
77 args_list$REPORT_HTML = c('report_html', 'r', '1', 'character')
78 args_list$REPORT_DIR = c('report_dir', 'd', '1', 'character')
79 args_list$SINK_MESSAGE = c('sink_message', 's', '1', 'character')
80 ##--------3. .Rmd templates in the tool directory ----------
81 args_list$TOOL_TEMPLATE_RMD = c('tool_template_rmd', 't', '1', 'character')
82 ##-----------------------------------------------------------
83 opt = getopt(t(as.data.frame(args_list)))
84
85
86
87 ##=======STEP 2: create report directory (optional)==========
88 ##
89 ##===========================================================
90 dir.create(opt$report_dir)
91
92 ##=STEP 3: replace placeholders in .Rmd with argument values=
93 ##
94 ##===========================================================
95 #++ need to replace placeholders with args values one by one+
96 readLines(opt$tool_template_rmd) %>%
97 (function(x) {
98 gsub('ECHO', opt$echo, x)
99 }) %>%
100 (function(x) {
101 gsub('REPORT_DIR', opt$report_dir, x)
102 }) %>%
103 (function(x) {
104 fileConn = file('tool_template.Rmd')
105 writeLines(x, con=fileConn)
106 close(fileConn)
107 })
108
109
110 ##=============STEP 4: render .Rmd templates=================
111 ##
112 ##===========================================================
113 render('tool_template.Rmd', output_file = opt$report_html)
114
115
116 ##--------end of code rendering .Rmd templates----------------
117 sink()
118 ##=========== End of sinking output=============================