Mercurial > repos > mingchen0919 > rmarkdown_bdss_client

annotate bdss_client_sra_pe_render.R @ 4:206c59e498e7 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
author mingchen0919
date Wed, 11 Oct 2017 11:31:48 -0400
parents c707a4178832
children 246cb7315673
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
1 ##======= Handle arguments from command line ========
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
2 # setup R error handline to go to stderr
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
3 options(show.error.messages=FALSE,
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
4 error=function(){
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
5 cat(geterrmessage(), file=stderr())
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
6 quit("no", 1, F)
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
7 })
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
8
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
9 # we need that to not crash galaxy with an UTF8 error on German LC settings.
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
10 loc = Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
11
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
12 # suppress warning
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
13 options(warn = -1)
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
14
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
15 options(stringsAsFactors=FALSE, useFancyQuotes=FALSE)
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
16 args = commandArgs(trailingOnly=TRUE)
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
17
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
18 suppressPackageStartupMessages({
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
19 library(getopt)
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
20 library(tools)
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
21 })
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
22
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
23 #/////////////////////// SINK WARNINGS AND ERRORS TO A FILE FOR DEBUGGING ///////////
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
24 zz = file('warnings_and_errors.txt')
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
25 sink(zz)
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
26 sink(zz, type = 'message')
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
27
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
28 # column 1: the long flag name
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
29 # column 2: the short flag alias. A SINGLE character string
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
30 # column 3: argument mask
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
31 # 0: no argument
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
32 # 1: argument required
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
33 # 2: argument is optional
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
34 # column 4: date type to which the flag's argument shall be cast.
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
35 # possible values: logical, integer, double, complex, character.
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
36 ##------- 1. input data ---------------------
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
37 spec_list=list()
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
38 spec_list$SRA_ACCESSION = c('sra_accession', 'i', '1', 'character')
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
39 spec_list$FORMAT = c('format', 'f', '1', 'character')
3
c707a4178832 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
mingchen0919
parents: 0
diff changeset
40 spec_list$SRA_BOOLEAN = c('sra_boolean', 'S', '1', 'character')
0
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
41 spec_list$ECHO = c('echo', 'e', '1', 'character')
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
42 ##--------2. output report and outputs --------------
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
43 spec_list$REPORT_HTML = c('report_html', 'r', '1', 'character')
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
44 spec_list$OUTPUT_DIR = c('output_dir', 'd', '1', 'character')
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
45 spec_list$SINK_OUTPUT = c('sink_message', 's', '1', 'character')
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
46 ##--------3. Rmd templates in the tool directory ----------
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
47 spec_list$FASTQ_DUMP_PE_RMD = c('fastq_dump_pe_rmd', 't', '1', 'character')
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
48
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
49 spec = t(as.data.frame(spec_list))
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
50 opt = getopt(spec)
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
51
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
52 #------ Load libraries ---------
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
53 library(rmarkdown)
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
54 library(htmltools)
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
55 library(dplyr)
4
206c59e498e7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
mingchen0919
parents: 3
diff changeset
56 library(RCurl)
0
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
57
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
58 #----- 1. create the report directory ------------------------
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
59 dir.create(opt$output_dir)
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
60
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
61 #----- 2. generate Rmd files with Rmd templates --------------
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
62 # a. templates without placeholder variables:
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
63 # copy templates from tool directory to the working directory.
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
64 # b. templates with placeholder variables:
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
65 # substitute variables with user input values and place them in the working directory.
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
66
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
67 #----- 01 fastq_dump_pe.Rmd -----------------------
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
68 readLines(opt$fastq_dump_pe_rmd) %>%
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
69 (function(x) {
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
70 gsub('SRA_ACCESSION', opt$sra_accession, x)
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
71 }) %>%
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
72 (function(x) {
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
73 gsub('FORMAT', opt$format, x)
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
74 }) %>%
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
75 (function(x) {
3
c707a4178832 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
mingchen0919
parents: 0
diff changeset
76 gsub('SRA_BOOLEAN', opt$sra_boolean, x)
c707a4178832 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
mingchen0919
parents: 0
diff changeset
77 }) %>%
c707a4178832 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
mingchen0919
parents: 0
diff changeset
78 (function(x) {
0
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
79 gsub('ECHO', opt$echo, x)
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
80 }) %>%
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
81 (function(x) {
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
82 gsub('OUTPUT_DIR', opt$output_dir, x)
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
83 }) %>%
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
84 (function(x) {
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
85 fileConn = file('fastq_dump_pe.Rmd')
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
86 writeLines(x, con=fileConn)
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
87 close(fileConn)
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
88 })
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
89
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
90 #------ 3. render all Rmd files --------
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
91 render('fastq_dump_pe.Rmd', output_file = opt$report_html)
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
92
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
93
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
94 #-------4. manipulate outputs -----------------------------
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
95
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
96
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
97
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
98
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
99
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
100 sink()
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
101 #/////////// END OF SINK OUTPUT ///////////////////////////