Mercurial > repos > mingchen0919 > rmarkdown_collection_builder

annotate collection_list_paired_render.R @ 49:7a65e6827c25 draft

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit a7ad932a1725b4ef26d522040c5395ae0026fb35-dirty
author mingchen0919
date Tue, 26 Sep 2017 13:12:19 -0400
parents 68da32dbc6e2
children
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2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
mingchen0919
parents:
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1 ##======= Handle arguments from command line ========
2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
mingchen0919
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2 # setup R error handline to go to stderr
2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
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3 options(show.error.messages=FALSE,
2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
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4 error=function(){
2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
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5 cat(geterrmessage(), file=stderr())
2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
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6 quit("no", 1, F)
2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
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7 })
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2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
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9 # we need that to not crash galaxy with an UTF8 error on German LC settings.
2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
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10 loc = Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
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2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
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12 # suppress warning
2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
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13 options(warn = -1)
2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
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2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
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15 options(stringsAsFactors=FALSE, useFancyQuotes=FALSE)
2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
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16 args = commandArgs(trailingOnly=TRUE)
2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
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18 suppressPackageStartupMessages({
2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
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19 library(getopt)
2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
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20 library(tools)
2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
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21 })
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2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
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23 # column 1: the long flag name
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24 # column 2: the short flag alias. A SINGLE character string
2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
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25 # column 3: argument mask
2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
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26 # 0: no argument
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27 # 1: argument required
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28 # 2: argument is optional
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29 # column 4: date type to which the flag's argument shall be cast.
2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
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30 # possible values: logical, integer, double, complex, character.
2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
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31 ##------- 1. input data ---------------------
2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
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32 spec_list=list()
2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
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33 spec_list$FORWARD_FILE_LIST = c('forward_file_list', 'L', '1', 'character')
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34 spec_list$REVERSE_FILE_LIST = c('reverse_file_list', 'R', '1', 'character')
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35 spec_list$ECHO = c('echo', 'e', '1', 'character')
2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
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36 spec_list$FORMAT = c('format', 'f', '1', 'character')
2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
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37 ##--------2. output report and outputs --------------
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38 spec_list$OUTPUT_HTML = c('list_paired_collection_html', 'r', '1', 'character')
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39 spec_list$OUTPUT_DIR = c('list_paired_collection_dir', 'd', '1', 'character')
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40 ##--------3. Rmd templates in the tool directory ----------
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41 spec_list$LIST_COLLECTION_RMD = c('list_collection_rmd', 't', '1', 'character')
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42
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43 spec = t(as.data.frame(spec_list))
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44 opt = getopt(spec)
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45 ##====== End of arguments handling ==========
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46
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47 #------ Load libraries ---------
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48 library(rmarkdown)
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49 library(htmltools)
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50 library(dplyr)
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51
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52 #----- 1. create the report directory ------------------------
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53 system(paste0('mkdir -p ', opt$list_paired_collection_dir))
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54
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55 #----- 2. generate Rmd files with Rmd templates --------------
2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
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56 # a. templates without placeholder variables:
2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
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57 # copy templates from tool directory to the working directory.
2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
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58 # b. templates with placeholder variables:
2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
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59 # substitute variables with user input values and place them in the working directory.
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60
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61 #----- 01 list_collection.Rmd -----------------------
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62 readLines(opt$list_collection_rmd) %>%
2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
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63 (function(x) {
2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
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64 gsub('ECHO', opt$echo, x)
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65 }) %>%
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66 (function(x) {
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67 gsub('FORMAT', opt$format, x)
2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
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68 }) %>%
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69 (function(x) {
2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
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70 gsub('FORWARD_FILE_LIST', opt$forward_file_list, x)
2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
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71 }) %>%
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72 (function(x) {
2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
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73 gsub('REVERSE_FILE_LIST', opt$reverse_file_list, x)
2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
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74 }) %>%
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75 (function(x) {
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76 fileConn = file('list_paired_collection.Rmd')
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77 writeLines(x, con=fileConn)
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78 close(fileConn)
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79 })
2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
mingchen0919
parents:
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80
2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
mingchen0919
parents:
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81 #------ 3. render all Rmd files --------
2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
mingchen0919
parents:
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82 render('list_paired_collection.Rmd', output_file = opt$list_paired_collection_html)
2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
mingchen0919
parents:
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83
2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
mingchen0919
parents:
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84
48
68da32dbc6e2 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit a7ad932a1725b4ef26d522040c5395ae0026fb35-dirty
mingchen0919
parents: 28
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85 #-------4. manipulate outputs -----------------------------