Mercurial > repos > mingchen0919 > rmarkdown_collection_builder

annotate collection_list_render.R @ 1:6be61cb4a1d5 draft

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 6df7b8ef3a603f7792ed5815ff324ede8a7b2b0b-dirty
author mingchen0919
date Mon, 25 Sep 2017 16:19:52 -0400
parents 78018b735124
children 56b68a320c0e
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78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
mingchen0919
parents:
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1 ##======= Handle arguments from command line ========
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
mingchen0919
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2 # setup R error handline to go to stderr
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
mingchen0919
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3 options(show.error.messages=FALSE,
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
mingchen0919
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4 error=function(){
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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5 cat(geterrmessage(), file=stderr())
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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6 quit("no", 1, F)
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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7 })
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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9 # we need that to not crash galaxy with an UTF8 error on German LC settings.
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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10 loc = Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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12 # suppress warning
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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13 options(warn = -1)
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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15 options(stringsAsFactors=FALSE, useFancyQuotes=FALSE)
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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16 args = commandArgs(trailingOnly=TRUE)
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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18 suppressPackageStartupMessages({
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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19 library(getopt)
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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20 library(tools)
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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21 })
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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23 # column 1: the long flag name
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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24 # column 2: the short flag alias. A SINGLE character string
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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25 # column 3: argument mask
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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26 # 0: no argument
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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27 # 1: argument required
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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28 # 2: argument is optional
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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29 # column 4: date type to which the flag's argument shall be cast.
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
mingchen0919
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30 # possible values: logical, integer, double, complex, character.
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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31 ##------- 1. input data ---------------------
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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32 spec_list=list()
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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33 spec_list$FILE_LIST = c('file_list', 'l', '1', 'character')
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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34 spec_list$ECHO = c('echo', 'e', '1', 'character')
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35 spec_list$FORMAT = c('echo', 'f', '1', 'character')
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78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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36 ##--------2. output report and outputs --------------
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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37 spec_list$REPORT = c('report', 'r', '1', 'character')
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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38 spec_list$OUTPUT_DIR = c('list_collection_dir', 'd', '1', 'character')
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
mingchen0919
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39 ##--------3. Rmd templates in the tool directory ----------
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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40 spec_list$LIST_COLLECTION_RMD = c('list_collection_rmd', 't', '1', 'character')
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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41
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42 spec = t(as.data.frame(spec_list))
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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43 opt = getopt(spec)
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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44 ##====== End of arguments handling ==========
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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45
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46 #------ Load libraries ---------
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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47 library(rmarkdown)
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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48 library(htmltools)
1
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49 library(dplyr)
0
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51 #----- 1. create the report directory ------------------------
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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52 system(paste0('mkdir -p ', opt$list_collection_dir))
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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53
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54 #----- 2. generate Rmd files with Rmd templates --------------
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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55 # a. templates without placeholder variables:
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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56 # copy templates from tool directory to the working directory.
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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57 # b. templates with placeholder variables:
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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58 # substitute variables with user input values and place them in the working directory.
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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59
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60 #----- 01 list_collection.Rmd -----------------------
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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61 readLines(opt$list_collection_rmd) %>%
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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62 (function(x) {
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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63 gsub('ECHO', opt$echo, x)
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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64 }) %>%
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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65 (function(x) {
1
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66 gsub('FORMAT', opt$echo, x)
6be61cb4a1d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 6df7b8ef3a603f7792ed5815ff324ede8a7b2b0b-dirty
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67 }) %>%
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68 (function(x) {
0
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69 gsub('FILE_LIST', opt$file_list, x)
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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70 }) %>%
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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71 (function(x) {
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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72 gsub('OUTPUT_DIR', opt$list_collection_dir, x)
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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73 }) %>%
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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74 (function(x) {
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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75 fileConn = file('list_collection.Rmd')
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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76 writeLines(x, con=fileConn)
78018b735124 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
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77 close(fileConn)
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78 })
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79
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80 #------ 3. render all Rmd files --------
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81 render('list_collection.Rmd', output_file = opt$report)
0
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83 #-------4. manipulate outputs -----------------------------