Mercurial > repos > mingchen0919 > rmarkdown_collection_builder

annotate collection_list_render.R @ 0:87c21e14f221 draft

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
author mingchen0919
date Mon, 25 Sep 2017 12:15:23 -0400
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children f85a6bcf940e
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87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
parents:
diff changeset
1 ##======= Handle arguments from command line ========
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
parents:
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2 # setup R error handline to go to stderr
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
parents:
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3 options(show.error.messages=FALSE,
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
parents:
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4 error=function(){
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
parents:
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5 cat(geterrmessage(), file=stderr())
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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6 quit("no", 1, F)
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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7 })
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
parents:
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8
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
parents:
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9 # we need that to not crash galaxy with an UTF8 error on German LC settings.
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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10 loc = Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
parents:
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11
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
parents:
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12 # suppress warning
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
parents:
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13 options(warn = -1)
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
parents:
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14
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
parents:
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15 options(stringsAsFactors=FALSE, useFancyQuotes=FALSE)
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
parents:
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16 args = commandArgs(trailingOnly=TRUE)
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
parents:
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87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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18 suppressPackageStartupMessages({
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
parents:
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19 library(getopt)
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
parents:
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20 library(tools)
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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21 })
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
parents:
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87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
parents:
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23 # column 1: the long flag name
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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24 # column 2: the short flag alias. A SINGLE character string
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
parents:
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25 # column 3: argument mask
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
parents:
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26 # 0: no argument
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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27 # 1: argument required
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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28 # 2: argument is optional
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
parents:
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29 # column 4: date type to which the flag's argument shall be cast.
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
parents:
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30 # possible values: logical, integer, double, complex, character.
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
parents:
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31 ##------- 1. input data ---------------------
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
parents:
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32 spec_list=list()
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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33 spec_list$READS = c('file_list', 'l', '1', 'character')
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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34 spec_list$ECHO = c('echo', 'e', '1', 'character')
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
parents:
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35 ##--------2. output report and outputs --------------
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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36 spec_list$LIST_COLLECTION = c('list_collection', 'o', '1', 'character')
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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37 spec_list$REPORT = c('report', 'r', '1', 'character')
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
parents:
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38 ##--------3. Rmd templates in the tool directory ----------
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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39 spec_list$LIST_COLLECTION_RMD = c('list_collection_rmd', 't', '1', 'character')
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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40
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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41 spec = t(as.data.frame(spec_list))
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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42 opt = getopt(spec)
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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43 ##====== End of arguments handling ==========
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
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44
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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45 #------ Load libraries ---------
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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46 library(rmarkdown)
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
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47 library(htmltools)
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
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48
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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49 #----- 1. create the report directory ------------------------
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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50 # this tool does not require an report directory
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
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51
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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52 #----- 2. generate Rmd files with Rmd templates --------------
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
parents:
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53 # a. templates without placeholder variables:
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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54 # copy templates from tool directory to the working directory.
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
parents:
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55 # b. templates with placeholder variables:
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
parents:
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56 # substitute variables with user input values and place them in the working directory.
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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57
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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58 #----- 01 list_collection.Rmd -----------------------
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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59 readLines(opt$list_collection_rmd) %>%
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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60 (function(x) {
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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61 gsub('ECHO', opt$echo, x)
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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62 }) %>%
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
parents:
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63 (function(x) {
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
parents:
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64 fileConn = file('list_collection.Rmd')
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
parents:
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65 writeLines(x, con=fileConn)
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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66 close(fileConn)
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
parents:
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67 })
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
parents:
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68
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
parents:
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69 #------ 3. render all Rmd files --------
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
parents:
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70 render('list_collection.Rmd', output_file = opt$list_collection_html)
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
parents:
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71
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
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72 #-------4. manipulate outputs -----------------------------