Mercurial > repos > mingchen0919 > rmarkdown_wgcna

annotate wgcna_preprocessing_render.R @ 0:4275479ada3a draft

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
author mingchen0919
date Tue, 08 Aug 2017 12:35:50 -0400
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4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
mingchen0919
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1 ##======= Handle arguments from command line ========
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
mingchen0919
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2 # setup R error handline to go to stderr
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
mingchen0919
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3 options(show.error.messages=FALSE,
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
mingchen0919
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4 error=function(){
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
mingchen0919
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5 cat(geterrmessage(), file=stderr())
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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6 quit("no", 1, F)
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
mingchen0919
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7 })
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
mingchen0919
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9 # we need that to not crash galaxy with an UTF8 error on German LC settings.
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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10 loc = Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
mingchen0919
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12 # suppress warning
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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13 options(warn = -1)
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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15 options(stringsAsFactors=FALSE, useFancyQuotes=FALSE)
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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16 args = commandArgs(trailingOnly=TRUE)
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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18 suppressPackageStartupMessages({
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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19 library(getopt)
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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20 library(tools)
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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21 })
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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23 # column 1: the long flag name
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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24 # column 2: the short flag alias. A SINGLE character string
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
mingchen0919
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25 # column 3: argument mask
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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26 # 0: no argument
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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27 # 1: argument required
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
mingchen0919
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28 # 2: argument is optional
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
mingchen0919
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29 # column 4: date type to which the flag's argument shall be cast.
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
mingchen0919
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30 # possible values: logical, integer, double, complex, character.
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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31 spec_list=list()
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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33 ##------- 1. input data ---------------------
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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34 spec_list$ECHO = c('echo', 'e', '1', 'character')
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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35 spec_list$EXPRESSION_DATA = c('expression_data', 'E', '1', 'character')
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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38 ##--------2. output report and report site directory --------------
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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39 spec_list$OUTPUT_HTML = c('wgcna_preprocessing_html', 'o', '1', 'character')
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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40 spec_list$OUTPUT_DIR = c('wgcna_preprocessing_dir', 'd', '1', 'character')
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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41 spec_list$PREPROCESSING_WORKSPACE = c('preprocessing_workspace', 'w', '1', 'character')
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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43 ##--------3. Rmd templates sitting in the tool directory ----------
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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44
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45 spec_list$WGCNA_PREPROCESSING_RMD = c('wgcna_preprocessing_rmd', 'D', '1', 'character')
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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47
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49 ##------------------------------------------------------------------
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50
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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51 spec = t(as.data.frame(spec_list))
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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52 opt = getopt(spec)
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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53 # arguments are accessed by long flag name (the first column in the spec matrix)
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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54 # NOT by element name in the spec_list
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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55 # example: opt$help, opt$expression_file
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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56 ##====== End of arguments handling ==========
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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57
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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58 #------ Load libraries ---------
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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59 library(rmarkdown)
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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60 library(WGCNA)
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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61 library(DT)
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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62 library(htmltools)
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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63
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64
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65 #----- 1. create the report directory ------------------------
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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66 system(paste0('mkdir -p ', opt$wgcna_preprocessing_dir))
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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67
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69 #----- 2. generate Rmd files with Rmd templates --------------
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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70 # a. templates without placeholder variables:
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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71 # copy templates from tool directory to the working directory.
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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72 # b. templates with placeholder variables:
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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73 # substitute variables with user input values and place them in the working directory.
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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74
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75
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76 #----- 01 wgcna_preprocessing.Rmd -----------------------
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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77 readLines(opt$wgcna_preprocessing_rmd) %>%
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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78 (function(x) {
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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79 gsub('ECHO', opt$echo, x)
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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80 }) %>%
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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81 (function(x) {
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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82 gsub('EXPRESSION_DATA', opt$expression_data, x)
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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83 }) %>%
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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84 (function(x) {
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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85 gsub('OUTPUT_DIR', opt$wgcna_preprocessing_dir, x)
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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86 }) %>%
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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87 (function(x) {
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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88 gsub('PREPROCESSING_WORKSPACE', opt$preprocessing_workspace, x)
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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89 }) %>%
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
mingchen0919
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90 (function(x) {
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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91 fileConn = file('wgcna_preprocessing.Rmd')
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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92 writeLines(x, con=fileConn)
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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93 close(fileConn)
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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94 })
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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95
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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96
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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97 #------ 3. render all Rmd files --------
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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98 render('wgcna_preprocessing.Rmd', output_file = opt$wgcna_preprocessing_html)
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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99
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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100 #-------4. manipulate outputs -----------------------------
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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101
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102