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2
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1 library(getopt)
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2 library(rmarkdown)
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3 library(htmltools)
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4 library(dplyr)
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5 library(stringr)
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6
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7 ##============ Sink warnings and errors to a file ==============
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8 ## use the sink() function to wrap all code within it.
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9 ##==============================================================
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10 zz = file('warnings_and_errors.txt')
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11 sink(zz)
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12 sink(zz, type = 'message')
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13 ##---------below is the code for rendering .Rmd templates-----
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14
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15 ##=============STEP 1: handle command line arguments==========
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16 ##
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17 ##============================================================
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18 # column 1: the long flag name
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19 # column 2: the short flag alias. A SINGLE character string
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20 # column 3: argument mask
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21 # 0: no argument
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22 # 1: argument required
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23 # 2: argument is optional
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24 # column 4: date type to which the flag's argument shall be cast.
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25 # possible values: logical, integer, double, complex, character.
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26 #-------------------------------------------------------------
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27 #++++++++++++++++++++ Best practice ++++++++++++++++++++++++++
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28 # 1. short flag alias should match the flag in the command section in the XML file.
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29 # 2. long flag name can be any legal R variable names
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30 # 3. two names in args_list can have common string but one name should not be a part of another name.
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31 # for example, one name is "ECHO", if another name is "ECHO_XXX", it will cause problems.
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32 #+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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33 args_list=list()
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34 ##------- 1. input data ---------------------
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35 args_list$ECHO = c('echo', 'e', '1', 'character')
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36 args_list$INPUT_BAM = c('input_bam', 'b', '1', 'character')
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37 args_list$INPUT_BAM_NAME = c('input_bam_name', 'n', '1', 'character')
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38 ##--------2. output report and outputs --------------
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39 args_list$REPORT_HTML = c('report_html', 'r', '1', 'character')
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40 args_list$REPORT_DIR = c('report_dir', 'd', '1', 'character')
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41 args_list$SINK_MESSAGE = c('sink_message', 's', '1', 'character')
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42 ##--------3. .Rmd templates in the tool directory ----------
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43 args_list$TOOL_TEMPLATE_RMD = c('tool_template_rmd', 't', '1', 'character')
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44 ##-----------------------------------------------------------
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45 opt = getopt(t(as.data.frame(args_list)))
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46
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47
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48
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49 ##=======STEP 2: create report directory (optional)==========
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50 ##
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51 ##===========================================================
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52 dir.create(opt$report_dir)
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53
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54 ##=STEP 3: replace placeholders in .Rmd with argument values=
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55 ##
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56 ##===========================================================
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57 #++ need to replace placeholders with args values one by one+
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58 readLines(opt$tool_template_rmd) %>%
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59 (function(x) {
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60 gsub('ECHO', opt$echo, x)
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61 }) %>%
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62 (function(x) {
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63 gsub('REPORT_DIR', opt$report_dir, x)
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64 }) %>%
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65 (function(x) {
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66 fileConn = file('rmarkdown_samtools_flagstat.Rmd')
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67 writeLines(x, con=fileConn)
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68 close(fileConn)
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69 })
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70
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71
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72 ##=============STEP 4: render .Rmd templates=================
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73 ##
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74 ##===========================================================
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75 render('rmarkdown_samtools_flagstat.Rmd', output_file = opt$report_html)
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76
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77
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78 ##--------end of code rendering .Rmd templates----------------
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79 sink()
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80 ##=========== End of sinking output=============================
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