Mercurial > repos > mingchen0919 > rmarkdown_bdss_client

annotate bdss_client_sra_se_render.R @ 20:531c00a2acbf draft

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit b3bd3152ad843fa878cb043b8abb88397ddbba4e-dirty
author mingchen0919
date Sat, 14 Oct 2017 17:15:39 -0400
parents 246cb7315673
children
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20
531c00a2acbf planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit b3bd3152ad843fa878cb043b8abb88397ddbba4e-dirty
mingchen0919
parents: 17
diff changeset
1 library(getopt)
531c00a2acbf planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit b3bd3152ad843fa878cb043b8abb88397ddbba4e-dirty
mingchen0919
parents: 17
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2 library(rmarkdown)
531c00a2acbf planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit b3bd3152ad843fa878cb043b8abb88397ddbba4e-dirty
mingchen0919
parents: 17
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3 library(htmltools)
531c00a2acbf planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit b3bd3152ad843fa878cb043b8abb88397ddbba4e-dirty
mingchen0919
parents: 17
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4 library(dplyr)
531c00a2acbf planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit b3bd3152ad843fa878cb043b8abb88397ddbba4e-dirty
mingchen0919
parents: 17
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5 library(RCurl)
531c00a2acbf planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit b3bd3152ad843fa878cb043b8abb88397ddbba4e-dirty
mingchen0919
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6
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mingchen0919
parents: 4
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8 ##============ Sink warnings and errors to a file ==============
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mingchen0919
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9 ## use the sink() function to wrap all code within it.
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10 ##==============================================================
0
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11 zz = file('warnings_and_errors.txt')
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
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12 sink(zz)
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13 sink(zz, type = 'message')
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14 ##---------below is the code for rendering .Rmd templates-----
0
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mingchen0919
parents: 4
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16 ##=============STEP 1: handle command line arguments==========
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mingchen0919
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17 ##
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mingchen0919
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18 ##============================================================
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mingchen0919
parents: 4
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19 # column 1: the long flag name
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mingchen0919
parents: 4
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20 # column 2: the short flag alias. A SINGLE character string
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mingchen0919
parents: 4
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21 # column 3: argument mask
246cb7315673 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 65f2ce692f3c46ccea55ee47f3c2cb2f8a2bb36f-dirty
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22 # 0: no argument
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mingchen0919
parents: 4
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23 # 1: argument required
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mingchen0919
parents: 4
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24 # 2: argument is optional
246cb7315673 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 65f2ce692f3c46ccea55ee47f3c2cb2f8a2bb36f-dirty
mingchen0919
parents: 4
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25 # column 4: date type to which the flag's argument shall be cast.
246cb7315673 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 65f2ce692f3c46ccea55ee47f3c2cb2f8a2bb36f-dirty
mingchen0919
parents: 4
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26 # possible values: logical, integer, double, complex, character.
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mingchen0919
parents: 4
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27 #-------------------------------------------------------------
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mingchen0919
parents: 4
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28 #++++++++++++++++++++ Best practice ++++++++++++++++++++++++++
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mingchen0919
parents: 4
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29 # 1. short flag alias should match the flag in the command section in the XML file.
246cb7315673 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 65f2ce692f3c46ccea55ee47f3c2cb2f8a2bb36f-dirty
mingchen0919
parents: 4
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30 # 2. long flag name can be any legal R variable names
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mingchen0919
parents: 4
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31 # 3. two names in args_list can have common string but one name should not be a part of another name.
246cb7315673 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 65f2ce692f3c46ccea55ee47f3c2cb2f8a2bb36f-dirty
mingchen0919
parents: 4
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32 # for example, one name is "ECHO", if another name is "ECHO_XXX", it will cause problems.
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33 #+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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mingchen0919
parents: 4
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34 ##------- 1. input data ---------------------
246cb7315673 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 65f2ce692f3c46ccea55ee47f3c2cb2f8a2bb36f-dirty
mingchen0919
parents: 4
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35 args_list=list()
246cb7315673 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 65f2ce692f3c46ccea55ee47f3c2cb2f8a2bb36f-dirty
mingchen0919
parents: 4
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36 args_list$SRA_ACCESSION = c('sra_accession', 'i', '1', 'character')
246cb7315673 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 65f2ce692f3c46ccea55ee47f3c2cb2f8a2bb36f-dirty
mingchen0919
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37 args_list$FORMAT = c('format', 'f', '1', 'character')
246cb7315673 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 65f2ce692f3c46ccea55ee47f3c2cb2f8a2bb36f-dirty
mingchen0919
parents: 4
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38 args_list$SRA_BOOLEAN = c('sra_boolean', 'S', '1', 'character')
246cb7315673 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 65f2ce692f3c46ccea55ee47f3c2cb2f8a2bb36f-dirty
mingchen0919
parents: 4
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39 args_list$ECHO = c('echo', 'e', '1', 'character')
246cb7315673 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 65f2ce692f3c46ccea55ee47f3c2cb2f8a2bb36f-dirty
mingchen0919
parents: 4
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40 ##--------2. output report and outputs --------------
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41 args_list$REPORT_HTML = c('report_html', 'r', '1', 'character')
246cb7315673 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 65f2ce692f3c46ccea55ee47f3c2cb2f8a2bb36f-dirty
mingchen0919
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42 args_list$REPORT_DIR = c('report_dir', 'd', '1', 'character')
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mingchen0919
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43 args_list$SINK_OUTPUT = c('sink_message', 's', '1', 'character')
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mingchen0919
parents: 4
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44 ##--------3. Rmd templates in the tool directory ----------
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45 args_list$bdss_client_sra_se_RMD = c('bdss_client_sra_se_rmd', 't', '1', 'character')
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46
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47 opt = getopt(t(as.data.frame(args_list)))
246cb7315673 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 65f2ce692f3c46ccea55ee47f3c2cb2f8a2bb36f-dirty
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48
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49
20
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50 ##=======STEP 2: create report directory (optional)==========
17
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51 ##
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52 ##===========================================================
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53 dir.create(opt$report_dir)
246cb7315673 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 65f2ce692f3c46ccea55ee47f3c2cb2f8a2bb36f-dirty
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54
20
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mingchen0919
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55 ##=STEP 3: replace placeholders in .Rmd with argument values=
17
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56 ##
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57 ##===========================================================
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58 #++ need to replace placeholders with args values one by one+
246cb7315673 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 65f2ce692f3c46ccea55ee47f3c2cb2f8a2bb36f-dirty
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59 #----- 01 bdss_client_sra_se.Rmd -----------------------
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mingchen0919
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60 readLines(opt$bdss_client_sra_se_rmd) %>%
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61 (function(x) {
246cb7315673 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 65f2ce692f3c46ccea55ee47f3c2cb2f8a2bb36f-dirty
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62 gsub('SRA_ACCESSION', opt$sra_accession, x)
246cb7315673 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 65f2ce692f3c46ccea55ee47f3c2cb2f8a2bb36f-dirty
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63 }) %>%
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mingchen0919
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64 (function(x) {
246cb7315673 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 65f2ce692f3c46ccea55ee47f3c2cb2f8a2bb36f-dirty
mingchen0919
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65 gsub('FORMAT', opt$format, x)
246cb7315673 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 65f2ce692f3c46ccea55ee47f3c2cb2f8a2bb36f-dirty
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66 }) %>%
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67 (function(x) {
246cb7315673 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 65f2ce692f3c46ccea55ee47f3c2cb2f8a2bb36f-dirty
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68 gsub('SRA_BOOLEAN', opt$sra_boolean, x)
246cb7315673 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 65f2ce692f3c46ccea55ee47f3c2cb2f8a2bb36f-dirty
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69 }) %>%
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mingchen0919
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70 (function(x) {
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mingchen0919
parents: 4
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71 gsub('ECHO', opt$echo, x)
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mingchen0919
parents: 4
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72 }) %>%
246cb7315673 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 65f2ce692f3c46ccea55ee47f3c2cb2f8a2bb36f-dirty
mingchen0919
parents: 4
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73 (function(x) {
246cb7315673 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 65f2ce692f3c46ccea55ee47f3c2cb2f8a2bb36f-dirty
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74 gsub('REPORT_DIR', opt$report_dir, x)
246cb7315673 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 65f2ce692f3c46ccea55ee47f3c2cb2f8a2bb36f-dirty
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parents: 4
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75 }) %>%
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parents: 4
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76 (function(x) {
246cb7315673 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 65f2ce692f3c46ccea55ee47f3c2cb2f8a2bb36f-dirty
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77 fileConn = file('bdss_client_sra_se.Rmd')
246cb7315673 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 65f2ce692f3c46ccea55ee47f3c2cb2f8a2bb36f-dirty
mingchen0919
parents: 4
diff changeset
78 writeLines(x, con=fileConn)
246cb7315673 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 65f2ce692f3c46ccea55ee47f3c2cb2f8a2bb36f-dirty
mingchen0919
parents: 4
diff changeset
79 close(fileConn)
246cb7315673 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 65f2ce692f3c46ccea55ee47f3c2cb2f8a2bb36f-dirty
mingchen0919
parents: 4
diff changeset
80 })
246cb7315673 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 65f2ce692f3c46ccea55ee47f3c2cb2f8a2bb36f-dirty
mingchen0919
parents: 4
diff changeset
81
20
531c00a2acbf planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit b3bd3152ad843fa878cb043b8abb88397ddbba4e-dirty
mingchen0919
parents: 17
diff changeset
82 ##=============STEP 4: render .Rmd templates=================
17
246cb7315673 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 65f2ce692f3c46ccea55ee47f3c2cb2f8a2bb36f-dirty
mingchen0919
parents: 4
diff changeset
83 ##
246cb7315673 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 65f2ce692f3c46ccea55ee47f3c2cb2f8a2bb36f-dirty
mingchen0919
parents: 4
diff changeset
84 ##===========================================================
246cb7315673 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 65f2ce692f3c46ccea55ee47f3c2cb2f8a2bb36f-dirty
mingchen0919
parents: 4
diff changeset
85 render('bdss_client_sra_se.Rmd', output_file = opt$report_html)
246cb7315673 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 65f2ce692f3c46ccea55ee47f3c2cb2f8a2bb36f-dirty
mingchen0919
parents: 4
diff changeset
86
0
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
87
17
246cb7315673 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 65f2ce692f3c46ccea55ee47f3c2cb2f8a2bb36f-dirty
mingchen0919
parents: 4
diff changeset
88 ##--------end of code rendering .Rmd templates----------------
0
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
89 sink()
17
246cb7315673 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 65f2ce692f3c46ccea55ee47f3c2cb2f8a2bb36f-dirty
mingchen0919
parents: 4
diff changeset
90 ##=========== End of sinking output=============================