Mercurial > repos > mingchen0919 > rmarkdown_mirdeep2
annotate mirdeep2_render.R @ 0:963905bcb754 draft
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
author | mingchen0919 |
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date | Tue, 08 Aug 2017 13:14:41 -0400 |
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rev | line source |
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963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
changeset
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1 ##======= Handle arguments from command line ======== |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
changeset
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2 # setup R error handline to go to stderr |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
changeset
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3 options(show.error.messages=FALSE, |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
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4 error=function(){ |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
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5 cat(geterrmessage(), file=stderr()) |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
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6 quit("no", 1, F) |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
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7 }) |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
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8 |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
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9 # we need that to not crash galaxy with an UTF8 error on German LC settings. |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
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10 loc = Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
changeset
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11 |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
changeset
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12 # suppress warning |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
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13 options(warn = -1) |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
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14 |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
changeset
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15 options(stringsAsFactors=FALSE, useFancyQuotes=FALSE) |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
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16 args = commandArgs(trailingOnly=TRUE) |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
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17 |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
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18 suppressPackageStartupMessages({ |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
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19 library(getopt) |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
changeset
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20 library(tools) |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
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21 }) |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
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22 |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
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changeset
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23 # column 1: the long flag name |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
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24 # column 2: the short flag alias. A SINGLE character string |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
changeset
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25 # column 3: argument mask |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
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26 # 0: no argument |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
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changeset
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27 # 1: argument required |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
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28 # 2: argument is optional |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
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29 # column 4: date type to which the flag's argument shall be cast. |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
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30 # possible values: logical, integer, double, complex, character. |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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31 spec_list=list() |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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32 |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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33 ##------- 1. input data --------------------- |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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34 spec_list$ECHO = c('echo', 'e', '1', 'character') |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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35 spec_list$COLLASPED_READS = c('collapsed_reads', 'a', '1', 'character') |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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36 spec_list$REFERENCE_GENOME = c('reference_genome', 'b', '1', 'character') |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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37 spec_list$READS_MAPPING = c('reads_mapping', 'c', '1', 'character') |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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38 |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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39 ##--------2. output report and report site directory -------------- |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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40 spec_list$OUTPUT_HTML = c('mirdeep2_html', 'o', '1', 'character') |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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41 spec_list$OUTPUT_DIR = c('mirdeep2_output_dir', 'd', '1', 'character') |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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42 spec_list$CSV_RESULT = c('csv_result', 'r', '1', 'character') |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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43 spec_list$HTML_RESULT = c('html_result', 't', '1', 'character') |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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44 spec_list$REPORT_LOG = c('report_log', 'u', '1', 'character') |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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45 |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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46 ##---------other parameters--------- |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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47 spec_list$SPECIES_MATURE_MIRNA = c('species_mature_mirna', 'f', '2', 'character') |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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48 spec_list$SPECIES_RELATED_MATURE_MIRRNA = c('related_species_mature_mirna', 'g', '2', 'character') |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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49 spec_list$PRECURSOR_SEQUENCES = c('precursor_sequences', 'h', '2', 'character') |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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50 spec_list$MIN_READ_STACK_HEIGHT = c('min_read_stack_height', 'j', '2', 'character') |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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51 spec_list$MIN_SCORE_CUTOFF = c('min_score_cutoff', 'k', '2', 'character') |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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52 spec_list$RANDFOLD_ANALYSIS = c('randfold_analysis', 'l', '2', 'character') |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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53 spec_list$MAX_PRECURSOR_NUMBER = c('max_precursor_number', 'm', '2', 'character') |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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54 spec_list$SPECIES = c('species', 'n', '2', 'character') |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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55 spec_list$SWITCH = c('switch', 'q', '2', 'character') |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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56 |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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57 ##--------3. Rmd templates sitting in the tool directory ---------- |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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58 |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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59 ## _site.yml and index.Rmd files |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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60 spec_list$SITE_YML = c('site_yml', 's', 1, 'character') |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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61 spec_list$INDEX_Rmd = c('index_rmd', 'i', 1, 'character') |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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62 |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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63 ## other Rmd body template files |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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64 spec_list$MIRDEEP2_RMD = c('mirdeep2_rmd', 'p', '1', 'character') |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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65 |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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66 |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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67 |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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68 ##------------------------------------------------------------------ |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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69 |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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70 spec = t(as.data.frame(spec_list)) |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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71 opt = getopt(spec) |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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72 # arguments are accessed by long flag name (the first column in the spec matrix) |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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73 # NOT by element name in the spec_list |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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74 # example: opt$help, opt$expression_file |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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75 ##====== End of arguments handling ========== |
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76 |
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77 #------ Load libraries --------- |
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78 library(rmarkdown) |
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79 library(plyr) |
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80 # library(stringr) |
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81 library(dplyr) |
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82 # library(highcharter) |
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83 # library(DT) |
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84 # library(reshape2) |
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85 # library(plotly) |
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86 # library(formattable) |
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87 library(htmltools) |
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88 |
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89 |
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90 #----- 1. create the report directory ------------------------ |
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91 paste0('mkdir -p ', opt$mirdeep2_output_dir) %>% |
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92 system() |
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93 |
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94 #----- 2. generate Rmd files with Rmd templates -------------- |
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95 # a. templates without placeholder variables: |
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96 # copy templates from tool directory to the working directory. |
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97 # b. templates with placeholder variables: |
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98 # substitute variables with user input values and place them in the working directory. |
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99 |
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100 |
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101 #----- mirdeep2.Rmd ----------------------- |
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102 readLines(opt$mirdeep2_rmd) %>% |
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103 (function(x) { |
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104 gsub('ECHO', opt$echo, x) |
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105 }) %>% |
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106 (function(x) { |
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107 gsub('COLLAPSED_READS', opt$collapsed_reads, x) |
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108 }) %>% |
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109 (function(x) { |
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110 gsub('REFERENCE_GENOME', opt$reference_genome, x) |
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111 }) %>% |
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112 (function(x) { |
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113 gsub('READS_MAPPING', opt$reads_mapping, x) |
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114 }) %>% |
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115 (function(x) { |
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116 gsub('SPECIES_MATURE_MIRNA', opt$species_mature_mirna, x) |
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117 }) %>% |
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118 (function(x) { |
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119 gsub('SPECIES_RELATED_MATURE_MIRNA', opt$related_species_mature_mirna, x) |
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120 }) %>% |
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121 (function(x) { |
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122 gsub('PRECURSOR_SEQUENCES', opt$precursor_sequences, x) |
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123 }) %>% |
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124 (function(x) { |
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125 gsub('MIN_READ_STACK_HEIGHT', opt$min_read_stack_height, x) |
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126 }) %>% |
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127 (function(x) { |
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128 gsub('MIN_SCORE_CUTOFF', opt$min_score_cutoff, x) |
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129 }) %>% |
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130 (function(x) { |
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131 gsub('RANDFOLD_ANALYSIS', opt$randfold_analysis, x) |
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132 }) %>% |
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133 (function(x) { |
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134 gsub('MAX_PRECURSOR_NUMBER', opt$max_precursor_number, x) |
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135 }) %>% |
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136 (function(x) { |
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137 gsub('SPECIES', opt$species, x) |
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138 }) %>% |
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139 (function(x) { |
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140 gsub('SWITCH', opt$switch, x) |
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141 }) %>% |
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142 (function(x) { |
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143 gsub('OUTPUT_DIR', opt$mirdeep2_output_dir, x) |
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144 }) %>% |
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145 (function(x) { |
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146 fileConn = file('mirdeep2.Rmd') |
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147 writeLines(x, con=fileConn) |
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148 close(fileConn) |
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149 }) |
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150 |
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151 |
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152 #------ 3. render all Rmd files with render() -------- |
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153 render('mirdeep2.Rmd',output_file = opt$mirdeep2_html) |
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154 |
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155 |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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156 #-------4. manipulate outputs ----------------------------- |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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157 # a. copy non-site files |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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158 file.copy('result.csv', opt$csv_result, recursive=TRUE) |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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159 file.copy('result.html', opt$html_result, recursive=TRUE) |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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160 file.copy('report.log', opt$report_log, recursive=TRUE) |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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changeset
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161 |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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162 |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
changeset
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163 |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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diff
changeset
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164 |