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annotate w4mcorcov_output.R @ 10:9a52306991b3 draft

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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552
author eschen42
date Sat, 01 Sep 2018 11:33:03 -0400
parents 50f60f94c034
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
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1
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
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2 # turn off all plotting devices
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
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3 dev.off.all <- function() {
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
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4 while (!is.null(dev.list())) { dev.off() }
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
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5 }
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
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6
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7 # capture plot and write to PDF; then close any devices opened in the process
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
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8 plot2pdf <- function(
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
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9 file.name
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10 , plot.function
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
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11 , width = 12
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
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12 , height = 12
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
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13 ) {
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
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14 # capture plot and write to PDF
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
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15 cur.dev <- dev.list()
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
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16 filename <- file.name
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
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17 pdf(file = filename, width = width, height = height)
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
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18 plot.function()
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
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19 # close any devices opened in the process
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20 dev.off()
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21 if (is.null(cur.dev)) {
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22 dev.off.all()
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
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23 } else {
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
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24 while ( length(dev.list()) > length(cur.dev) ) { dev.off() }
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
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25 }
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
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26 }
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
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27
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28 # print and capture plot and write to PDF; then close any devices opened in the process
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
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29 # This is needed for ggplot which does not print the plot when invoked within a function.
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
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30 print2pdf <- function(
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
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31 file.name
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32 , plot.function
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
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33 , width = 12
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
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34 , height = 12
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
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35 ) {
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
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36 plot2pdf(
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
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37 file.name = file.name
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38 , width = width
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
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39 , height = height
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
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40 , plot.function = function() {
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41 print(plot.function())
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42 }
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
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43 )
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
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44 }
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
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45
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46 iso8601.znow <- function()
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
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47 {
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48 strftime(as.POSIXlt(Sys.time(), "UTC"), "%Y-%m-%dT%H:%M:%SZ")
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49 }
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50
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51 # pdf.name <- function(name)
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52 # {
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53 # paste0(name, "_", iso8601.filename.fragment(), ".pdf")
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54 # }
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55 #
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56 # tsv.name <- function(name)
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57 # {
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58 # paste0(name, "_", iso8601.filename.fragment(), ".tsv")
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59 # }
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60 #
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61
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62 tsv_action_factory <- function(file, colnames, append) {
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63 return (
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64 function(tsv) {
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65 write.table(
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66 x = tsv
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67 , file = file
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68 , sep = "\t"
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69 , quote = FALSE
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70 , row.names = FALSE
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71 , col.names = colnames
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72 , append = append
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73 )
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74 }
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75 )
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76 }
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