Mercurial > repos > azomics > edit_fcs_markers

annotate editFCSmarkers.R @ 0:02b2412598b6 draft default tip

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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
author azomics
date Mon, 22 Jun 2020 20:07:30 -0400
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02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
azomics
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1 #!/usr/bin/Rscript
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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2 # modify channels and marker names in FCS
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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3 #
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4 ######################################################################
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5 # Copyright (c) 2017 Northrop Grumman.
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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6 # All rights reserved.
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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7 ######################################################################
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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8 #
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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9 # Cristel Thomas
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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10 # Version 2 - May 2018
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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11 # Modified to take in marker/channel names by name rather than index
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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12 #
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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13 library(flowCore)
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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14
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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15 checkCandM <- function(m_set, channels=vector(), markers=vector()){
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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16 if (m_set[[3]]){
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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17 in_file <- m_set[[1]] %in% channels
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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18 } else {
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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19 in_file <- m_set[[1]] %in% markers
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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20 }
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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21 if (sum(in_file)==0) {
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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22 warning("Given original columns are either not in the channels or in the markers of the read object. Will fail.")
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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23 return(FALSE)
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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24 }
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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25 return(TRUE)
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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26 }
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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27
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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28 modifyMarkersFCS <- function(input, output="", report="", flag_fcs=F,
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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29 marker_sets=list()) {
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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30
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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31 fcs <- read.FCS(input, transformation=F)
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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32 original_channels <- colnames(fcs)
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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33 original_markers <- as.vector(pData(parameters(fcs))$desc)
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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34 nb <- length(original_channels)
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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35 ## check if markers are in FCS files
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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36 check_markers <- sapply(marker_sets, checkCandM, channels=original_channels,
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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37 markers=original_markers)
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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38 if (sum(check_markers)==0) {
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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39 quit(save = "no", status = 13, runLast = FALSE)
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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40 }
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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41
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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42 post_channels <- colnames(fcs)
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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43 post_markers <- as.vector(pData(parameters(fcs))$desc)
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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44
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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45 for (m_set in marker_sets) {
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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46 if (m_set[[3]]){
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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47 chan_to_replace <- post_channels %in% m_set[[1]]
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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48 for (i in 1:nb){
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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49 if (chan_to_replace[[i]]){
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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50 post_channels[[i]] <- m_set[[2]][[match(post_channels[[i]], m_set[[1]])[1]]]
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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51 }
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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52 }
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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53 } else {
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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54 marker_to_replace <- post_markers %in% m_set[[1]]
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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55 for (i in 1:nb){
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56 if (marker_to_replace[[i]]){
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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57 post_markers[[i]] <- m_set[[2]][[match(post_markers[[i]], m_set[[1]])[1]]]
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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58 pm <- paste("$P", as.character(i), "S", sep="")
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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59 fcs@description[[pm]] <- post_markers[[i]]
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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60 }
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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61 }
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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62 }
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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63 }
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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64
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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65 colnames(fcs) <- post_channels
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66 pData(parameters(fcs))$desc <- post_markers
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67
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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68 # write report
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69 sink(report)
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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70 cat("###########################\n")
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71 cat("## BEFORE RENAMING ##\n")
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72 cat("###########################\nFCS Channels\n")
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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73 cat("---------------------------\n")
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74 cat(original_channels,"---------------------------", "FCS Markers","---------------------------",original_markers, sep="\n")
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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75 cat("\n###########################\n")
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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76 cat("## AFTER RENAMING ##\n")
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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77 cat("###########################\nFCS Channels\n")
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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78 cat("---------------------------\n")
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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79 cat(post_channels,"---------------------------","FCS Markers","---------------------------", post_markers, sep="\n")
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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80 sink()
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81
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82 # output fcs
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83 if (flag_fcs) {
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84 write.FCS(fcs, output)
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85 } else {
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86 saveRDS(fcs, file = output)
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87 }
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88 }
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89
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90 checkFCS <- function(fcsfile, out_file ="", report="", flag_fcs=FALSE,
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91 marker_sets=list()) {
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92 isValid <- F
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93 tryCatch({
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94 isValid <- isFCSfile(fcsfile)
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95 }, error = function(ex) {
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96 print(paste(ex))
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97 })
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98
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99 if (isValid) {
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100 modifyMarkersFCS(fcsfile, out_file, report, flag_fcs, marker_sets)
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101 } else {
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102 quit(save = "no", status = 10, runLast = FALSE)
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103 }
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104 }
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105
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106 ################################################################################
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107 ################################################################################
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108 args <- commandArgs(trailingOnly = TRUE)
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109 flag_fcs <- if (args[3]=="FCS") TRUE else FALSE
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110
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111 items <- args[5:length(args)]
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112 marker_sets <- list()
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113 j <- 1
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114 for (i in seq(1, length(items), 3)) {
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115 if (items[i]=="None" || items[i]== "" || items[i]== "i.e.:TLR 6, TLR6PE") {
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116 quit(save = "no", status = 11, runLast = FALSE)
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117 }
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118 if (items[i+1]=="None" || items[i+1]=="" || items[i+1]=="i.e.:TLR6") {
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119 quit(save = "no", status = 12, runLast = FALSE)
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120 }
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121
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122 old_names <- strsplit(items[i], ",")[[1]]
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123 to_replace <- sapply(old_names, trimws)
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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124 replacement <- sapply(strsplit(items[i+1], ",")[[1]], trimws)
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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125 flag_channel <- if (items[i+2]=="C") TRUE else FALSE
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126 m_set <- list(to_replace, replacement, flag_channel)
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127 marker_sets[[j]] <- m_set
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128 j <- j + 1
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129 }
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130
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131 checkFCS(args[1], args[2], args[4], flag_fcs, marker_sets)