Mercurial > repos > azomics > fcs_merge_downsample

annotate FCSMergeDownsample.R @ 1:04afe468b234 draft default tip

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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit d62d7d86dafd09575d91ddb6d07a8dd6a6dc4a27"
author azomics
date Mon, 06 Jul 2020 19:22:44 -0400
parents 8e568997abda
children
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8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
azomics
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diff changeset
1 #!/usr/bin/Rscript
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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2 # Aggregate FCS files Module for Galaxy
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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3 # with FlowSOM AggregateFlowFrames
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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4 ######################################################################
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
azomics
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5 # Copyright (c) 2017 Northrop Grumman.
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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6 # All rights reserved.
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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7 ######################################################################
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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8 #
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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9 # Version 1
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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10 # Cristel Thomas
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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11 #
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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12 #
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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13 library(FlowSOM)
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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14 library(flowCore)
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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15
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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16 downsampleMergeFCS <- function(fcs_files, nb_cells, output="", flag_fcs=FALSE) {
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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17 ff <- AggregateFlowFrames(fcs_files, nb_cells, writeOutput = FALSE)
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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18 n <- length(colnames(ff)) - 2
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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19 exprs(ff) <- exprs(ff)[,1:n]
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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20 if (flag_fcs) {
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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21 write.FCS(ff, output)
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
azomics
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22 } else {
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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23 saveRDS(ff, file=output)
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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24 }
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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25 }
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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26
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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27 checkFCSfiles <- function(fcsfiles, ds_factor=0.1, out_file ="",
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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28 flag_fcs=FALSE) {
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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29 isValid <- F
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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30 nb_events <- 0
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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31 markerCheck <- T
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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32
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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33 for (i in 1:length(fcsfiles)){
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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34 is_file_valid <- F
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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35 tryCatch({
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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36 fcs <- read.FCS(fcsfiles[i], transformation=FALSE)
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
azomics
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37 is_file_valid <- T
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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38 nb_events <- nb_events + as.numeric(fcs@description$`$TOT`)
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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39 }, error = function(ex) {
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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40 print(paste(ex))
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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41 })
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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42 if (is_file_valid){
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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43 if (i == 1) {
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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44 m1 <- as.vector(pData(parameters(fcs))$desc)
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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45 } else {
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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46 m2 <- as.vector(pData(parameters(fcs))$desc)
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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47 if (is.na(all(m1==m2))) {
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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48 mm1 <- is.na(m1)
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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49 mm2 <- is.na(m2)
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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50 if (all(mm1==mm2)){
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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51 if (!all(m1==m2, na.rm=TRUE)){
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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52 markerCheck <- F
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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53 }
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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54 } else {
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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55 markerCheck <- F
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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56 }
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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57 } else if (!all(m1==m2)) {
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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58 markerCheck <- F
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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59 }
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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60 }
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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61 } else {
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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62 quit(save = "no", status = 10, runLast = FALSE)
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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63 }
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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64 }
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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65
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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66 if (markerCheck) {
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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67 isValid <- T
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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68 } else {
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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69 quit(save = "no", status = 12, runLast = FALSE)
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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70 }
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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71
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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72 ## translate ds_factor to nb of events
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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73 nb_cell <- floor(ds_factor*nb_events)
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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74
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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75 if (isValid) {
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
azomics
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76 downsampleMergeFCS(fcsfiles, nb_cell, out_file, flag_fcs)
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
azomics
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77 } else {
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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78 quit(save = "no", status = 10, runLast = FALSE)
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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79 }
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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80 }
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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81
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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82 args <- commandArgs(trailingOnly = TRUE)
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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83 flag_fcs <- FALSE
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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84
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
azomics
parents:
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85 if (args[2] == "FCS"){
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
azomics
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86 flag_fcs <- TRUE
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
azomics
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87 }
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
azomics
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88
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
azomics
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89 if (args[3] == "" || args[3] == "i.e.:0.1 or 10X") {
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
azomics
parents:
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90 factor <- 0.1
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
azomics
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91 } else {
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
azomics
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92 #rm last X if it's there
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
azomics
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93 ds <- gsub("X", "", args[3])
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
azomics
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94 if (!is.na(as.numeric(ds))) {
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
azomics
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95 factor <- as.numeric(ds)
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
azomics
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96 if (factor > 1 && factor <= 100) {
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
azomics
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diff changeset
97 factor <- as.numeric(ds) / 100
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
azomics
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98 } else if (factor > 100){
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
azomics
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99 quit(save = "no", status = 11, runLast = FALSE)
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
azomics
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diff changeset
100 }
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
azomics
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diff changeset
101 } else {
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
azomics
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diff changeset
102 quit(save = "no", status = 11, runLast = FALSE)
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
azomics
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103 }
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
azomics
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104 }
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
azomics
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105
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
azomics
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106 nb_files <- (length(args) - 3)
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
azomics
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107 fcsfiles <- character(nb_files)
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
azomics
parents:
diff changeset
108 j <- 1
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
azomics
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109 ## get files and file names
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
azomics
parents:
diff changeset
110 for (i in 4:length(args)) {
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
azomics
parents:
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111 fcsfiles[[j]] <- args[i]
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
azomics
parents:
diff changeset
112 j <- j + 1
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
azomics
parents:
diff changeset
113 }
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
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114
8e568997abda "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
azomics
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diff changeset
115 checkFCSfiles(fcsfiles, factor, args[1], flag_fcs)