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annotate FCSflowAI.R @ 1:34397a84faf1 draft

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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
author azomics
date Tue, 23 Jun 2020 18:34:02 -0400
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children fab7c5deeb65
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34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
azomics
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1 #!/usr/bin/env Rscript
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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2 #
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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3 # Authors: Gianni Monaco
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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4 #
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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5 # Reference: flowAI: automatic and interactive anomaly discerning
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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6 # tools for flow cytometry data.
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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7 # Gianni Monaco, Hao Chen, Michael Poidinger, Jinmiao Chen,
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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8 # Joao Pedro de Magalhaes and Anis Larbi
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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9 # Bioinformatics (2016)
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10 # doi: 10.1093/bioinformatics/btw191
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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11 #
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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13 library(flowAI)
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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14 library(methods)
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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16 # parse arguments
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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18 args <- commandArgs(trailingOnly = TRUE)
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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20 remFS <- if(args[4]) c("FSC", "SSC") else NULL
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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22 flow_auto_qc(
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23 fcsfiles = args[1],
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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24 remove_from = args[2],
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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25 alphaFR = as.numeric(args[3]),
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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26 ChRemoveFS = remFS,
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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27 outlierFS = args[5],
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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28 pen_valueFS = as.numeric(args[6]),
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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29 sideFM = args[7],
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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30 fcs_QC = ifelse(args[9] == "None", FALSE, "_QC"),
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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31 fcs_highQ = ifelse(args[10] == "None", FALSE, "_highQ"),
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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32 fcs_lowQ = ifelse(args[11] == "None", FALSE, "_lowQ"),
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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33 folder_results = FALSE)
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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35 try(file.rename(dir(".", pattern = ".*_QC.html"), args[8]), silent =TRUE)
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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36 try(file.rename(dir(".", pattern = ".*_QC.fcs"), args[9]), silent =TRUE)
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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37 try(file.rename(dir(".", pattern = ".*_highQ.fcs"), args[10]), silent =TRUE)
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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38 try(file.rename(dir(".", pattern = ".*_lowQ.fcs"), args[11]), silent =TRUE)