Mercurial > repos > azomics > metacyto_preprocess

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"planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
author azomics
date Sun, 25 Jul 2021 10:36:03 +0000
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bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
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diff changeset
1 #!/usr/bin/env Rscript
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
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2 ######################################################################
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
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3 # Copyright (c) 2018 Northrop Grumman.
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
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4 # All rights reserved.
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
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5 ######################################################################
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
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6 #
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
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7 # Version 1 - January 2018
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
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8 # Author: Cristel Thomas
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
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9 #
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
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10 #
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
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11
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
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12 library(flowCore)
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
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13 library(MetaCyto)
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
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14
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
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15 compare_lists <- function(m1, m2) {
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
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16 list_check <- T
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
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17 if (is.na(all(m1 == m2))) {
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
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18 mm1 <- is.na(m1)
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
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19 mm2 <- is.na(m2)
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
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20 if (all(mm1 == mm2)) {
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
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21 if (!all(m1 == m2, na.rm = TRUE)) {
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
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22 list_check <- F
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
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23 }
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
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24 } else {
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
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25 list_check <- F
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
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26 }
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
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27 } else if (!all(m1 == m2)) {
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
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28 list_check <- F
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
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29 }
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
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30 return(list_check)
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
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31 }
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
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32
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
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33
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
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34 run_batch_processing <- function(sampling_size = 5000, flag_default = T,
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
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35 to_exclude, outdir = "", outfile = "",
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
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36 labels, assays, factors, fcspaths, fcsnames) {
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
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37 # Create meta_data object
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
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38 fp <- unlist(fcspaths)
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
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39 file_counts <- lengths(fcspaths)
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
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40 group_names <- rep(labels, times = file_counts)
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
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41 group_bs <- rep(factors, times = file_counts)
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
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42 group_types <- rep(assays, times = file_counts)
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
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43
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
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44 meta_data <- data.frame(fcs_files = fp, study_id = group_names)
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
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45
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
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46 # excluded_parameters
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
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47 default_param <- c("FSC-A", "FSC-H", "FSC-W", "FSC", "SSC-A", "SSC-H",
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
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48 "SSC-W", "SSC", "Time", "Cell_length", "cell_length",
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
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49 "CELL_LENGTH")
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
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50 excluded_parameters <- if (flag_default) default_param else to_exclude
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
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51 # Run preprocessing.batch
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
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52 preprocessing.batch(inputMeta = meta_data,
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
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53 assay = group_types,
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
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54 b = group_bs,
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
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55 fileSampleSize = sampling_size,
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
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56 outpath = outdir,
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
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57 excludeTransformParameters = excluded_parameters)
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
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58
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
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59 # deal with outputs
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
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60 # output[2]: a csv file summarizing the pre-processing result.
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
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61 ## -> open file to pull info and print out filenames rather than path.
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
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62 tmp_csv <- file.path(outdir, "processed_sample_summary.csv")
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
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63 tmp <- read.csv(tmp_csv)
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
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64 tmp$old_index <- seq(1, length(tmp$fcs_names))
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
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65
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
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66 fn <- unlist(fcsnames)
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
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67 df <- data.frame(fcs_files = fp, filenames = fn)
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
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68
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
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69 # merge two data frames by ID
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
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70 total <- merge(tmp, df, by = "fcs_files")
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
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71 total2 <- total[order(total$old_index), ]
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
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72 to_drop <- c("fcs_names", "fcs_files", "old_index")
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
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73 newdf <- total2[, !(names(total2) %in% to_drop)]
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
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74 write.table(newdf, file = outfile, quote = F, row.names = F, col.names = T, sep = "\t")
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
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75
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
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76 file.remove(tmp_csv)
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
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diff changeset
77 }
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
78
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
79 check_fcs <- function(sampling = 5000, flag_default = TRUE, to_exclude,
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
80 outdir = "", outfile = "", labels, assays, factors,
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
81 fcspaths, fcsnames) {
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
82
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
83 if (length(labels) > length(unique(labels))) {
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
84 # we have repeated group names, all group names need to be different
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
85 print("ERROR: repeated labels among groups, make sure that labels are all different for groups.")
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
86 print("The following labels are repeated")
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
87 table(labels)[table(labels) > 1]
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
88 quit(save = "no", status = 13, runLast = FALSE)
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
89 }
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
90
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
91 marker_pb <- FALSE
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
92 for (i in seq_len(length(fcspaths))) {
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
93 for (n in seq_len(length(fcspaths[[i]]))) {
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
94 marker_check <- FALSE
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
95 marker_channel <- FALSE
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
96 tryCatch({
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
97 fcs <- read.FCS(fcspaths[[i]][[n]], transformation = FALSE)
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
98 }, error = function(ex) {
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
99 print(paste("File is not a valid FCS file:", fnames[[i]][[n]], ex))
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
100 quit(save = "no", status = 10, runLast = FALSE)
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
101 })
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
102
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
103 if (n == 1) {
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
104 m1 <- as.vector(pData(parameters(fcs))$desc)
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
105 c1 <- colnames(fcs)
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
106 } else {
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
107 m2 <- as.vector(pData(parameters(fcs))$desc)
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
108 c2 <- colnames(fcs)
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
109 marker_check <- compare_lists(m1, m2)
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
110 marker_channel <- compare_lists(c1, c2)
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
111 }
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
112 if (n > 1 && marker_check == F) {
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
113 marker_pb <- TRUE
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
114 print(paste("Marker discrepancy detected in markers -- group", labels[[i]]))
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
115 } else if (n > 1 && marker_channel == F) {
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
116 marker_pb <- TRUE
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
117 print(paste("Marker discrepancy detected in channels -- group", labels[[i]]))
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
118 }
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
119 }
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
120 }
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
121
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
122 if (marker_pb) {
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
123 quit(save = "no", status = 12, runLast = FALSE)
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
124 } else {
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
125 run_batch_processing(sampling, flag_default, to_exclude, outdir, outfile,
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
126 labels, assays, factors, fcspaths, fcsnames)
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
127 }
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
128 }
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
129
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
130 ################################################################################
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
131 ################################################################################
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
132 args <- commandArgs(trailingOnly = TRUE)
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
133
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
134 # Arg 1: sub_sampling number
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
135 # Arg 2: output dir for processed FCS files for check_fcs and run_batch_processing
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
136 # Arg 3: Main output file (text file)
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
137 # Arg 4: excluded params
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
138 # Arg 5: Group 1 Name
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
139 # Arg 6: Group 1 format
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
140 # Arg 7: Group 1 Scaling factor
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
141 # Cycle through files in group 1
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
142 # Arg : file path in Galaxy
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
143 # Arg : desired real file name
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
144 # Cycle through at at least one additional group
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
145 # Arg : 'new_panel' - used as some sort of delimiter
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
146 # Arg : Group n+1 Name
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
147 # Arg : Group n+1 format
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
148 # Arg : Group n+1 Scaling factor
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
149 ## Cycle through files in that group
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
150 ## Arg : file path in Galaxy
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
151 ## Arg : desired real file path
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
152
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
153 sub_sampling <- NULL
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
154 if (as.numeric(args[1]) > 0) {
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
155 sub_sampling <- as.numeric(args[1])
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
156 }
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
157
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
158 # parameters to exclude => args[4]
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
159 to_exclude <- vector()
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
160 flag_default <- FALSE
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
161 i <- 1
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
162 if (args[4] == "None" || args[4] == "") {
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
163 flag_default <- TRUE
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
164 } else {
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
165 excluded <- unlist(strsplit(args[4], ","))
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
166 for (channel in excluded) {
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
167 stripped_chan <- gsub(" ", "", channel, fixed = TRUE)
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
168 if (!is.na(stripped_chan)) {
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
169 to_exclude[[i]] <- stripped_chan
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
170 }
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
171 i <- i + 1
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
172 }
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
173 }
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
174
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
175 # handle group cycle in arguments to produce iterable panels
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
176 tot_args <- length(args)
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
177 tmpargs <- paste(args[5:tot_args], collapse = "=%=")
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
178 tmppanels <- strsplit(tmpargs, "=%=new_panel=%=")
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
179 nb_panel <- length(tmppanels[[1]])
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
180
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
181 labels <- vector(mode = "character", length = nb_panel)
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
182 assay_types <- vector(mode = "character", length = nb_panel)
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
183 scaling_factors <- vector(mode = "numeric", length = nb_panel)
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
184 filepaths <- list()
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
185 filenames <- list()
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
186
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
187 # iterate over panels (groups of fcs files)
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
188 j <- 1
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
189 for (pnl in tmppanels[[1]]) {
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
190 tmppanel <- strsplit(pnl, "=%=")
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
191 # number of FCS files
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
192 nb_files <- (length(tmppanel[[1]]) - 3) / 2
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
193 tmplist <- character(nb_files)
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
194 tmpnames <- character(nb_files)
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
195 if (tmppanel[[1]][[1]] == "None" || tmppanel[[1]][[1]] == "") {
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
196 print(paste("ERROR: Empty group name/label for group ", j))
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
197 quit(save = "no", status = 11, runLast = FALSE)
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
198 } else {
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
199 labels[[j]] <- tmppanel[[1]][[1]]
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
200 }
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
201 # assay type
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
202 assay_types[[j]] <- tmppanel[[1]][[2]]
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
203
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
204 scaling_factors[[j]] <- 0
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
205 if (as.numeric(tmppanel[[1]][[3]]) > 0) {
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
206 scaling_factors[[j]] <- 1 / as.numeric(tmppanel[[1]][[3]])
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
207 }
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
208
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
209 k <- 1
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
210 for (m in 4:length(tmppanel[[1]])) {
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
211 if (!m %% 2) {
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
212 tmplist[[k]] <- tmppanel[[1]][[m]]
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
213 tmpnames[[k]] <- tmppanel[[1]][[m + 1]]
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
214 k <- k + 1
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
215 }
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
216 }
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
217 filepaths[[tmppanel[[1]][1]]] <- tmplist
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
218 filenames[[tmppanel[[1]][1]]] <- tmpnames
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
219 j <- j + 1
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
220 }
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
221
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
222 check_fcs(sub_sampling, flag_default, to_exclude, args[2], args[3], labels,
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
223 assay_types, scaling_factors, filepaths, filenames)
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
224
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
225 # check_fcs <- function(sampling = 5000, flag_default = TRUE, to_exclude,
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
226 # outdir = "", outfile = "", labels, assays, factors,
bf6470882a15 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
azomics
parents:
diff changeset
227 # fcspaths, fcsnames)