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"planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
author azomics
date Wed, 28 Jul 2021 22:02:38 +0000
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94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
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1 #!/usr/bin/env Rscript
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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2 ######################################################################
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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3 # Copyright (c) 2018 Northrop Grumman.
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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4 # All rights reserved.
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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5 ######################################################################
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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6 #
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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7 # Version 1 - January 2018
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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8 # Author: Cristel Thomas
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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9 #
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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10 #
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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11
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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12 library(flowCore)
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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13 library(MetaCyto)
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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15 check_cluster_def <- function(cl_def) {
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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16 if (cl_def == "" || cl_def == "None") {
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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17 quit(save = "no", status = 14, runLast = FALSE)
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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18 } else {
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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19 tmp <- gsub(" ", "", cl_def, fixed = TRUE)
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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20 clean_def <- gsub(",", "|", tmp, fixed = TRUE)
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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21 return(toupper(clean_def))
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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22 }
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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23 }
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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25 path_to_group_file <- function(path_to_result) {
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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26 grp <- basename(dirname(path_to_result))
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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27 return(paste(grp, "fcs", sep = ".", collapse = NULL))
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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28 }
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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30 group_file_to_group_name <- function(result_file) {
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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31 return(strsplit(result_file, ".", fixed = TRUE)[[1]][1])
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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32 }
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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34
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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35 search_cluster_panels <- function(df, fcspaths, fcsnames, outdir="", uc="",
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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36 clusters=vector()) {
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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37
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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38 working_dir <- "tmp_metacyto"
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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39 working_out <- "tmp_metacyto_out"
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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40 dir.create(working_dir)
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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41 dir.create(outdir)
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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42
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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43 # reformat summary -- expects csv + 'fcs_names' && 'fcs_files'
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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44 new_df <- file.path(working_dir, "processed_sample_summary.csv")
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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45 df$fcs_names <- df$filenames
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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46 df$fcs_files <- df$filenames
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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47 write.csv(df, file = new_df, row.names = F)
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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48
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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49 # move && rename FCS files to same directory
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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50 for (i in seq_len(length(fcspaths))) {
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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51 new_file <- file.path(working_dir, fcsnames[[i]])
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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52 file.copy(fcspaths[[i]], new_file)
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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53 }
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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54
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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55 searchCluster.batch(preprocessOutputFolder = working_dir,
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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56 outpath = working_out,
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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57 clusterLabel = clusters)
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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58
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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59 result_files <- list.files(working_out,
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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60 pattern = "cluster_stats_in_each_sample",
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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61 recursive = T,
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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62 full.names = T)
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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63
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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64 nb_groups <- length(fcsnames)
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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65 no_results <- vector()
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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66 if (length(result_files) != nb_groups) {
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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67 groups_with_results <- sapply(result_files, path_to_group_file)
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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68 ## one or more groups with no results, figure out which
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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69 no_results <- setdiff(fcsnames, groups_with_results)
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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70 }
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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71
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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72 if (length(no_results) == nb_groups) {
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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73 sink(uc)
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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74 cat("No clusters were found in none of the groups.")
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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75 sink()
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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76 } else {
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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77 unused_clrs <- list()
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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diff changeset
78
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
79 if (length(no_results > 0)) {
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
80 grp_no_results <- sapply(no_results, group_file_to_group_name)
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
81 unused_clrs <- data.frame("cluster_label" = "any", "not_found_in" = grp_no_results)
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
82 }
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
83
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
84 for (result in result_files) {
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
85 group_name <- strsplit(result, .Platform$file.sep)[[1]][2]
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
86 new_filename <- paste(c(group_name, "cluster_stats.txt"), collapse = "_")
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
87 new_path <- file.path(outdir, new_filename)
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
88 tmp_df <- read.csv(result)
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
89
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
90 used_clr <- as.character(unique(tmp_df$label))
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
91 if (length(used_clr) != length(clusters)) {
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
92 unused <- setdiff(clusters, used_clr)
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
93 tmp_udf <- data.frame("cluster_label" = unused, "not_found_in" = group_name)
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
94 unused_clrs <- rbind(unused_clrs, tmp_udf)
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
95 }
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
96 colnames(tmp_df)[[1]] <- "group_name"
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
97 write.table(tmp_df, new_path, quote = F, row.names = F, col.names = T, sep = "\t")
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
98 }
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
99
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
100 if (is.null(dim(unused_clrs))) {
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
101 sink(uc)
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
102 cat("All provided cluster definition were found in all provided FCS files.")
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
103 sink()
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
104 } else {
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
105 write.table(unused_clrs, uc, quote = F, row.names = F, col.names = T, sep = "\t")
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
106 }
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
107 }
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
108 }
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
109
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
110
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
111 check_input <- function(report="", outdir="", list_unused="", list_clusters="",
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
112 fcs_files=list(), grp_names=list(), clusters=vector()) {
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
113 # check FCS files
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
114 fcspaths <- unlist(fcs_files)
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
115 fcsnames <- unlist(grp_names)
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
116 ct_files <- 0
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
117 some_pb <- FALSE
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
118 for (i in seq_len(length(fcspaths))) {
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
119 is_file_valid <- FALSE
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
120 tryCatch({
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
121 fcs <- read.FCS(fcspaths[[i]], transformation = FALSE)
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
122 is_file_valid <- TRUE
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
123 }, error = function(ex) {
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
124 print(paste("File is not a valid FCS file:", fcsnames[[i]], ex))
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
125 })
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
126 if (is_file_valid) {
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
127 metacyto_pp_check <- if ("sample_id" %in% colnames(fcs)) TRUE else FALSE
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
128 if (metacyto_pp_check) {
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
129 idx <- length(colnames(fcs))
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
130 ct_files <- ct_files + max(fcs@exprs[, idx])
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
131 } else {
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
132 quit(save = "no", status = 11, runLast = FALSE)
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
133 }
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
134 } else {
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
135 some_pb <- TRUE
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
136 }
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
137 }
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
138 # check summary file format
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
139 df <- read.table(report, sep = "\t", header = T, colClasses = "character")
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
140 nm <- colnames(df)
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
141 check_ab <- if ("antibodies" %in% nm) TRUE else FALSE
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
142 check_sdy <- if ("study_id" %in% nm) TRUE else FALSE
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
143
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
144 if (check_sdy && check_ab) {
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
145 # check that summary index compatible with FCSs in collection - by number of files == index nb
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
146 if (ct_files != length(df$antibodies)) {
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
147 quit(save = "no", status = 12, runLast = FALSE)
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
148 }
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
149 } else {
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
150 quit(save = "no", status = 13, runLast = FALSE)
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
151 }
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
152
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
153 if (some_pb) {
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
154 quit(save = "no", status = 10, runLast = FALSE)
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
155 } else {
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
azomics
parents:
diff changeset
156 write.table(clusters, list_clusters, quote = F, row.names = F, col.names = F)
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157 search_cluster_panels(df, fcspaths, fcsnames, outdir, list_unused, clusters)
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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158 }
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159 }
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160
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161 ################################################################################
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162 ################################################################################
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163 args <- commandArgs(trailingOnly = TRUE)
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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164
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165 i <- grep(args, pattern = "FCS_FILES")
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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166
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167 cluster_def <- vector()
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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168 cl_df <- args[3]
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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169 if (i > 6) {
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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170 ii <- i - 1
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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171 more_cl <- args[6:ii]
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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172 cl_df <- c(cl_df, more_cl)
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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173 }
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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174 cluster_def <- sapply(cl_df, check_cluster_def)
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175
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176 fcs_files <- list()
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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177 fcs_names <- list()
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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178 j <- 1
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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179 m <- i + 1
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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180 tmp_fcs <- args[m:length(args)]
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181
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182 for (k in seq_len(length(tmp_fcs))) {
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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183 if (k %% 2) {
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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184 fcs_files[[j]] <- tmp_fcs[[k]]
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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185 fcs_names[[j]] <- tmp_fcs[[k + 1]]
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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186 j <- j + 1
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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187 }
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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188 }
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189
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190 check_input(args[1], args[2], args[4], args[5], fcs_files, fcs_names,
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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191 cluster_def)