Mercurial > repos > azomics > metacyto_checkpanel
annotate metacyto_checkpanel.R @ 0:67d79ba0f7aa draft default tip
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
author | azomics |
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date | Tue, 27 Jul 2021 21:47:56 +0000 |
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67d79ba0f7aa
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
azomics
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1 #!/usr/bin/env Rscript |
67d79ba0f7aa
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
azomics
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2 ###################################################################### |
67d79ba0f7aa
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
azomics
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3 # Copyright (c) 2018 Northrop Grumman. |
67d79ba0f7aa
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
azomics
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4 # All rights reserved. |
67d79ba0f7aa
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
azomics
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5 ###################################################################### |
67d79ba0f7aa
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
azomics
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6 # |
67d79ba0f7aa
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
azomics
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7 # Version 1 - January 2018 |
67d79ba0f7aa
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
azomics
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8 # Author: Cristel Thomas |
67d79ba0f7aa
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
azomics
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9 # |
67d79ba0f7aa
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
azomics
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10 # |
67d79ba0f7aa
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
azomics
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11 |
67d79ba0f7aa
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
azomics
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12 library(MetaCyto) |
67d79ba0f7aa
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
azomics
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13 |
67d79ba0f7aa
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
azomics
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14 check_panel <- function(df, outfile = "") { |
67d79ba0f7aa
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
azomics
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15 report <- panelSummary(df, ".", cluster = F, width = 30, height = 20) |
67d79ba0f7aa
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
azomics
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16 markers <- data.frame("Markers" = row.names(report)) |
67d79ba0f7aa
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
azomics
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17 s <- cbind(markers, report) |
67d79ba0f7aa
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
azomics
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18 write.table(s, file = outfile, quote = F, row.names = F, col.names = T, sep = "\t") |
67d79ba0f7aa
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
azomics
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19 } |
67d79ba0f7aa
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
azomics
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20 |
67d79ba0f7aa
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
azomics
parents:
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21 check_input_format <- function(infile = "", outfile = "") { |
67d79ba0f7aa
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
azomics
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22 df <- read.table(infile, sep = "\t", header = T, colClasses = "character") |
67d79ba0f7aa
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
azomics
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23 nm <- colnames(df) |
67d79ba0f7aa
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
azomics
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24 check_ab <- if ("antibodies" %in% nm) TRUE else FALSE |
67d79ba0f7aa
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
azomics
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25 check_sdy <- if ("study_id" %in% nm) TRUE else FALSE |
67d79ba0f7aa
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
azomics
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26 |
67d79ba0f7aa
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
azomics
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27 if (check_sdy && check_ab) { |
67d79ba0f7aa
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
azomics
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28 check_panel(df, outfile) |
67d79ba0f7aa
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
azomics
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29 } else { |
67d79ba0f7aa
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
azomics
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30 quit(save = "no", status = 10, runLast = FALSE) |
67d79ba0f7aa
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
azomics
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31 } |
67d79ba0f7aa
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
azomics
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32 } |
67d79ba0f7aa
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
azomics
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33 |
67d79ba0f7aa
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
azomics
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34 ################################################################################ |
67d79ba0f7aa
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
azomics
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35 args <- commandArgs(trailingOnly = TRUE) |
67d79ba0f7aa
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
azomics
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36 |
67d79ba0f7aa
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
azomics
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37 check_input_format(args[1], args[2]) |