Mercurial > repos > iuc > isoformswitchanalyzer

annotate IsoformSwitchAnalyzeR.R @ 1:2c4e879a81cf draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7d278967f9c8d2c6ce0a8f83be2c444822746bbf
author iuc
date Fri, 19 May 2023 21:26:00 +0000
parents f3fefb6d8254
children 2b0a6af4b85e
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f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
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1 # Load the IsoformSwitchAnalyzeR library
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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2 library(IsoformSwitchAnalyzeR,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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3 quietly = TRUE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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4 warn.conflicts = FALSE)
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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5 library(argparse, quietly = TRUE, warn.conflicts = FALSE)
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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6 library(dplyr, quietly = TRUE, warn.conflicts = FALSE)
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2c4e879a81cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7d278967f9c8d2c6ce0a8f83be2c444822746bbf
iuc
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7 library(ggplot2, quietly = TRUE, warn.conflicts = FALSE)
2c4e879a81cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7d278967f9c8d2c6ce0a8f83be2c444822746bbf
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f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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10 # setup R error handling to go to stderr
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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11 options(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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12 show.error.messages = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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13 error = function() {
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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14 cat(geterrmessage(), file = stderr())
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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15 q("no", 1, FALSE)
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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16 }
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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17 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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19 # we need that to not crash galaxy with an UTF8 error on German LC settings.
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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20 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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22 ################################################################################
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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23 ### Input Processing
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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24 ################################################################################
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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27 # Collect arguments from command line
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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28 parser <- ArgumentParser(description = "IsoformSwitcheR R script")
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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29
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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30 parser$add_argument("--modeSelector")
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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31 parser$add_argument("--parentDir", required = FALSE, help = "Parent directory")
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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32 parser$add_argument("--readLength",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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33 required = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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34 type = "integer",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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35 help = "Read length (required for stringtie)")
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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36 parser$add_argument("--annotation", required = FALSE, help = "Annotation")
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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37 parser$add_argument("--transcriptome", required = FALSE, help = "Transcriptome")
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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38 parser$add_argument(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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39 "--fixStringTieAnnotationProblem",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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40 action = "store_true",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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41 required = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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42 help = "Fix StringTie annotation problem"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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43 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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44 parser$add_argument("--countFiles", required = FALSE, help = "Count files")
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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45 parser$add_argument("--toolSource", required = FALSE, help = "Tool source")
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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46 parser$add_argument("--rObject", required = FALSE, help = "R object")
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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47 parser$add_argument("--IFcutoff",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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48 required = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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49 type = "numeric",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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50 help = "IFcutoff")
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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51 parser$add_argument(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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52 "--geneExpressionCutoff",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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53 required = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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54 type = "numeric",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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55 help = "Gene expression cutoff"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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56 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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57 parser$add_argument(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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58 "--isoformExpressionCutoff",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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59 required = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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60 type = "numeric",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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61 help = "Isoform expression cutoff"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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62 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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63 parser$add_argument("--alpha",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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64 required = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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65 type = "numeric",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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66 help = "")
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67 parser$add_argument("--dIFcutoff",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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68 required = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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69 type = "numeric",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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70 help = "dIF cutoff")
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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71 parser$add_argument(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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72 "--onlySigIsoforms",
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73 required = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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74 action = "store_true",
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75 help = "Only significative isoforms"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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76 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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77 parser$add_argument(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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78 "--filterForConsequences",
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79 required = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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80 action = "store_true",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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81 help = "Filter for consequences"
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82 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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83 parser$add_argument(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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84 "--removeSingleIsformGenes",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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85 required = FALSE,
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86 action = "store_true",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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87 help = "Remove single isoform genes"
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88 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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89 parser$add_argument(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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diff changeset
90 "--keepIsoformInAllConditions",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
91 required = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
92 action = "store_true",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
93 help = "Keep isoform in all conditions"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
94 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
95 parser$add_argument(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
96 "--correctForConfoundingFactors",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
97 required = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
98 action = "store_true",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
99 help = "Correct for confunding factors"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
100 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
101 parser$add_argument(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
102 "--overwriteIFvalues",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
103 required = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
104 action = "store_true",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
105 help = "Overwrite IF values"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
106 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
107 parser$add_argument(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
108 "--reduceToSwitchingGenes",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
109 required = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
110 action = "store_true",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
111 help = "Reduce to switching genes"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
112 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
113 parser$add_argument(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
114 "--reduceFurtherToGenesWithConsequencePotential",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
115 required = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
116 action = "store_true",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
117 help = "Reduce further to genes with consequence potential"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
118 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
119 parser$add_argument(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
120 "--keepIsoformInAllConditions2",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
121 required = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
122 action = "store_true",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
123 help = "Keep isoform in ll conditions"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
124 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
125 parser$add_argument("--minORFlength",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
126 required = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
127 type = "integer",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
128 help = "")
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
129 parser$add_argument("--orfMethod", required = FALSE, help = "ORF methods")
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
130 parser$add_argument("--PTCDistance",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
131 required = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
132 type = "integer",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
133 help = "")
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
134 parser$add_argument(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
135 "--removeShortAAseq",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
136 required = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
137 action = "store_true",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
138 help = "Remove short aminoacid sequences"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
139 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
140 parser$add_argument(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
141 "--removeLongAAseq",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
142 required = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
143 action = "store_true",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
144 help = "Remove long aminoacid sequences"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
145 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
146 parser$add_argument(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
147 "--removeORFwithStop",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
148 required = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
149 action = "store_true",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
150 help = "Remove ORF with stop codon"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
151 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
152 parser$add_argument(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
153 "--onlySwitchingGenes",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
154 required = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
155 action = "store_true",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
156 help = "Only switching genes"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
157 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
158 parser$add_argument("--analysisMode", required = FALSE, help = "Analyze all isoforms with differential usage or single genes")
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
159 parser$add_argument(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
160 "--genesToPlot",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
161 type = "integer",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
162 default = 10,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
163 required = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
164 help = "Number of genes to plot"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
165 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
166 parser$add_argument("--gene", required = FALSE, help = "Gene ID to analyze")
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
167 parser$add_argument(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
168 "--sortByQvals",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
169 action = "store_true",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
170 required = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
171 help = "Sort genes by Q-val values"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
172 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
173 parser$add_argument("--countGenes",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
174 action = "store_true",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
175 required = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
176 help = "Count genes")
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
177 parser$add_argument(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
178 "--asFractionTotal",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
179 action = "store_true",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
180 required = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
181 help = "Plot gene expresson as fraction of total"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
182 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
183 parser$add_argument("--plotGenes",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
184 action = "store_true",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
185 required = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
186 help = "Plot genes instead of isoforms")
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
187 parser$add_argument(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
188 "--simplifyLocation",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
189 action = "store_true",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
190 required = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
191 help = "Simplify localtion"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
192 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
193 parser$add_argument(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
194 "--removeEmptyConsequences",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
195 action = "store_true",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
196 required = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
197 help = "Remove empty consequences"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
198 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
199 parser$add_argument(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
200 "--analysisOppositeConsequence",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
201 action = "store_true",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
202 required = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
203 help = "Analysi opposite consequences"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
204 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
205 parser$add_argument("--pathToCPATresultFile",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
206 required = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
207 help = "Path to CPAT result file")
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
208 parser$add_argument("--pathToCPC2resultFile",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
209 required = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
210 help = "Path to CPC2 result file")
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
211 parser$add_argument("--pathToPFAMresultFile",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
212 required = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
213 help = "Path to PFAM result file")
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
214 parser$add_argument("--pathToNetSurfP2resultFile",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
215 required = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
216 help = "Path to NetSurfP2 result file")
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
217 parser$add_argument("--pathToSignalPresultFile",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
218 required = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
219 help = "Path to signalP result file")
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
220 parser$add_argument("--pathToIUPred2AresultFile",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
221 required = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
222 help = "Path to IUPred2A result file")
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
223 parser$add_argument("--codingCutoff",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
224 required = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
225 type = "numeric",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
226 help = "Codding cutoff")
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
227 parser$add_argument(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
228 "--removeNoncodingORFs",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
229 action = "store_true",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
230 required = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
231 help = "Remove non-coding ORFs"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
232 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
233 parser$add_argument(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
234 "--minSignalPeptideProbability",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
235 required = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
236 type = "numeric",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
237 help = "Minimul signal peptide probability"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
238 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
239 parser$add_argument(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
240 "--smoothingWindowSize",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
241 type = "integer",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
242 required = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
243 help = "Smoothing windows size"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
244 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
245 parser$add_argument(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
246 "--probabilityCutoff",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
247 required = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
248 type = "double",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
249 help = "Probability cutoff"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
250 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
251 parser$add_argument("--minIdrSize",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
252 required = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
253 type = "integer",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
254 help = "Min Idr size")
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
255 parser$add_argument(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
256 "--annotateBindingSites",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
257 action = "store_true",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
258 required = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
259 help = "Annotate binding sites"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
260 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
261 parser$add_argument(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
262 "--minIdrBindingSize",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
263 required = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
264 type = "integer",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
265 help = "Minimun Idr binding size"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
266 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
267 parser$add_argument(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
268 "--minIdrBindingOverlapFrac",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
269 required = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
270 type = "numeric",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
271 help = ""
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
272 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
273 parser$add_argument("--ntCutoff",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
274 required = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
275 type = "integer",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
276 help = "Nucleotide cutoff")
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iuc
parents:
diff changeset
277 parser$add_argument("--ntFracCutoff",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
278 required = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
279 type = "numeric",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
280 help = "Nucleotide fraction cutoff")
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
281 parser$add_argument(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
282 "--ntJCsimCutoff",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
283 required = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
284 type = "numeric",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
285 help = "Nucleotide Jaccard simmilarity cutoff"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
286 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
287 parser$add_argument("--AaCutoff",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
288 required = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
289 type = "integer",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
290 help = "Aminoacid cutoff")
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
291 parser$add_argument("--AaFracCutoff",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
292 required = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
293 type = "numeric",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
294 help = "Aminoacid fraction cutoff")
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
295 parser$add_argument(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
296 "--AaJCsimCutoff",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
297 required = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
298 type = "numeric",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
299 help = "Aminoacid Jaccard similarity cutoff"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
300 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
301 parser$add_argument(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
302 "--removeNonConseqSwitches",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
303 action = "store_true",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
304 required = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
305 help = "Remove switches without consequences"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
306 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
307 parser$add_argument(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
308 "--rescaleTranscripts",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
309 action = "store_true",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
310 required = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
311 help = "Rescale transcripts"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
312 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
313 parser$add_argument(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
314 "--reverseMinus",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
315 action = "store_true",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
316 required = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
317 help = "Reverse minus"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
318 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
319 parser$add_argument(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
320 "--addErrorbars",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
321 action = "store_true",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
322 required = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
323 help = "Add error bars"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
324 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
325
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
326
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
327 args <- parser$parse_args()
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
328
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
329 # Data import
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
330 ###################
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
331
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
332 if (args$modeSelector == "data_import") {
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
333
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
334 quantificationData <- importIsoformExpression(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
335 parentDir = args$parentDir,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
336 addIsofomIdAsColumn = TRUE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
337 readLength = args$readLength
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
338 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
339
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
340 ### Make design matrix
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
341 myDesign <- data.frame(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
342 sampleID = colnames(quantificationData$abundance)[-1],
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
343 condition = gsub(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
344 "[[:digit:]]+",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
345 "",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
346 colnames(quantificationData$abundance)[-1]
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
347 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
348 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
349
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
350 if (args$toolSource == "stringtie") {
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
351 SwitchList <- importRdata(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
352 isoformCountMatrix = quantificationData$counts,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
353 isoformRepExpression = quantificationData$abundance,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
354 designMatrix = myDesign,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
355 isoformExonAnnoation = args$annotation,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
356 isoformNtFasta = args$transcriptome,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
357 showProgress = TRUE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
358 fixStringTieAnnotationProblem = args$fixStringTieAnnotationProblem
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
359 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
360 } else {
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
361 SwitchList <- importRdata(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
362 isoformCountMatrix = quantificationData$counts,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
363 isoformRepExpression = quantificationData$abundance,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
364 designMatrix = myDesign,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
365 isoformExonAnnoation = args$annotation,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
366 isoformNtFasta = args$transcriptome,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
367 showProgress = TRUE
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
368 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
369 }
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
370
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
371
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
372 geneCountMatrix <- extractGeneExpression(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
373 SwitchList,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
374 extractCounts = TRUE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
375 addGeneNames = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
376 addIdsAsColumns = FALSE
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
377 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
378
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
379 if (args$countFiles == "collection") {
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
380
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
381 expressionDF <- data.frame(geneCountMatrix)
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
382
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
383 myDesign$condition[length(myDesign$condition)]
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
384
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
385 dataframe_factor1 <- expressionDF %>% select(matches(myDesign$condition[1]))
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
386 dataframe_factor2 <- expressionDF %>% select(matches(myDesign$condition[length(myDesign$condition)]))
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
387
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
388
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
389 lf1 <- as.list(as.data.frame(dataframe_factor1))
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
390 sampleNames1 <- colnames(as.data.frame(dataframe_factor1))
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
391
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
392 lf2 <- as.list(as.data.frame(dataframe_factor2))
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
393 sampleNames2 <- colnames(as.data.frame(dataframe_factor2))
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
394
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
395 geneNames <- row.names(as.data.frame(expressionDF))
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
396
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
397
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
398 for (index in seq_along(lf1)) {
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
399 tabular_expression <- data.frame(geneNames, lf1[index])
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
400 colnames(tabular_expression) <-
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
401 c("Geneid", sampleNames1[index])
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
402 filename <-
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
403 paste(sampleNames1[index], "dataset.tabular", sep = "_")
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
404 output_path <- paste("./count_files/factor1/", filename, sep = "")
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
405 write.table(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
406 tabular_expression,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
407 output_path,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
408 sep = "\t",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
409 row.names = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
410 quote = FALSE
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
411 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
412 }
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
413 for (index in seq_along(lf2)) {
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
414 tabular_expression <- data.frame(geneNames, lf2[index])
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
415 colnames(tabular_expression) <-
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
416 c("Geneid", sampleNames2[index])
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
417 filename <-
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
418 paste(sampleNames2[index], "dataset.tabular", sep = "_")
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
419 output_path <- paste("./count_files/factor2/", filename, sep = "")
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
420 write.table(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
421 tabular_expression,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
422 output_path,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
423 sep = "\t",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
424 row.names = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
425 quote = FALSE
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
426 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
427 }
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
428 } else if (args$countFiles == "matrix") {
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
429 expressionDF <- data.frame(geneCountMatrix)
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
430 geneNames <- row.names(expressionDF)
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
431
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
432 expressionDF <- cbind(geneNames, expressionDF)
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
433 write.table(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
434 as.data.frame(expressionDF),
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
435 "./count_files/matrix.tabular",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
436 sep = "\t",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
437 row.names = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
438 quote = FALSE
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
439 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
440 write.table(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
441 as.data.frame(myDesign),
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
442 "./count_files/samples.tabular",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
443 sep = "\t",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
444 row.names = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
445 quote = FALSE
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
446 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
447 }
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
448
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
449 save(SwitchList, file = "SwitchList.Rda")
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
450
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
451 }
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
452
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
453 if (args$modeSelector == "first_step") {
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
454
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
455 # First part of the analysis
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
456 #############################
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
457
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
458 load(file = args$rObject)
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
459
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
460 ### Filter
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
461 SwitchList <- preFilter(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
462 SwitchList,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
463 IFcutoff = args$IFcutoff,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
464 geneExpressionCutoff = args$geneExpressionCutoff,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
465 isoformExpressionCutoff = args$isoformExpressionCutoff,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
466 removeSingleIsoformGenes = args$removeSingleIsformGenes,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
467 onlySigIsoforms = args$onlySigIsoforms,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
468 keepIsoformInAllConditions = args$keepIsoformInAllConditions,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
469 alpha = args$alpha,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
470 dIFcutoff = args$dIFcutoff,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
471 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
472
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
473 ### Test for isoform switches
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
474 SwitchList <- isoformSwitchTestDEXSeq(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
475 SwitchList,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
476 alpha = args$alpha,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
477 dIFcutoff = args$dIFcutoff,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
478 correctForConfoundingFactors = args$correctForConfoundingFactors,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
479 overwriteIFvalues = args$overwriteIFvalues,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
480 reduceToSwitchingGenes = args$reduceToSwitchingGenes,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
481 reduceFurtherToGenesWithConsequencePotential = args$reduceFurtherToGenesWithConsequencePotential,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
482 onlySigIsoforms = args$onlySigIsoforms,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
483 keepIsoformInAllConditions = args$keepIsoformInAllConditions2,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
484 showProgress = TRUE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
485 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
486
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
487 SwitchList <- analyzeNovelIsoformORF(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
488 SwitchList,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
489 analysisAllIsoformsWithoutORF = TRUE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
490 minORFlength = args$minORFlength,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
491 orfMethod = args$orfMethod,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
492 PTCDistance = args$PTCDistance,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
493 startCodons = "ATG",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
494 stopCodons = c("TAA", "TAG", "TGA"),
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
495 showProgress = TRUE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
496 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
497
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
498 ### Extract Sequences
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
499 SwitchList <- extractSequence(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
500 SwitchList,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
501 onlySwitchingGenes = args$onlySwitchingGenes,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
502 alpha = args$alpha,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
503 dIFcutoff = args$dIFcutoff,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
504 extractNTseq = TRUE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
505 extractAAseq = TRUE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
506 removeShortAAseq = args$removeShortAAseq,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
507 removeLongAAseq = args$removeLongAAseq,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
508 removeORFwithStop = args$removeORFwithStop,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
509 addToSwitchAnalyzeRlist = TRUE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
510 writeToFile = TRUE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
511 pathToOutput = getwd(),
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
512 outputPrefix = "isoformSwitchAnalyzeR_isoform",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
513 forceReExtraction = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
514 quiet = FALSE
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
515 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
516
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
517 ### Summary
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
518 switchSummary <- extractSwitchSummary(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
519 SwitchList,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
520 filterForConsequences = args$filterForConsequences,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
521 alpha = args$alpha,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
522 dIFcutoff = args$dIFcutoff,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
523 onlySigIsoforms = args$onlySigIsoforms,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
524 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
525
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
526 save(SwitchList, file = "SwitchList.Rda")
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
527 write.table(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
528 switchSummary,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
529 file = "switchSummary.tsv",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
530 quote = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
531 sep = "\t",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
532 col.names = TRUE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
533 row.names = FALSE
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
534 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
535
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
536 }
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
537
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
538 if (args$modeSelector == "second_step") {
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
539
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
540 # Second part of the analysis
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
541 #############################
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
542
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
543 load(file = args$rObject)
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
544
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
545 ### Add annotation
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
546 if (!is.null(args$pathToCPATresultFile)) {
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
547 SwitchList <- analyzeCPAT(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
548 SwitchList,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
549 pathToCPATresultFile = args$pathToCPATresultFile,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
550 codingCutoff = args$codingCutoff,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
551 removeNoncodinORFs = args$removeNoncodingORFs
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
552 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
553 }
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
554
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
555 if (!is.null(args$pathToCPC2resultFile)) {
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
556 SwitchList <- analyzeCPC2(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
557 SwitchList,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
558 pathToCPC2resultFile = args$pathToCPC2resultFile,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
559 removeNoncodinORFs = args$removeNoncodingORFs
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
560 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
561 }
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
562
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
563 if (!is.null(args$pathToPFAMresultFile)) {
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
564 pfamFiles <- list.files(path = args$pathToPFAMresultFile,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
565 full.names = TRUE)
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
566
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
567 SwitchList <- analyzePFAM(SwitchList,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
568 pathToPFAMresultFile = pfamFiles,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
569 showProgress = FALSE)
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
570 }
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
571
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
572 if (!is.null(args$pathToNetSurfP2resultFile)) {
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
573 netsurfFiles <- list.files(path = args$pathToNetSurfP2resultFile,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
574 full.names = TRUE)
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
575
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
576 SwitchList <- analyzeNetSurfP2(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
577 SwitchList,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
578 pathToNetSurfP2resultFile = netsurfFiles,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
579 smoothingWindowSize = args$smoothingWindowSize,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
580 probabilityCutoff = args$probabilityCutoff,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
581 minIdrSize = args$minIdrSize,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
582 showProgress = TRUE
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
583 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
584 }
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
585
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
586 if (!is.null(args$pathToIUPred2AresultFile)) {
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
587 SwitchList <- analyzeIUPred2A(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
588 SwitchList,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
589 pathToIUPred2AresultFile = args$pathToIUPred2AresultFile,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
590 smoothingWindowSize = args$smoothingWindowSize,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
591 probabilityCutoff = args$probabilityCutoff,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
592 minIdrSize = args$minIdrSize,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
593 annotateBindingSites = args$annotateBindingSites,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
594 minIdrBindingSize = args$minIdrBindingSize,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
595 minIdrBindingOverlapFrac = args$minIdrBindingOverlapFrac,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
596 showProgress = TRUE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
597 quiet = FALSE
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
598 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
599 }
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
600
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
601 if (!is.null(args$pathToSignalPresultFile)) {
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
602 signalpFiles <- list.files(path = args$pathToSignalPresultFile,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
603 full.names = TRUE)
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
604
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
605 SwitchList <- analyzeSignalP(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
606 SwitchList,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
607 pathToSignalPresultFile = signalpFiles,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
608 minSignalPeptideProbability = args$minSignalPeptideProbability
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
609 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
610 }
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
611
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
612 SwitchList <- analyzeAlternativeSplicing(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
613 SwitchList,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
614 onlySwitchingGenes = args$onlySwitchingGenes,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
615 alpha = args$alpha,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
616 dIFcutoff = args$dIFcutoff,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
617 showProgress = TRUE
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
618 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
619
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
620 SwitchList <- analyzeIntronRetention(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
621 SwitchList,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
622 onlySwitchingGenes = args$onlySwitchingGenes,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
623 alpha = args$alpha,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
624 dIFcutoff = args$dIFcutoff,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
625 showProgress = TRUE
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
626 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
627
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
628 consequences <- c(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
629 "intron_retention",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
630 "NMD_status",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
631 "isoform_seq_similarity",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
632 "ORF_genomic",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
633 "tss",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
634 "tts"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
635 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
636
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
637 if (!is.null(args$pathToCPATresultFile) ||
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
638 !is.null(args$pathToCPC2resultFile)) {
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
639 updatedConsequences <- c(consequences, "coding_potential")
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
640 consequences <- updatedConsequences
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
641 }
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
642
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
643 if (!is.null(args$pathToPFAMresultFile)) {
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
644 updatedConsequences <- c(consequences, "domains_identified")
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
645 consequences <- updatedConsequences
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
646 }
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
647
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
648 if (!is.null(args$pathToSignalPresultFile)) {
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
649 updatedConsequences <- c(consequences, "signal_peptide_identified")
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
650 consequences <- updatedConsequences
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
651 }
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
652
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
653 if (!is.null(args$pathToNetSurfP2resultFile) ||
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
654 !is.null(args$pathToIUPred2AresultFile)) {
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
655 updatedConsequences <- c(consequences, "IDR_identified", "IDR_type")
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
656 consequences <- updatedConsequences
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
657 }
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
658
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
659 SwitchList <- analyzeSwitchConsequences(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
660 SwitchList,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
661 consequencesToAnalyze = consequences,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
662 alpha = args$alpha,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
663 dIFcutoff = args$dIFcutoff,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
664 onlySigIsoforms = args$onlySigIsoforms,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
665 ntCutoff = args$ntCutoff,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
666 ntJCsimCutoff = args$ntJCsimCutoff,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
667 AaCutoff = args$AaCutoff,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
668 AaFracCutoff = args$AaFracCutoff,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
669 AaJCsimCutoff = args$AaJCsimCutoff,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
670 removeNonConseqSwitches = args$removeNonConseqSwitches,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
671 showProgress = TRUE
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
672 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
673
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
674
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
675 ### Visual analysis
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
676 # Top genes
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
677
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
678 if (args$analysisMode == "single") {
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
679
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
680 outputFile <- file.path(getwd(), "single_gene.pdf")
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
681
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
682 pdf(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
683 file = outputFile,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
684 onefile = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
685 height = 6,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
686 width = 9
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
687 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
688
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
689 switchPlot(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
690 SwitchList,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
691 gene = args$gene,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
692 condition1 = myDesign$condition[1],
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
693 condition2 = myDesign$condition[length(myDesign$condition)],
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
694 IFcutoff = args$IFcutoff,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
695 dIFcutoff = args$dIFcutoff,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
696 rescaleTranscripts = args$rescaleTranscripts,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
697 reverseMinus = args$reverseMinus,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
698 addErrorbars = args$addErrorbars,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
699 logYaxis = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
700 localTheme = theme_bw(base_size = 8)
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
701 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
702 dev.off()
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
703
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
704 } else {
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
705 mostSwitchingGene <-
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
706 extractTopSwitches(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
707 SwitchList,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
708 n = Inf,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
709 filterForConsequences = args$filterForConsequences,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
710 extractGenes = TRUE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
711 alpha = args$alpha,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
712 dIFcutoff = args$dIFcutoff,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
713 inEachComparison = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
714 sortByQvals = args$sortByQvals
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
715 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
716
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
717 write.table(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
718 mostSwitchingGene,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
719 file = "mostSwitchingGene.tsv",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
720 quote = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
721 sep = "\t",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
722 col.names = TRUE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
723 row.names = FALSE
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
724 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
725
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
726
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
727 switchPlotTopSwitches(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
728 SwitchList,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
729 alpha = args$alpha,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
730 dIFcutoff = args$dIFcutoff,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
731 onlySigIsoforms = args$onlySigIsoforms,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
732 n = args$genesToPlot,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
733 sortByQvals = args$sortByQvals,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
734 pathToOutput = getwd(),
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
735 fileType = "pdf"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
736 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
737
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
738 outputFile <-
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
739 file.path(getwd(), "extractConsequencesSummary.pdf")
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
740
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
741 pdf(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
742 file = outputFile,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
743 onefile = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
744 height = 6,
1
2c4e879a81cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7d278967f9c8d2c6ce0a8f83be2c444822746bbf
iuc
parents: 0
diff changeset
745 width = 12
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
746 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
747
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
748 consequenceSummary <- extractConsequenceSummary(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
749 SwitchList,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
750 consequencesToAnalyze = "all",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
751 includeCombined = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
752 asFractionTotal = args$asFractionTotal,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
753 alpha = args$alpha,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
754 dIFcutoff = args$dIFcutoff,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
755 plot = TRUE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
756 plotGenes = args$plotGenes,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
757 simplifyLocation = args$simplifyLocation,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
758 removeEmptyConsequences = args$removeEmptyConsequences,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
759 returnResult = TRUE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
760 localTheme = theme_bw()
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
761 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
762 dev.off()
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
763
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
764 write.table(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
765 consequenceSummary,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
766 file = "consequencesSummary.tsv",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
767 quote = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
768 sep = "\t",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
769 col.names = TRUE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
770 row.names = FALSE
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
771 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
772
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
773
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
774 outputFile <- file.path(getwd(), "consequencesEnrichment.pdf")
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
775 pdf(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
776 file = outputFile,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
777 onefile = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
778 height = 6,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
779 width = 9
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
780 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
781 consequenceEnrichment <- extractConsequenceEnrichment(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
782 SwitchList,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
783 consequencesToAnalyze = "all",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
784 alpha = args$alpha,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
785 dIFcutoff = args$dIFcutoff,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
786 countGenes = args$countGenes,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
787 analysisOppositeConsequence = args$analysisOppositeConsequence,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
788 plot = TRUE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
789 localTheme = theme_bw(base_size = 12),
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
790 minEventsForPlotting = 10,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
791 returnResult = TRUE
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
792 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
793 dev.off()
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
794
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
795 write.table(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
796 consequenceEnrichment,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
797 file = "consequencesEnrichment.tsv",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
798 quote = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
799 sep = "\t",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
800 col.names = TRUE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
801 row.names = FALSE
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
802 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
803
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
804
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
805 outputFile <- file.path(getwd(), "splicingEnrichment.pdf")
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
806 pdf(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
807 file = outputFile,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
808 onefile = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
809 height = 6,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
810 width = 9
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
811 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
812 splicingEnrichment <- extractSplicingEnrichment(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
813 SwitchList,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
814 splicingToAnalyze = "all",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
815 alpha = args$alpha,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
816 dIFcutoff = args$dIFcutoff,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
817 onlySigIsoforms = args$onlySigIsoforms,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
818 countGenes = args$countGenes,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
819 plot = TRUE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
820 minEventsForPlotting = 10,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
821 returnResult = TRUE
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
822 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
823 dev.off()
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
824
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
825 write.table(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
826 splicingEnrichment,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
827 file = "splicingEnrichment.tsv",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
828 quote = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
829 sep = "\t",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
830 col.names = TRUE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
831 row.names = FALSE
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
832 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
833
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
834
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
835 outputFile <- file.path(getwd(), "splicingSummary.pdf")
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
836 pdf(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
837 file = outputFile,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
838 onefile = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
839 height = 6,
1
2c4e879a81cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7d278967f9c8d2c6ce0a8f83be2c444822746bbf
iuc
parents: 0
diff changeset
840 width = 12
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
841 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
842 splicingSummary <- extractSplicingSummary(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
843 SwitchList,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
844 splicingToAnalyze = "all",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
845 asFractionTotal = args$asFractionTotal,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
846 alpha = args$alpha,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
847 dIFcutoff = args$dIFcutoff,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
848 onlySigIsoforms = args$onlySigIsoforms,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
849 plot = TRUE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
850 plotGenes = args$plotGenes,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
851 localTheme = theme_bw(),
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
852 returnResult = TRUE
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
853 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
854 dev.off()
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
855
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
856 write.table(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
857 splicingSummary,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
858 file = "splicingSummary.tsv",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
859 quote = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
860 sep = "\t",
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
861 col.names = TRUE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
862 row.names = FALSE
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
863 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
864
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
865
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
866 ### Volcano like plot:
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
867 outputFile <- file.path(getwd(), "volcanoPlot.pdf")
1
2c4e879a81cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7d278967f9c8d2c6ce0a8f83be2c444822746bbf
iuc
parents: 0
diff changeset
868
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
869 pdf(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
870 file = outputFile,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
871 onefile = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
872 height = 6,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
873 width = 9
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
874 )
1
2c4e879a81cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7d278967f9c8d2c6ce0a8f83be2c444822746bbf
iuc
parents: 0
diff changeset
875
2c4e879a81cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7d278967f9c8d2c6ce0a8f83be2c444822746bbf
iuc
parents: 0
diff changeset
876 p <- ggplot(data = SwitchList$isoformFeatures, aes(x = dIF, y = -log10(isoform_switch_q_value))) +
2c4e879a81cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7d278967f9c8d2c6ce0a8f83be2c444822746bbf
iuc
parents: 0
diff changeset
877 geom_point(
2c4e879a81cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7d278967f9c8d2c6ce0a8f83be2c444822746bbf
iuc
parents: 0
diff changeset
878 aes(color = abs(dIF) > 0.1 & isoform_switch_q_value < 0.05), # default cutoff
2c4e879a81cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7d278967f9c8d2c6ce0a8f83be2c444822746bbf
iuc
parents: 0
diff changeset
879 size = 1
2c4e879a81cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7d278967f9c8d2c6ce0a8f83be2c444822746bbf
iuc
parents: 0
diff changeset
880 ) +
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
881 geom_hline(yintercept = -log10(0.05), linetype = "dashed") + # default cutoff
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
882 geom_vline(xintercept = c(-0.1, 0.1), linetype = "dashed") + # default cutoff
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
883 facet_wrap(~ condition_2) +
1
2c4e879a81cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7d278967f9c8d2c6ce0a8f83be2c444822746bbf
iuc
parents: 0
diff changeset
884 #facet_grid(condition_1 ~ condition_2) + # alternative to facet_wrap if you have overlapping conditions
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
885 scale_color_manual("Signficant\nIsoform Switch", values = c("black", "red")) +
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
886 labs(x = "dIF", y = "-Log10 ( Isoform Switch Q Value )") +
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
887 theme_bw()
1
2c4e879a81cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7d278967f9c8d2c6ce0a8f83be2c444822746bbf
iuc
parents: 0
diff changeset
888 print(p)
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
889 dev.off()
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
890
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
891 ### Switch vs Gene changes:
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
892 outputFile <- file.path(getwd(), "switchGene.pdf")
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
893 pdf(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
894 file = outputFile,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
895 height = 6,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
896 width = 9
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
897 )
1
2c4e879a81cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7d278967f9c8d2c6ce0a8f83be2c444822746bbf
iuc
parents: 0
diff changeset
898 p <- ggplot(data = SwitchList$isoformFeatures,
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
899 aes(x = gene_log2_fold_change, y = dIF)) +
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
900 geom_point(aes(color = abs(dIF) > 0.1 &
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
901 isoform_switch_q_value < 0.05),
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
902 size = 1) +
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
903 facet_wrap(~ condition_2) +
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
904 geom_hline(yintercept = 0, linetype = "dashed") +
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
905 geom_vline(xintercept = 0, linetype = "dashed") +
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
906 scale_color_manual("Signficant\nIsoform Switch", values = c("black", "red")) +
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
907 labs(x = "Gene log2 fold change", y = "dIF") +
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
908 theme_bw()
1
2c4e879a81cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7d278967f9c8d2c6ce0a8f83be2c444822746bbf
iuc
parents: 0
diff changeset
909 print(p)
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
910 dev.off()
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
911
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
912 outputFile <- file.path(getwd(), "splicingGenomewide.pdf")
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
913 pdf(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
914 file = outputFile,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
915 onefile = FALSE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
916 height = 6,
1
2c4e879a81cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7d278967f9c8d2c6ce0a8f83be2c444822746bbf
iuc
parents: 0
diff changeset
917 width = 14
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
918 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
919 splicingGenomeWide <- extractSplicingGenomeWide(
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
920 SwitchList,
1
2c4e879a81cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7d278967f9c8d2c6ce0a8f83be2c444822746bbf
iuc
parents: 0
diff changeset
921 featureToExtract = "isoformUsage",
2c4e879a81cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7d278967f9c8d2c6ce0a8f83be2c444822746bbf
iuc
parents: 0
diff changeset
922 splicingToAnalyze = "all",
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
923 plot = TRUE,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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parents:
diff changeset
924 returnResult = TRUE
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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parents:
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925 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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parents:
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926 dev.off()
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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927 }
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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parents:
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928 save(SwitchList, file = "SwitchList.Rda")
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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parents:
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929
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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930 }