Mercurial > repos > iuc > isoformswitchanalyzer

annotate IsoformSwitchAnalyzeR.R @ 7:d3377a16d881 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
author iuc
date Wed, 14 Jan 2026 09:30:42 +0000
parents b3f292d9f35d
children
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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,
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d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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3 quietly = TRUE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
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4 warn.conflicts = FALSE
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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5 )
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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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6 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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7 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
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8 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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9
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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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11 # 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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12 options(
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d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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13 show.error.messages = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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14 error = function() {
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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15 cat(geterrmessage(), file = stderr())
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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16 q("no", 1, FALSE)
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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17 }
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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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18 )
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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20 # 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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21 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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23 ################################################################################
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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24 ### Input Processing
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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25 ################################################################################
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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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28 # 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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29 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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f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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31 parser$add_argument("--modeSelector")
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32 parser$add_argument("--parentDir", required = FALSE, help = "Parent directory")
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b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
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33 parser$add_argument("--condition",
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d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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34 action = "append",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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35 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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36 help = "Conditions"
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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37 )
5
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38 parser$add_argument("--sampleID",
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d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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39 action = "append",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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40 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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41 help = "SampleID"
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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42 )
5
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
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43 parser$add_argument("--replicate",
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d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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44 action = "append",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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45 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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46 help = "Replicates"
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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47 )
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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48 parser$add_argument("--cofactors",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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49 action = "append",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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50 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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51 help = "Cofactors (comma-separated values)"
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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52 )
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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53 parser$add_argument("--cofactorNames",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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54 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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55 help = "Cofactor names (comma-separated)"
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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56 )
0
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57 parser$add_argument("--readLength",
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58 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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59 type = "integer",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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60 help = "Read length (required for stringtie)"
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61 )
5
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62 parser$add_argument("--pairedSamples", action = "store_true", required = FALSE, help = "Paired samples")
0
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63 parser$add_argument("--annotation", required = FALSE, help = "Annotation")
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64 parser$add_argument("--stringtieAnnotation", required = FALSE, help = "Stringtie annotation")
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f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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65 parser$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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66 parser$add_argument(
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67 "--fixStringTieAnnotationProblem",
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68 action = "store_true",
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69 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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70 help = "Fix StringTie annotation problem"
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71 )
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72 parser$add_argument("--countFiles", required = FALSE, help = "Count files")
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73 parser$add_argument("--toolSource", required = FALSE, help = "Tool source")
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74 parser$add_argument("--rObject", required = FALSE, help = "R object")
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75 parser$add_argument("--IFcutoff",
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76 required = FALSE,
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77 type = "numeric",
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78 help = "IFcutoff"
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79 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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80 parser$add_argument(
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81 "--geneExpressionCutoff",
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82 required = FALSE,
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83 type = "numeric",
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84 help = "Gene expression cutoff"
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85 )
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86 parser$add_argument(
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87 "--isoformExpressionCutoff",
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88 required = FALSE,
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diff changeset
89 type = "numeric",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
90 help = "Isoform expression cutoff"
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
91 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
92 parser$add_argument("--alpha",
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
93 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
94 type = "numeric",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
95 help = ""
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
96 )
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
97 parser$add_argument("--dIFcutoff",
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
98 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
99 type = "numeric",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
100 help = "dIF cutoff"
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
101 )
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
102 parser$add_argument(
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
103 "--onlySigIsoforms",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
104 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
105 action = "store_true",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
106 help = "Only significative isoforms"
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
107 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
108 parser$add_argument(
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
109 "--filterForConsequences",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
110 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
111 action = "store_true",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
112 help = "Filter for consequences"
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
113 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
114 parser$add_argument(
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
115 "--removeSingleIsformGenes",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
116 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
117 action = "store_true",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
118 help = "Remove single isoform genes"
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
119 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
120 parser$add_argument(
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
121 "--keepIsoformInAllConditions",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
122 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
123 action = "store_true",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
124 help = "Keep isoform in all conditions"
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
125 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
126 parser$add_argument(
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
127 "--correctForConfoundingFactors",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
128 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
129 action = "store_true",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
130 help = "Correct for confunding factors"
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
131 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
132 parser$add_argument(
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
133 "--overwriteIFvalues",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
134 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
135 action = "store_true",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
136 help = "Overwrite IF values"
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
137 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
138 parser$add_argument(
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
139 "--removeNonConvensionalChr",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
140 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
141 action = "store_true",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
142 help = "Remove non-conventional chromosomes"
2
2b0a6af4b85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a
iuc
parents: 1
diff changeset
143 )
2b0a6af4b85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a
iuc
parents: 1
diff changeset
144 parser$add_argument(
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
145 "--reduceToSwitchingGenes",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
146 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
147 action = "store_true",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
148 help = "Reduce to switching genes"
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
149 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
150 parser$add_argument(
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
151 "--reduceFurtherToGenesWithConsequencePotential",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
152 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
153 action = "store_true",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
154 help = "Reduce further to genes with consequence potential"
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
155 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
156 parser$add_argument(
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
157 "--keepIsoformInAllConditions2",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
158 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
159 action = "store_true",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
160 help = "Keep isoform in ll conditions"
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
161 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
162 parser$add_argument("--minORFlength",
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
163 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
164 type = "integer",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
165 help = ""
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
166 )
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
167 parser$add_argument("--orfMethod", required = FALSE, help = "ORF methods")
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
168 parser$add_argument("--PTCDistance",
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
169 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
170 type = "integer",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
171 help = ""
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
172 )
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
173 parser$add_argument(
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
174 "--removeShortAAseq",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
175 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
176 action = "store_true",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
177 help = "Remove short aminoacid sequences"
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
178 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
179 parser$add_argument(
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
180 "--removeLongAAseq",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
181 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
182 action = "store_true",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
183 help = "Remove long aminoacid sequences"
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
184 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
185 parser$add_argument(
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
186 "--removeORFwithStop",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
187 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
188 action = "store_true",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
189 help = "Remove ORF with stop codon"
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
190 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
191 parser$add_argument(
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
192 "--onlySwitchingGenes",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
193 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
194 action = "store_true",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
195 help = "Only switching genes"
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
196 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
197 parser$add_argument("--analysisMode", required = FALSE, help = "Analyze all isoforms with differential usage or single genes")
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
198 parser$add_argument(
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
199 "--genesToPlot",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
200 type = "integer",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
201 default = 10,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
202 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
203 help = "Number of genes to plot"
0
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$add_argument("--gene", required = FALSE, help = "Gene ID to analyze")
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
206 parser$add_argument(
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
207 "--sortByQvals",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
208 action = "store_true",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
209 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
210 help = "Sort genes by Q-val values"
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
211 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
212 parser$add_argument("--countGenes",
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
213 action = "store_true",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
214 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
215 help = "Count genes"
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
216 )
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
217 parser$add_argument(
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
218 "--asFractionTotal",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
219 action = "store_true",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
220 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
221 help = "Plot gene expresson as fraction of total"
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
222 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
223 parser$add_argument("--plotGenes",
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
224 action = "store_true",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
225 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
226 help = "Plot genes instead of isoforms"
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
227 )
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
228 parser$add_argument(
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
229 "--simplifyLocation",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
230 action = "store_true",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
231 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
232 help = "Simplify localtion"
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
233 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
234 parser$add_argument(
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
235 "--removeEmptyConsequences",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
236 action = "store_true",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
237 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
238 help = "Remove empty consequences"
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
239 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
240 parser$add_argument(
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
241 "--analysisOppositeConsequence",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
242 action = "store_true",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
243 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
244 help = "Analysi opposite consequences"
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
245 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
246 parser$add_argument("--pathToCPATresultFile",
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
247 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
248 help = "Path to CPAT result file"
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
249 )
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
250 parser$add_argument("--pathToCPC2resultFile",
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
251 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
252 help = "Path to CPC2 result file"
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
253 )
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
254 parser$add_argument("--pathToPFAMresultFile",
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
255 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
256 help = "Path to PFAM result file"
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
257 )
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
258 parser$add_argument("--pathToNetSurfP2resultFile",
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
259 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
260 help = "Path to NetSurfP2 result file"
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
261 )
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
262 parser$add_argument("--pathToSignalPresultFile",
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
263 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
264 help = "Path to signalP result file"
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
265 )
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
266 parser$add_argument("--pathToIUPred2AresultFile",
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
267 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
268 help = "Path to IUPred2A result file"
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
269 )
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
270 parser$add_argument("--codingCutoff",
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
271 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
272 type = "numeric",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
273 help = "Codding cutoff"
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
274 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
275 parser$add_argument(
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
276 "--removeNoncodingORFs",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
277 action = "store_true",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
278 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
279 help = "Remove non-coding ORFs"
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
280 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
281 parser$add_argument(
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
282 "--minSignalPeptideProbability",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
283 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
284 type = "numeric",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
285 help = "Minimul signal peptide probability"
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
286 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
287 parser$add_argument(
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
288 "--smoothingWindowSize",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
289 type = "integer",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
290 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
291 help = "Smoothing windows size"
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
292 )
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
293 parser$add_argument(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
294 "--probabilityCutoff",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
295 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
296 type = "double",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
297 help = "Probability cutoff"
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
298 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
299 parser$add_argument("--minIdrSize",
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
300 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
301 type = "integer",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
302 help = "Min Idr size"
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
303 )
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
304 parser$add_argument(
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
305 "--annotateBindingSites",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
306 action = "store_true",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
307 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
308 help = "Annotate binding sites"
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
309 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
310 parser$add_argument(
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
311 "--minIdrBindingSize",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
312 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
313 type = "integer",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
314 help = "Minimun Idr binding size"
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
315 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
316 parser$add_argument(
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
317 "--minIdrBindingOverlapFrac",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
318 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
319 type = "numeric",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
320 help = ""
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
321 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
322 parser$add_argument("--ntCutoff",
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
323 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
324 type = "integer",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
325 help = "Nucleotide cutoff"
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
326 )
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
327 parser$add_argument("--ntFracCutoff",
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
328 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
329 type = "numeric",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
330 help = "Nucleotide fraction cutoff"
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
331 )
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
332 parser$add_argument(
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
333 "--ntJCsimCutoff",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
334 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
335 type = "numeric",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
336 help = "Nucleotide Jaccard simmilarity cutoff"
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
337 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
338 parser$add_argument("--AaCutoff",
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
339 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
340 type = "integer",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
341 help = "Aminoacid cutoff"
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
342 )
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
343 parser$add_argument("--AaFracCutoff",
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
344 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
345 type = "numeric",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
346 help = "Aminoacid fraction cutoff"
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
347 )
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
348 parser$add_argument(
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
349 "--AaJCsimCutoff",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
350 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
351 type = "numeric",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
352 help = "Aminoacid Jaccard similarity cutoff"
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
353 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
354 parser$add_argument(
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
355 "--removeNonConseqSwitches",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
356 action = "store_true",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
357 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
358 help = "Remove switches without consequences"
0
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 parser$add_argument(
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
361 "--rescaleTranscripts",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
362 action = "store_true",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
363 required = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
364 help = "Rescale transcripts"
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
365 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
366 parser$add_argument(
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
367 "--reverseMinus",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
368 action = "store_true",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
369 required = FALSE,
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370 help = "Reverse minus"
0
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371 )
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372 parser$add_argument(
7
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373 "--addErrorbars",
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374 action = "store_true",
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375 required = FALSE,
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376 help = "Add error bars"
0
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377 )
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378
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379
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380 args <- parser$parse_args()
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381
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382 # Data import
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383 ###################
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384
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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385 if (args$modeSelector == "data_import") {
7
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386 quantificationData <- importIsoformExpression(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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387 parentDir = args$parentDir,
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388 addIsofomIdAsColumn = TRUE,
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389 readLength = args$readLength
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390 )
0
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391
7
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392 if (!args$pairedSamples) {
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393 ### Make design matrix
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394 if (!is.null(args$cofactors)) {
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395 # Split comma-separated cofactor values for each sample
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396 cofactor_list <- lapply(args$cofactors, function(x) {
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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397 strsplit(x, ",")[[1]]
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398 })
5
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399
7
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400 cofactor_names <- strsplit(as.character(args$cofactorNames), ",")[[1]]
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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diff changeset
401
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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402 # Create design matrix with cofactors as additional columns
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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403 myDesign <- data.frame(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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diff changeset
404 sampleID = args$sampleID,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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diff changeset
405 condition = args$condition
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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diff changeset
406 )
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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407
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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diff changeset
408 # Add cofactor columns with actual names
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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diff changeset
409 for (i in seq_along(cofactor_names)) {
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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diff changeset
410 cofactor_col <- sapply(cofactor_list, function(x) x[i])
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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411 myDesign[[cofactor_names[i]]] <- cofactor_col
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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diff changeset
412 }
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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diff changeset
413 } else {
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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parents: 5
diff changeset
414 myDesign <- data.frame(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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diff changeset
415 sampleID = args$sampleID,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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diff changeset
416 condition = args$condition
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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diff changeset
417 )
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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diff changeset
418 }
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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diff changeset
419 } else {
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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diff changeset
420 if (!is.null(args$cofactors)) {
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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diff changeset
421 # Split comma-separated cofactor values for each sample
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
422 cofactor_list <- lapply(args$cofactors, function(x) {
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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diff changeset
423 strsplit(x, ",")[[1]]
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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diff changeset
424 })
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
425
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
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diff changeset
426 cofactor_names <- strsplit(as.character(args$cofactorNames), ",")[[1]]
2
2b0a6af4b85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a
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parents: 1
diff changeset
427
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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diff changeset
428 # Create design matrix with cofactors as additional columns
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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diff changeset
429 myDesign <- data.frame(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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diff changeset
430 sampleID = args$sampleID,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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diff changeset
431 condition = args$condition,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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diff changeset
432 replicate = args$replicate
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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diff changeset
433 )
2
2b0a6af4b85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a
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parents: 1
diff changeset
434
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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diff changeset
435 # Add cofactor columns with actual names
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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parents: 5
diff changeset
436 for (i in seq_along(cofactor_names)) {
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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diff changeset
437 cofactor_col <- sapply(cofactor_list, function(x) x[i])
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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diff changeset
438 myDesign[[cofactor_names[i]]] <- cofactor_col
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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diff changeset
439 }
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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diff changeset
440 } else {
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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parents: 5
diff changeset
441 myDesign <- data.frame(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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diff changeset
442 sampleID = args$sampleID,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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diff changeset
443 condition = args$condition,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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diff changeset
444 replicate = args$replicate
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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diff changeset
445 )
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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diff changeset
446 }
2
2b0a6af4b85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a
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parents: 1
diff changeset
447 }
2b0a6af4b85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a
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diff changeset
448
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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diff changeset
449 comparisons <- as.data.frame(cbind(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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diff changeset
450 condition_1 = myDesign$condition[1],
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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diff changeset
451 condition_2 = myDesign$condition[length(myDesign$condition)]
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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diff changeset
452 ))
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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parents: 5
diff changeset
453
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
454 if (args$toolSource == "stringtie") {
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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diff changeset
455 if (!is.null(args$stringtieAnnotation)) {
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
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diff changeset
456 SwitchList <- importRdata(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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diff changeset
457 isoformCountMatrix = quantificationData$counts,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
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diff changeset
458 isoformRepExpression = quantificationData$abundance,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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diff changeset
459 designMatrix = myDesign,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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diff changeset
460 removeNonConvensionalChr = args$removeNonConvensionalChr,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
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diff changeset
461 isoformExonAnnoation = args$stringtieAnnotation,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
462 isoformNtFasta = args$transcriptome,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
463 addAnnotatedORFs = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
464 showProgress = TRUE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
465 comparisonsToMake = comparisons,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
466 fixStringTieAnnotationProblem = args$fixStringTieAnnotationProblem
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
467 )
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
468
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
469 SwitchList <- addORFfromGTF(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
470 SwitchList,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
471 removeNonConvensionalChr = args$removeNonConvensionalChr,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
472 pathToGTF = args$annotation
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
473 )
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
474 } else {
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
475 SwitchList <- importRdata(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
476 isoformCountMatrix = quantificationData$counts,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
477 isoformRepExpression = quantificationData$abundance,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
478 designMatrix = myDesign,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
479 removeNonConvensionalChr = args$removeNonConvensionalChr,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
480 isoformNtFasta = args$transcriptome,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
481 isoformExonAnnoation = args$annotation,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
482 showProgress = TRUE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
483 comparisonsToMake = comparisons,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
484 fixStringTieAnnotationProblem = args$fixStringTieAnnotationProblem
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
485 )
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
486 }
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
487 } else {
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
488 SwitchList <- importRdata(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
489 isoformCountMatrix = quantificationData$counts,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
490 isoformRepExpression = quantificationData$abundance,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
491 designMatrix = myDesign,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
492 removeNonConvensionalChr = args$removeNonConvensionalChr,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
493 isoformExonAnnoation = args$annotation,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
494 isoformNtFasta = args$transcriptome,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
495 showProgress = TRUE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
496 comparisonsToMake = comparisons
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
497 )
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
498 }
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
499
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
500 geneCountMatrix <- extractGeneExpression(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
501 SwitchList,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
502 extractCounts = TRUE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
503 addGeneNames = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
504 addIdsAsColumns = FALSE
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
505 )
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
506
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
507 if (args$countFiles == "collection") {
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
508 expressionDF <- data.frame(geneCountMatrix)
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
509
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
510 myDesign$condition[length(myDesign$condition)]
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
511
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
512 dataframe_factor1 <- expressionDF %>% select(matches(myDesign$condition[1]))
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
513 dataframe_factor2 <- expressionDF %>% select(matches(myDesign$condition[length(myDesign$condition)]))
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
514
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
515
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
516 lf1 <- as.list(as.data.frame(dataframe_factor1))
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
517 sampleNames1 <- colnames(as.data.frame(dataframe_factor1))
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
518
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
519 lf2 <- as.list(as.data.frame(dataframe_factor2))
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
520 sampleNames2 <- colnames(as.data.frame(dataframe_factor2))
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
521
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
522 geneNames <- row.names(as.data.frame(expressionDF))
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
523
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
524
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
525 for (index in seq_along(lf1)) {
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
526 tabular_expression <- data.frame(geneNames, lf1[index])
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
527 colnames(tabular_expression) <-
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
528 c("Geneid", sampleNames1[index])
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
529 filename <-
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
530 paste(sampleNames1[index], "dataset.tabular", sep = "_")
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
531 output_path <- paste("./count_files/factor1/", filename, sep = "")
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
532 write.table(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
533 tabular_expression,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
534 output_path,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
535 sep = "\t",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
536 row.names = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
537 quote = FALSE
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
538 )
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
539 }
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
540 for (index in seq_along(lf2)) {
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
541 tabular_expression <- data.frame(geneNames, lf2[index])
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
542 colnames(tabular_expression) <-
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
543 c("Geneid", sampleNames2[index])
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
544 filename <-
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
545 paste(sampleNames2[index], "dataset.tabular", sep = "_")
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
546 output_path <- paste("./count_files/factor2/", filename, sep = "")
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
547 write.table(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
548 tabular_expression,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
549 output_path,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
550 sep = "\t",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
551 row.names = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
552 quote = FALSE
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
553 )
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
554 }
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
555 } else if (args$countFiles == "matrix") {
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
556 expressionDF <- data.frame(geneCountMatrix)
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
557 geneNames <- row.names(expressionDF)
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
558
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
559 expressionDF <- cbind(geneNames, expressionDF)
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
560 write.table(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
561 as.data.frame(expressionDF),
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
562 "./count_files/matrix.tabular",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
563 sep = "\t",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
564 row.names = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
565 quote = FALSE
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
566 )
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
567 write.table(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
568 as.data.frame(myDesign),
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
569 "./count_files/samples.tabular",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
570 sep = "\t",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
571 row.names = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
572 quote = FALSE
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
573 )
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
574 }
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
575
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
576 save(SwitchList, file = "SwitchList.Rda")
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
577 }
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
578
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
579 if (args$modeSelector == "first_step") {
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
580 # First part of the analysis
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
581 #############################
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
582
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
583 load(file = args$rObject)
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
584
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
585 ### Filter
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
586 SwitchList <- preFilter(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
587 SwitchList,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
588 IFcutoff = args$IFcutoff,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
589 geneExpressionCutoff = args$geneExpressionCutoff,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
590 isoformExpressionCutoff = args$isoformExpressionCutoff,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
591 removeSingleIsoformGenes = args$removeSingleIsformGenes,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
592 onlySigIsoforms = args$onlySigIsoforms,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
593 keepIsoformInAllConditions = args$keepIsoformInAllConditions,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
594 alpha = args$alpha,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
595 dIFcutoff = args$dIFcutoff,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
596 )
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
597
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
598 ### Test for isoform switches
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
599 SwitchList <- isoformSwitchTestDEXSeq(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
600 SwitchList,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
601 alpha = args$alpha,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
602 dIFcutoff = args$dIFcutoff,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
603 correctForConfoundingFactors = args$correctForConfoundingFactors,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
604 overwriteIFvalues = args$overwriteIFvalues,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
605 reduceToSwitchingGenes = args$reduceToSwitchingGenes,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
606 reduceFurtherToGenesWithConsequencePotential = args$reduceFurtherToGenesWithConsequencePotential,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
607 onlySigIsoforms = args$onlySigIsoforms,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
608 keepIsoformInAllConditions = args$keepIsoformInAllConditions2,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
609 showProgress = TRUE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
610 )
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
611
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
612 # Analyze missing annotated isoforms by default
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
613 SwitchList <- analyzeNovelIsoformORF(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
614 SwitchList,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
615 analysisAllIsoformsWithoutORF = TRUE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
616 minORFlength = args$minORFlength,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
617 orfMethod = args$orfMethod,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
618 PTCDistance = args$PTCDistance,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
619 startCodons = "ATG",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
620 stopCodons = c("TAA", "TAG", "TGA"),
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
621 showProgress = TRUE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
622 )
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
623
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
624 ### Extract Sequences
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
625 SwitchList <- extractSequence(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
626 SwitchList,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
627 onlySwitchingGenes = args$onlySwitchingGenes,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
628 alpha = args$alpha,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
629 dIFcutoff = args$dIFcutoff,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
630 extractNTseq = TRUE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
631 extractAAseq = TRUE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
632 removeShortAAseq = args$removeShortAAseq,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
633 removeLongAAseq = args$removeLongAAseq,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
634 removeORFwithStop = args$removeORFwithStop,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
635 addToSwitchAnalyzeRlist = TRUE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
636 writeToFile = TRUE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
637 pathToOutput = getwd(),
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
638 outputPrefix = "isoformSwitchAnalyzeR_isoform",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
639 forceReExtraction = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
640 quiet = FALSE
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
641 )
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
642
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
643 ### Summary
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
644 switchSummary <- extractSwitchSummary(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
645 SwitchList,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
646 filterForConsequences = args$filterForConsequences,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
647 alpha = args$alpha,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
648 dIFcutoff = args$dIFcutoff,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
649 onlySigIsoforms = args$onlySigIsoforms,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
650 )
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
651
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
652 save(SwitchList, file = "SwitchList.Rda")
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
653 write.table(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
654 switchSummary,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
655 file = "switchSummary.tsv",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
656 quote = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
657 sep = "\t",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
658 col.names = TRUE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
659 row.names = FALSE
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
660 )
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
661 }
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
662
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
663 if (args$modeSelector == "second_step") {
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
664 # Second part of the analysis
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
665 #############################
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
666
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
667 load(file = args$rObject)
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
668
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
669 ### Add annotation
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
670 if (!is.null(args$pathToCPATresultFile)) {
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
671 SwitchList <- analyzeCPAT(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
672 SwitchList,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
673 pathToCPATresultFile = args$pathToCPATresultFile,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
674 codingCutoff = args$codingCutoff,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
675 removeNoncodinORFs = args$removeNoncodingORFs
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
676 )
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
677 }
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
678
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
679 if (!is.null(args$pathToCPC2resultFile)) {
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
680 SwitchList <- analyzeCPC2(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
681 SwitchList,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
682 pathToCPC2resultFile = args$pathToCPC2resultFile,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
683 removeNoncodinORFs = args$removeNoncodingORFs
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
684 )
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
685 }
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
686
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
687 if (!is.null(args$pathToPFAMresultFile)) {
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
688 pfamFiles <- list.files(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
689 path = args$pathToPFAMresultFile,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
690 full.names = TRUE
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
691 )
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
692
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
693 SwitchList <- analyzePFAM(SwitchList,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
694 pathToPFAMresultFile = pfamFiles,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
695 showProgress = FALSE
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
696 )
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
697 }
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
698
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
699 if (!is.null(args$pathToNetSurfP2resultFile)) {
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
700 netsurfFiles <- list.files(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
701 path = args$pathToNetSurfP2resultFile,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
702 full.names = TRUE
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
703 )
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
704
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
705 SwitchList <- analyzeNetSurfP2(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
706 SwitchList,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
707 pathToNetSurfP2resultFile = netsurfFiles,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
708 smoothingWindowSize = args$smoothingWindowSize,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
709 probabilityCutoff = args$probabilityCutoff,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
710 minIdrSize = args$minIdrSize,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
711 showProgress = TRUE
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
712 )
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
713 }
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
714
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
715 if (!is.null(args$pathToIUPred2AresultFile)) {
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
716 SwitchList <- analyzeIUPred2A(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
717 SwitchList,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
718 pathToIUPred2AresultFile = args$pathToIUPred2AresultFile,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
719 smoothingWindowSize = args$smoothingWindowSize,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
720 probabilityCutoff = args$probabilityCutoff,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
721 minIdrSize = args$minIdrSize,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
722 annotateBindingSites = args$annotateBindingSites,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
723 minIdrBindingSize = args$minIdrBindingSize,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
724 minIdrBindingOverlapFrac = args$minIdrBindingOverlapFrac,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
725 showProgress = TRUE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
726 quiet = FALSE
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
727 )
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
728 }
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
729
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
730 if (!is.null(args$pathToSignalPresultFile)) {
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
731 signalpFiles <- list.files(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
732 path = args$pathToSignalPresultFile,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
733 full.names = TRUE
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
734 )
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
735
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
736 SwitchList <- analyzeSignalP(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
737 SwitchList,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
738 pathToSignalPresultFile = signalpFiles,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
739 minSignalPeptideProbability = args$minSignalPeptideProbability
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
740 )
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
741 }
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
742
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
743 SwitchList <- analyzeAlternativeSplicing(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
744 SwitchList,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
745 onlySwitchingGenes = args$onlySwitchingGenes,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
746 alpha = args$alpha,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
747 dIFcutoff = args$dIFcutoff,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
748 showProgress = TRUE
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
749 )
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
750
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
751 SwitchList <- analyzeIntronRetention(
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
752 SwitchList,
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
753 onlySwitchingGenes = args$onlySwitchingGenes,
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
754 alpha = args$alpha,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
755 dIFcutoff = args$dIFcutoff,
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
756 showProgress = TRUE
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
757 )
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
758
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
759 consequences <- c(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
760 "intron_retention",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
761 "NMD_status",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
762 "isoform_seq_similarity",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
763 "ORF_genomic",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
764 "tss",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
765 "tts"
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
766 )
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
767
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
768 if (!is.null(args$pathToCPATresultFile) ||
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
769 !is.null(args$pathToCPC2resultFile)) {
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
770 updatedConsequences <- c(consequences, "coding_potential")
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
771 consequences <- updatedConsequences
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
772 }
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
773
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
774 if (!is.null(args$pathToPFAMresultFile)) {
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
775 updatedConsequences <- c(consequences, "domains_identified")
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
776 consequences <- updatedConsequences
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
777 }
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
778
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
779 if (!is.null(args$pathToSignalPresultFile)) {
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
780 updatedConsequences <- c(consequences, "signal_peptide_identified")
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
781 consequences <- updatedConsequences
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
782 }
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
783
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
784 if (!is.null(args$pathToNetSurfP2resultFile) ||
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
785 !is.null(args$pathToIUPred2AresultFile)) {
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
786 updatedConsequences <- c(consequences, "IDR_identified", "IDR_type")
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
787 consequences <- updatedConsequences
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
788 }
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
789
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
790 SwitchList <- analyzeSwitchConsequences(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
791 SwitchList,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
792 consequencesToAnalyze = consequences,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
793 alpha = args$alpha,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
794 dIFcutoff = args$dIFcutoff,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
795 onlySigIsoforms = args$onlySigIsoforms,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
796 ntCutoff = args$ntCutoff,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
797 ntJCsimCutoff = args$ntJCsimCutoff,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
798 AaCutoff = args$AaCutoff,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
799 AaFracCutoff = args$AaFracCutoff,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
800 AaJCsimCutoff = args$AaJCsimCutoff,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
801 removeNonConseqSwitches = args$removeNonConseqSwitches,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
802 showProgress = TRUE
0
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
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
806 ### Visual analysis
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
807 # Top genes
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
808
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
809 if (args$analysisMode == "single") {
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
810 outputFile <- file.path(getwd(), "single_gene.pdf")
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
811
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
812 pdf(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
813 file = outputFile,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
814 onefile = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
815 height = 6,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
816 width = 9
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
817 )
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
818
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
819 switchPlot(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
820 SwitchList,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
821 gene = args$gene,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
822 condition1 = myDesign$condition[1],
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
823 condition2 = myDesign$condition[length(myDesign$condition)],
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
824 IFcutoff = args$IFcutoff,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
825 dIFcutoff = args$dIFcutoff,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
826 rescaleTranscripts = args$rescaleTranscripts,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
827 reverseMinus = args$reverseMinus,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
828 addErrorbars = args$addErrorbars,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
829 logYaxis = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
830 localTheme = theme_bw(base_size = 8)
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
831 )
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
832 dev.off()
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
833 } else {
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
834 mostSwitchingGene <-
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
835 extractTopSwitches(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
836 SwitchList,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
837 n = Inf,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
838 filterForConsequences = args$filterForConsequences,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
839 extractGenes = TRUE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
840 alpha = args$alpha,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
841 dIFcutoff = args$dIFcutoff,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
842 inEachComparison = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
843 sortByQvals = args$sortByQvals
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
844 )
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
845
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
846 write.table(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
847 mostSwitchingGene,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
848 file = "mostSwitchingGene.tsv",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
849 quote = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
850 sep = "\t",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
851 col.names = TRUE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
852 row.names = FALSE
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
853 )
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
854
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
855
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
856 switchPlotTopSwitches(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
857 SwitchList,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
858 alpha = args$alpha,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
859 dIFcutoff = args$dIFcutoff,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
860 onlySigIsoforms = args$onlySigIsoforms,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
861 n = args$genesToPlot,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
862 sortByQvals = args$sortByQvals,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
863 pathToOutput = getwd(),
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
864 fileType = "pdf"
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
865 )
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
866
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
867 outputFile <-
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
868 file.path(getwd(), "extractConsequencesSummary.pdf")
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
869
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
870 pdf(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
871 file = outputFile,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
872 onefile = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
873 height = 6,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
874 width = 12
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
875 )
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
876
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
877 consequenceSummary <- extractConsequenceSummary(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
878 SwitchList,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
879 consequencesToAnalyze = "all",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
880 includeCombined = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
881 asFractionTotal = args$asFractionTotal,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
882 alpha = args$alpha,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
883 dIFcutoff = args$dIFcutoff,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
884 plot = TRUE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
885 plotGenes = args$plotGenes,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
886 simplifyLocation = args$simplifyLocation,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
887 removeEmptyConsequences = args$removeEmptyConsequences,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
888 returnResult = TRUE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
889 localTheme = theme_bw()
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
890 )
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
891 dev.off()
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
892
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
893 write.table(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
894 consequenceSummary,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
895 file = "consequencesSummary.tsv",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
896 quote = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
897 sep = "\t",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
898 col.names = TRUE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
899 row.names = FALSE
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
900 )
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
901
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
902
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
903 outputFile <- file.path(getwd(), "consequencesEnrichment.pdf")
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
904 pdf(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
905 file = outputFile,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
906 onefile = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
907 height = 6,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
908 width = 9
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
909 )
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
910 consequenceEnrichment <- extractConsequenceEnrichment(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
911 SwitchList,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
912 consequencesToAnalyze = "all",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
913 alpha = args$alpha,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
914 dIFcutoff = args$dIFcutoff,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
915 countGenes = args$countGenes,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
916 analysisOppositeConsequence = args$analysisOppositeConsequence,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
917 plot = TRUE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
918 localTheme = theme_bw(base_size = 12),
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
919 minEventsForPlotting = 10,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
920 returnResult = TRUE
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
921 )
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
922 dev.off()
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
923
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
924 write.table(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
925 consequenceEnrichment,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
926 file = "consequencesEnrichment.tsv",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
927 quote = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
928 sep = "\t",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
929 col.names = TRUE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
930 row.names = FALSE
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
931 )
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
932
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
933
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
934 outputFile <- file.path(getwd(), "splicingEnrichment.pdf")
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
935 pdf(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
936 file = outputFile,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
937 onefile = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
938 height = 6,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
939 width = 9
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
940 )
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
941 splicingEnrichment <- extractSplicingEnrichment(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
942 SwitchList,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
943 splicingToAnalyze = "all",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
944 alpha = args$alpha,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
945 dIFcutoff = args$dIFcutoff,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
946 onlySigIsoforms = args$onlySigIsoforms,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
947 countGenes = args$countGenes,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
948 plot = TRUE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
949 minEventsForPlotting = 10,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
950 returnResult = TRUE
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
951 )
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
952 dev.off()
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
953
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
954 write.table(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
955 splicingEnrichment,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
956 file = "splicingEnrichment.tsv",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
957 quote = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
958 sep = "\t",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
959 col.names = TRUE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
960 row.names = FALSE
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
961 )
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
962
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
963
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
964 outputFile <- file.path(getwd(), "splicingSummary.pdf")
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
965 pdf(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
966 file = outputFile,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
967 onefile = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
968 height = 6,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
969 width = 12
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
970 )
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
971 splicingSummary <- extractSplicingSummary(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
972 SwitchList,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
973 splicingToAnalyze = "all",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
974 asFractionTotal = args$asFractionTotal,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
975 alpha = args$alpha,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
976 dIFcutoff = args$dIFcutoff,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
977 onlySigIsoforms = args$onlySigIsoforms,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
978 plot = TRUE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
979 plotGenes = args$plotGenes,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
980 localTheme = theme_bw(),
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
981 returnResult = TRUE
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
982 )
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
983 dev.off()
4
512d6462f2ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 3
diff changeset
984
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
985 write.table(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
986 splicingSummary,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
987 file = "splicingSummary.tsv",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
988 quote = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
989 sep = "\t",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
990 col.names = TRUE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
991 row.names = FALSE
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
992 )
4
512d6462f2ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 3
diff changeset
993
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
994 write.table(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
995 SwitchList$switchConsequence,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
996 file = "switchConsequence_fulldata.tsv",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
997 quote = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
998 sep = "\t",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
999 col.names = TRUE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1000 row.names = FALSE
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1001 )
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1002
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1003 write.table(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1004 SwitchList$AlternativeSplicingAnalysis,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1005 file = "switchSplicing_fulldata.tsv",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1006 quote = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1007 sep = "\t",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1008 col.names = TRUE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1009 row.names = FALSE
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1010 )
1
2c4e879a81cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7d278967f9c8d2c6ce0a8f83be2c444822746bbf
iuc
parents: 0
diff changeset
1011
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1012 write.table(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1013 SwitchList$isoformFeatures,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1014 file = "IsoformFeatures.tsv",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1015 quote = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1016 sep = "\t",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1017 col.names = TRUE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1018 row.names = FALSE
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1019 )
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1020
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1021 ### Volcano like plot:
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1022 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
1023
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1024 pdf(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1025 file = outputFile,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1026 onefile = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1027 height = 6,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1028 width = 9
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1029 )
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1030
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1031 p <- ggplot(data = SwitchList$isoformFeatures, aes(x = dIF, y = -log10(isoform_switch_q_value))) +
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1032 geom_point(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1033 aes(color = abs(dIF) > 0.1 & isoform_switch_q_value < 0.05), # default cutoff
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1034 size = 1
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1035 ) +
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1036 geom_hline(yintercept = -log10(0.05), linetype = "dashed") + # default cutoff
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1037 geom_vline(xintercept = c(-0.1, 0.1), linetype = "dashed") + # default cutoff
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1038 facet_wrap(~condition_2) +
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1039 # facet_grid(condition_1 ~ condition_2) + # alternative to facet_wrap if you have overlapping conditions
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1040 scale_color_manual("Signficant\nIsoform Switch", values = c("black", "red")) +
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1041 labs(x = "dIF", y = "-Log10 ( Isoform Switch Q Value )") +
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1042 theme_bw()
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1043 print(p)
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1044 dev.off()
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1045
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1046 ### Switch vs Gene changes:
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1047 outputFile <- file.path(getwd(), "switchGene.pdf")
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1048 pdf(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1049 file = outputFile,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1050 height = 6,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1051 width = 9
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1052 )
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1053 p <- ggplot(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1054 data = SwitchList$isoformFeatures,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1055 aes(x = gene_log2_fold_change, y = dIF)
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1056 ) +
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1057 geom_point(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1058 aes(color = abs(dIF) > 0.1 &
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1059 isoform_switch_q_value < 0.05),
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1060 size = 1
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1061 ) +
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1062 facet_wrap(~condition_2) +
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1063 geom_hline(yintercept = 0, linetype = "dashed") +
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1064 geom_vline(xintercept = 0, linetype = "dashed") +
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1065 scale_color_manual("Signficant\nIsoform Switch", values = c("black", "red")) +
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1066 labs(x = "Gene log2 fold change", y = "dIF") +
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1067 theme_bw()
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1068 print(p)
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1069 dev.off()
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1070
7
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1071 outputFile <- file.path(getwd(), "splicingGenomewide.pdf")
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1072 pdf(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1073 file = outputFile,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1074 onefile = FALSE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1075 height = 6,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1076 width = 14
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1077 )
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1078 splicingGenomeWide <- extractSplicingGenomeWide(
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1079 SwitchList,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1080 featureToExtract = "isoformUsage",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1081 splicingToAnalyze = "all",
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1082 plot = TRUE,
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1083 returnResult = TRUE
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1084 )
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1085 dev.off()
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1086 }
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1087 save(SwitchList, file = "SwitchList.Rda")
0
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1088 }