Mercurial > repos > devteam > cummerbund
annotate test-data/dispersion.txt @ 0:e462121e8269 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
author | devteam |
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date | Mon, 09 Nov 2015 11:27:38 -0500 |
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children | aefbcaf15a94 |
rev | line source |
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0
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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1 |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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2 R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet" |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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3 Copyright (C) 2014 The R Foundation for Statistical Computing |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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4 Platform: x86_64-unknown-linux-gnu (64-bit) |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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5 |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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6 R is free software and comes with ABSOLUTELY NO WARRANTY. |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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7 You are welcome to redistribute it under certain conditions. |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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8 Type 'license()' or 'licence()' for distribution details. |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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9 |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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10 Natural language support but running in an English locale |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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11 |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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12 R is a collaborative project with many contributors. |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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13 Type 'contributors()' for more information and |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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14 'citation()' on how to cite R or R packages in publications. |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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15 |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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16 Type 'demo()' for some demos, 'help()' for on-line help, or |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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17 'help.start()' for an HTML browser interface to help. |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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18 Type 'q()' to quit R. |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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19 |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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20 > ## Feature Selection ## |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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21 > get_features <- function(myGenes, f="gene") { |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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22 + if (f == "isoforms") |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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23 + return(isoforms(myGenes)) |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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24 + else if (f == "tss") |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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25 + return(TSS(myGenes)) |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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26 + else if (f == "cds") |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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27 + return(CDS(myGenes)) |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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28 + else |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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29 + return(myGenes) |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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30 + } |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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31 > |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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32 > ## Main Function ## |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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33 > |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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34 > library(argparse) |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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35 Loading required package: proto |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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36 > |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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37 > parser <- ArgumentParser(description='Create a plot with cummeRbund') |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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38 > |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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39 > parser$add_argument('--type', dest='plotType', default='Density', required=TRUE) |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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40 > parser$add_argument('--height', dest='height', type='integer', default=960, required=TRUE) |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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41 > parser$add_argument('--width', dest='width', type='integer', default=1280, required=TRUE) |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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42 > parser$add_argument('--outfile', dest='filename', default="plot-unknown-0.png", required=TRUE) |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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43 > parser$add_argument('--input', dest='input_database', default="cuffData.db", required=TRUE) |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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44 > parser$add_argument('--smooth', dest='smooth', action="store_true", default=FALSE) |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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45 > parser$add_argument('--gene_selector', dest='gene_selector', action="store_true", default=FALSE) |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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46 > parser$add_argument('--replicates', dest='replicates', action="store_true", default=FALSE) |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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47 > parser$add_argument('--labcol', dest='labcol', action="store_true", default=FALSE) |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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48 > parser$add_argument('--labrow', dest='labrow', action="store_true", default=FALSE) |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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49 > parser$add_argument('--border', dest='border', action="store_true", default=FALSE) |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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50 > parser$add_argument('--summary', dest='summary', action="store_true", default=FALSE) |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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51 > parser$add_argument('--count', dest='count', action="store_true", default=FALSE) |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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52 > parser$add_argument('--error_bars', dest='error_bars', action="store_true", default=FALSE) |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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53 > parser$add_argument('--log10', dest='log10', action="store_true", default=FALSE) |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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54 > parser$add_argument('--features', dest='features', action="store", default="genes") |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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55 > parser$add_argument('--clustering', dest='clustering', action="store", default="both") |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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56 > parser$add_argument('--iter_max', dest='iter_max', action="store") |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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57 > parser$add_argument('--genes', dest='genes', action="append") |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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58 > parser$add_argument('--k', dest='k', action="store") |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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59 > parser$add_argument('--x', dest='x', action="store") |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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60 > parser$add_argument('--y', dest='y', action="store") |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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61 > |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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62 > args <- parser$parse_args() |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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63 > |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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64 > print(args) |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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65 $border |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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66 [1] FALSE |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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67 |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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68 $clustering |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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69 [1] "both" |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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70 |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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71 $count |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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72 [1] FALSE |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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73 |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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74 $error_bars |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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75 [1] FALSE |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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76 |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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77 $features |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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78 [1] "genes" |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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79 |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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80 $filename |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
81 [1] "plot-dispersion-0.png" |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
82 |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
83 $gene_selector |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
84 [1] FALSE |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
85 |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
86 $genes |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
87 NULL |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
88 |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
89 $height |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
90 [1] 960 |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
91 |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
92 $input_database |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
93 [1] "/tmp/tmp3exXG8/tmpuNktUy/database/files/000/dataset_25.dat" |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
94 |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
95 $iter_max |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
96 NULL |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
97 |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
98 $k |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
99 NULL |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
100 |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
101 $labcol |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
102 [1] FALSE |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
103 |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
104 $labrow |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
105 [1] FALSE |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
106 |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
107 $log10 |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
108 [1] FALSE |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
109 |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
110 $plotType |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
111 [1] "dispersion" |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
112 |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
113 $replicates |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
114 [1] FALSE |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
115 |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
116 $smooth |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
117 [1] FALSE |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
118 |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
119 $summary |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
120 [1] FALSE |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
121 |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
122 $width |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
123 [1] 1280 |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
124 |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
125 $x |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
126 NULL |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
127 |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
128 $y |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
129 NULL |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
130 |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
131 > |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
132 > #q() |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
133 > |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
134 > ## Load cummeRbund library |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
135 > library("cummeRbund") |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
136 Loading required package: BiocGenerics |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
137 Loading required package: parallel |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
138 |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
139 Attaching package: ‘BiocGenerics’ |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
140 |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
141 The following objects are masked from ‘package:parallel’: |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
142 |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
143 clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
144 clusterExport, clusterMap, parApply, parCapply, parLapply, |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
145 parLapplyLB, parRapply, parSapply, parSapplyLB |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
146 |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
147 The following object is masked from ‘package:stats’: |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
148 |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
149 xtabs |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
150 |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
151 The following objects are masked from ‘package:base’: |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
152 |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
153 anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
154 do.call, duplicated, eval, evalq, Filter, Find, get, intersect, |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
155 is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
156 pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
157 rownames, sapply, setdiff, sort, table, tapply, union, unique, |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
158 unlist, unsplit |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
159 |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
160 Loading required package: RSQLite |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
161 Loading required package: DBI |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
162 Loading required package: ggplot2 |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
163 Loading required package: reshape2 |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
164 Loading required package: fastcluster |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
165 |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
166 Attaching package: ‘fastcluster’ |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
167 |
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168 The following object is masked from ‘package:stats’: |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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169 |
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170 hclust |
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171 |
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172 Loading required package: rtracklayer |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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173 Loading required package: GenomicRanges |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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174 Loading required package: S4Vectors |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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175 Loading required package: stats4 |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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176 Loading required package: IRanges |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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177 Loading required package: GenomeInfoDb |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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178 Loading required package: Gviz |
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179 Loading required package: grid |
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180 |
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181 Attaching package: ‘cummeRbund’ |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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182 |
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183 The following object is masked from ‘package:GenomicRanges’: |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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184 |
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185 promoters |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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186 |
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187 The following object is masked from ‘package:IRanges’: |
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188 |
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189 promoters |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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190 |
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191 The following object is masked from ‘package:BiocGenerics’: |
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192 |
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193 conditions |
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194 |
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195 > |
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196 > ## Initialize cuff object |
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197 > cuff <- readCufflinks(dir = "", dbFile = args$input_database, rebuild = FALSE) |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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198 > |
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199 > ## Print out info |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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200 > print(cuff) |
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201 CuffSet instance with: |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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202 2 samples |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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203 87 genes |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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204 90 isoforms |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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205 88 TSS |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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206 0 CDS |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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207 87 promoters |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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208 88 splicing |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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209 0 relCDS |
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210 > sink("cuffdb_info.txt") |
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211 > print(cuff) |
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212 > print("SAMPLES:") |
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213 > samples(cuff) |
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214 > print("REPLICATES:") |
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215 > replicates(cuff) |
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216 > print("FEATURES:") |
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217 > print(annotation(genes(cuff))) |
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218 > cat(annotation(genes(cuff))[[1]],sep=",") |
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219 > sink() |
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220 > |
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221 > png(filename = args$filename, width = args$width, height = args$height, type=c('cairo-png')) |
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222 > tryCatch({ |
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223 + if (args$plotType == 'density') { |
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224 + csDensity(genes(cuff), replicates=args$replicates, logMode=args$log10) |
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225 + } |
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226 + else if (args$plotType == 'boxplot') { |
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227 + csBoxplot(genes(cuff), replicates=args$replicates, logMode=args$log10) |
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228 + } |
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229 + else if (args$plotType == 'mds') { |
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230 + MDSplot(genes(cuff), replicates=args$replicates) |
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231 + } |
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232 + else if (args$plotType == 'pca') { |
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233 + PCAplot(genes(cuff), "PC1", "PC2", replicates=args$replicates) |
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234 + } |
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235 + else if (args$plotType == 'dendrogram') { |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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236 + csDendro(genes(cuff), replicates=args$replicates) |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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237 + } |
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238 + else if (args$plotType == 'scatter') { |
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239 + if (args$gene_selector) { |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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240 + myGenes <- getGenes(cuff, args$genes) |
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241 + csScatter(get_features(myGenes, args$features), args$x, args$y, smooth=args$smooth, logMode=args$log10) |
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242 + } |
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243 + else { |
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244 + csScatter(genes(cuff), args$x, args$y, smooth=args$smooth, logMode=args$log10) |
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245 + } |
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246 + } |
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247 + else if (args$plotType == 'volcano') { |
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248 + if (args$gene_selector) { |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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249 + myGenes <- get_features(getGenes(cuff, args$genes), args$features) |
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250 + } |
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251 + else { |
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252 + myGenes <- genes(cuff) |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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253 + } |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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254 + csVolcano(myGenes, args$x, args$y) |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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255 + } |
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256 + else if (args$plotType == 'heatmap') { |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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257 + if (args$gene_selector) { |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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258 + myGenes <- getGenes(cuff, args$genes) |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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259 + } |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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260 + else { |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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261 + myGenes <- getGenes(cuff,annotation(genes(cuff))[[1]]) |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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262 + } |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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263 + csHeatmap(get_features(myGenes, args$features), clustering=args$clustering, labCol=args$labcol, labRow=args$labrow, border=args$border, logMode=args$log10) |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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264 + } |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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265 + else if (args$plotType == 'cluster') { |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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266 + myGenes <- getGenes(cuff, args$genes) |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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267 + csCluster(get_features(myGenes, args$features), k=args$k) |
e462121e8269
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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268 + } |
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269 + else if (args$plotType == 'dispersion') { |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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270 + dispersionPlot(genes(cuff)) |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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271 + } |
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272 + else if (args$plotType == 'fpkmSCV') { |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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273 + fpkmSCVPlot(genes(cuff)) |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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274 + } |
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275 + else if (args$plotType == 'scatterMatrix') { |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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276 + csScatterMatrix(genes(cuff)) |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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277 + } |
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278 + else if (args$plotType == 'expressionplot') { |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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279 + myGenes <- getGenes(cuff, args$genes) |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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280 + expressionPlot(get_features(myGenes, args$features), drawSummary=args$summary, showErrorbars=args$error_bars, replicates=args$replicates) |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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281 + } |
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282 + else if (args$plotType == 'expressionbarplot') { |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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283 + myGeneId <- args$genes |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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284 + myGenes <- getGenes(cuff, myGeneId) |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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285 + expressionBarplot(get_features(myGenes, args$features), showErrorbars=args$error_bars, replicates=args$replicates) |
e462121e8269
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286 + } |
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287 + else if (args$plotType == 'mds') { |
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288 + MDSplot(genes(cuff),replicates=args$replicates) |
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289 + } |
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290 + else if (args$plotType == 'pca') { |
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291 + PCAplot(genes(cuff),"PC1","PC2", replicates=args$replicates) |
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292 + } |
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293 + else if (args$plotType == 'maplot') { |
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294 + MAplot(genes(cuff), args$x, args$y, useCount=args$count) |
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295 + } |
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296 + else if (args$plotType == 'genetrack') { |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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297 + myGene <- getGene(cuff, args$genes) |
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298 + plotTracks(makeGeneRegionTrack(myGene)) |
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299 + } |
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300 + },error = function(e) { |
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301 + write(paste("Failed:", e, sep=" "), stderr()) |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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302 + q("no", 1, TRUE) |
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303 + }) |
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304 Fontconfig error: Cannot load default config file |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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305 > devname = dev.off() |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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306 > |
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307 > #end for |
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308 > |