Mercurial > repos > iuc > rgcca
annotate launcher.R @ 0:067d45e6caa9 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
author | iuc |
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date | Tue, 12 Jan 2021 10:12:04 +0000 |
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children | 4e73ea176c34 |
rev | line source |
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0
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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1 # Author: Etienne CAMENEN |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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2 # Date: 2020 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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3 # Contact: arthur.tenenhaus@centralesupelec.fr |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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4 # Key-words: omics, RGCCA, multi-block |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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5 # EDAM operation: analysis, correlation, visualisation |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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6 # |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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7 # Abstract: Performs multi-variate analysis (PCA, CCA, PLS, R/SGCCA, etc.) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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8 # and produces textual and graphical outputs (e.g. variables and individuals |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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9 # plots). |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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10 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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11 rm(list = ls()) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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12 graphics.off() |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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13 separator <- NULL |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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14 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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15 ########## Arguments ########## |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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16 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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17 # Parse the arguments from a command line launch |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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18 get_args <- function() { |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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19 option_list <- list( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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20 # File parameters |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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21 make_option( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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22 opt_str = c("-d", "--datasets"), |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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23 type = "character", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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24 metavar = "path list", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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25 help = "List of comma-separated file paths corresponding to the |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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26 blocks to be analyzed (one per block and without spaces between |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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27 them; e.g., path/file1.txt,path/file2.txt) [required]" |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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28 ), |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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29 make_option( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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30 opt_str = c("-c", "--connection"), |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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31 type = "character", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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32 metavar = "path", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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33 help = "Path of the file defining the connections between the blocks |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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34 [if not used, activates the superblock mode]" |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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35 ), |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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36 make_option( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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37 opt_str = "--group", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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38 type = "character", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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39 metavar = "path", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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40 help = "Path of the file coloring the individuals in the ad hoc |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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41 plot" |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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42 ), |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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43 make_option( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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44 opt_str = c("-r", "--response"), |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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45 type = "integer", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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46 metavar = "integer", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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47 help = "Position of the response file for the supervised mode within |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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48 the block path list [actives the supervised mode]" |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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49 ), |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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50 make_option( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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51 opt_str = "--names", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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52 type = "character", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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53 metavar = "character list", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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54 help = "List of comma-separated block names to rename them (one per |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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55 block; without spaces between them) [default: the block file names]" |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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56 ), |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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57 make_option( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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58 opt_str = c("-H", "--header"), |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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59 type = "logical", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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60 action = "store_false", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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61 help = "DO NOT consider the first row as the column header" |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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62 ), |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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63 make_option( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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64 opt_str = "--separator", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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65 type = "integer", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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66 metavar = "integer", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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67 default = opt[1], |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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68 help = "Character used to separate columns (1: tabulation, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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69 2: semicolon, 3: comma) [default: %default]" |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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70 ), |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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71 # Analysis parameter |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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72 make_option( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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73 opt_str = "--type", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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74 type = "character", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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75 metavar = "character", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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76 default = opt[2], |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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77 help = "Type of analysis [default: %default] (among: rgcca, pca, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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78 cca, gcca, cpca-w, hpca, maxbet-b, maxbet, maxdiff-b, maxdiff, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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79 maxvar-a, maxvar-b, maxvar, niles, r-maxvar, rcon-pca, ridge-gca, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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80 sabscor, ssqcor, ssqcor, ssqcov-1, ssqcov-2, ssqcov, sum-pca, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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81 sumcor, sumcov-1, sumcov-2, sumcov)" |
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82 ), |
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83 make_option( |
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84 opt_str = "--ncomp", |
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85 type = "character", |
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86 metavar = "integer list", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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87 default = opt[3], |
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88 help = "Number of components in the analysis for each block |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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89 [default: %default]. The number should be higher than 1 and lower |
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90 than the minimum number of variables among the blocks. It can be a |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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91 single values or a comma-separated list (e.g 2,2,3,2)." |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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92 ), |
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93 make_option( |
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94 opt_str = "--penalty", |
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95 type = "character", |
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96 metavar = "float list", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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97 default = opt[4], |
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98 help = "For RGCCA, a regularization parameter for each block (i.e., tau) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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99 [default: %default]. Tau varies from 0 (maximizing the correlation) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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100 to 1 (maximizing the covariance). For SGCCA, tau is automatically |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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101 set to 1 and shrinkage parameter can be defined instead for |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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102 automatic variable selection, varying from the square root of the |
067d45e6caa9
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103 variable number (the fewest selected variables) to 1 (all the |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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104 variables are included). It can be a single value or a |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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105 comma-separated list (e.g. 0,1,0.75,1)." |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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106 ), |
067d45e6caa9
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107 make_option( |
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108 opt_str = "--scheme", |
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109 type = "integer", |
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110 metavar = "integer", |
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111 default = opt[5], |
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112 help = "Link (i.e. scheme) function for covariance maximization |
067d45e6caa9
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113 (1: x, 2: x^2, 3: |x|, 4: x^4) [default: %default]. Onnly, the x |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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114 function ('horst scheme') penalizes structural negative correlation. |
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115 The x^2 function ('factorial scheme') discriminates more strongly |
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116 the blocks than the |x| ('centroid scheme') one." |
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117 ), |
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118 make_option( |
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119 opt_str = "--scale", |
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120 type = "logical", |
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121 action = "store_false", |
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122 help = "DO NOT scale the blocks (i.e., a data centering step is |
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123 always performed). Otherwise, each block is normalised and divided |
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124 by the squareroot of its number of variables." |
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125 ), |
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126 make_option( |
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127 opt_str = "--superblock", |
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128 type = "logical", |
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129 action = "store_false", |
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130 help = "DO NOT use a superblock (i.e. a concatenation of all the |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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131 blocks to visualize them all together in a consensus space). In |
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132 this case, all blocks are assumed to be connected or a connection |
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133 file could be used." |
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134 ), |
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135 # Graphical parameters |
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136 make_option( |
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137 opt_str = "--text", |
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138 type = "logical", |
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139 action = "store_false", |
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140 help = "DO NOT display the name of the points instead of shapes when |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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141 plotting" |
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142 ), |
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143 make_option( |
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144 opt_str = "--block", |
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145 type = "integer", |
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146 metavar = "integer", |
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147 default = opt[6], |
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148 help = "Position in the path list of the plotted block (0: the |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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149 superblock or, if not activated, the last one, 1: the fist one, |
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150 2: the 2nd, etc.)[default: the last one]" |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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151 ), |
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152 make_option( |
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153 opt_str = "--block_y", |
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154 type = "integer", |
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155 metavar = "integer", |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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156 help = "Position in the path list of the plotted block for the |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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157 Y-axis in the individual plot (0: the superblock or, if not |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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158 activated, the last one, 1: the fist one, 2: the 2nd, etc.) |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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159 [default: the last one]" |
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160 ), |
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161 make_option( |
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162 opt_str = "--compx", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
163 type = "integer", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
164 metavar = "integer", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
165 default = opt[7], |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
166 help = "Component used in the X-axis for biplots and the only |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
167 component used for histograms [default: %default] (should not be |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
168 higher than the number of components of the analysis)" |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
169 ), |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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170 make_option( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
171 opt_str = "--compy", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
172 type = "integer", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
173 metavar = "integer", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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174 default = opt[8], |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
175 help = "Component used in the Y-axis for biplots |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
176 [default: %default] (should not be higher than the number of |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
177 components of the analysis)" |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
178 ), |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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179 make_option( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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180 opt_str = "--nmark", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
181 type = "integer", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
182 metavar = "integer", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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183 default = opt[9], |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
184 help = "Number maximum of top variables in ad hoc plot |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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185 [default: %default]" |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
186 ), |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
187 # output parameters |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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188 make_option( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
189 opt_str = "--o1", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
190 type = "character", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
191 metavar = "path", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
192 default = opt[10], |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
193 help = "Path for the individual plot [default: %default]" |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
194 ), |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
195 make_option( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
196 opt_str = "--o2", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
197 type = "character", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
198 metavar = "path", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
199 default = opt[11], |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
200 help = "Path for the variable plot [default: %default]" |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
201 ), |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
202 make_option( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
203 opt_str = "--o3", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
204 type = "character", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
205 metavar = "path", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
206 default = opt[12], |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
207 help = "Path for the top variables plot [default: %default]" |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
208 ), |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
209 make_option( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
210 opt_str = "--o4", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
211 type = "character", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
212 metavar = "path", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
213 default = opt[13], |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
214 help = "Path for the explained variance plot [default: %default]" |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
215 ), |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
216 make_option( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
217 opt_str = "--o5", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
218 type = "character", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
219 metavar = "path", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
220 default = opt[14], |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
221 help = "Path for the design plot [default: %default]" |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
222 ), |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
223 make_option( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
224 opt_str = "--o6", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
225 type = "character", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
226 metavar = "path", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
227 default = opt[15], |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
228 help = "Path for the individual table [default: %default]" |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
229 ), |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
230 make_option( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
231 opt_str = "--o7", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
232 type = "character", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
233 metavar = "path", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
234 default = opt[16], |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
235 help = "Path for the variable table [default: %default]" |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
236 ), |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
237 make_option( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
238 opt_str = "--o8", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
239 type = "character", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
240 metavar = "path", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
241 default = opt[17], |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
242 help = "Path for the analysis results in RData [default: %default]" |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
243 ) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
244 ) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
245 return(optparse::OptionParser(option_list = option_list)) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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246 } |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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247 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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248 char_to_list <- function(x) { |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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249 strsplit(gsub(" ", "", as.character(x)), ",")[[1]] |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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250 } |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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251 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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252 check_arg <- function(opt) { |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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253 # Check the validity of the arguments opt : an optionParser object |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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254 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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255 if (is.null(opt$datasets)) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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256 stop_rgcca(paste0("datasets is required."), exit_code = 121) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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257 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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258 if (is.null(opt$scheme)) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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259 opt$scheme <- "factorial" |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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260 else if (!opt$scheme %in% seq(4)) { |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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261 stop_rgcca( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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262 paste0( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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263 "scheme should be comprise between 1 and 4 [by default: 2], not be equal to ", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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264 opt$scheme, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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265 "." |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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266 ), |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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267 exit_code = 122 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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268 ) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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269 } else { |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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270 schemes <- c("horst", "factorial", "centroid") |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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271 if (opt$scheme == 4) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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272 opt$scheme <- function(x) x ^ 4 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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273 else |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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274 opt$scheme <- schemes[opt$scheme] |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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275 } |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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276 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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277 if (!opt$separator %in% seq(3)) { |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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278 stop_rgcca( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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279 paste0( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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280 "separator should be comprise between 1 and 3 (1: Tabulation, 2: Semicolon, 3: Comma) [by default: 2], not be equal to ", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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281 opt$separator, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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282 "." |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
283 ), |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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284 exit_code = 123 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
285 ) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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286 } else { |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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287 separators <- c("\t", ";", ",") |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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288 opt$separator <- separators[opt$separator] |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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289 } |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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290 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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291 nmark <- NULL |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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292 RGCCA:::check_integer("nmark", opt$nmark, min = 2) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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293 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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294 for (x in c("ncomp", "penalty")) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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295 opt[[x]] <- char_to_list(opt[[x]]) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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296 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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297 return(opt) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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298 } |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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299 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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300 post_check_arg <- function(opt, rgcca) { |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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301 # Check the validity of the arguments after loading the blocks opt : an |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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302 # optionParser object blocks : a list of matrix |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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303 blocks <- NULL |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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304 for (x in c("block", "block_y")) { |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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305 if (!is.null(opt[[x]])) { |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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306 if (opt[[x]] == 0) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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307 opt[[x]] <- length(rgcca$call$blocks) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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308 opt[[x]] <- RGCCA:::check_blockx(x, opt[[x]], rgcca$call$blocks) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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309 } |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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310 } |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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311 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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312 if (any(opt$ncomp == 1)) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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313 opt$compy <- 1 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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314 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
315 for (x in c("compx", "compy")) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
316 opt[[x]] <- check_compx(x, opt[[x]], rgcca$call$ncomp, opt$block) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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317 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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318 return(opt) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
319 } |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
320 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
321 check_integer <- function(x, y = x, type = "scalar", float = FALSE, min = 1) { |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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322 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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|
323 if (is.null(y)) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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324 y <- x |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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325 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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|
326 if (type %in% c("matrix", "data.frame")) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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327 y_temp <- y |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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|
328 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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329 y <- suppressWarnings(as.double(as.matrix(y))) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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330 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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331 if (any(is.na(y))) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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332 stop_rgcca(paste(x, "should not be NA.")) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
333 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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334 if (!is(y, "numeric")) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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335 stop_rgcca(paste(x, "should be numeric.")) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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|
336 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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337 if (type == "scalar" && length(y) != 1) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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338 stop_rgcca(paste(x, "should be of length 1.")) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
339 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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340 if (!float) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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341 y <- as.integer(y) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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342 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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343 if (all(y < min)) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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344 stop_rgcca(paste0(x, " should be higher than or equal to ", min, ".")) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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345 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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346 if (type %in% c("matrix", "data.frame")) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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347 y <- matrix( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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348 y, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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349 dim(y_temp)[1], |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
350 dim(y_temp)[2], |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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351 dimnames = dimnames(y_temp) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
352 ) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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353 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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354 if (type == "data.frame") |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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355 as.data.frame(y) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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356 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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357 return(y) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
358 } |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
359 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
360 load_libraries <- function(librairies) { |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
361 for (l in librairies) { |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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362 if (!(l %in% installed.packages()[, "Package"])) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
363 utils::install.packages(l, repos = "cran.us.r-project.org") |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
364 suppressPackageStartupMessages( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
365 library( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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366 l, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
367 character.only = TRUE, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
368 warn.conflicts = FALSE, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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369 quietly = TRUE |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
370 )) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
371 } |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
372 } |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
373 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
374 stop_rgcca <- function( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
375 message, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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376 exit_code = "1", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
377 call = NULL) { |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
378 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
379 base::stop( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
380 structure( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
381 class = c(exit_code, "simpleError", "error", "condition"), |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
382 list(message = message, call. = NULL) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
383 )) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
384 } |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
385 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
386 ########## Main ########## |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
387 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
388 # Get arguments : R packaging install, need an opt variable with associated |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
389 # arguments |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
390 opt <- list( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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391 separator = 1, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
392 type = "rgcca", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
393 ncomp = 2, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
394 penalty = 1, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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395 scheme = 2, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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396 block = 0, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
397 compx = 1, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
398 compy = 2, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
399 nmark = 100, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
400 o1 = "individuals.pdf", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
401 o2 = "corcircle.pdf", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
402 o3 = "top_variables.pdf", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
403 o4 = "ave.pdf", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
404 o5 = "design.pdf", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
405 o6 = "individuals.tsv", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
406 o7 = "variables.tsv", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
407 o8 = "rgcca_result.RData", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
408 datasets = paste0("inst/extdata/", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
409 c("agriculture", "industry", "politic"), |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
410 ".tsv", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
411 collapse = ",") |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
412 ) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
413 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
414 load_libraries(c("ggplot2", "optparse", "scales", "igraph", "MASS", "rlang", "Deriv")) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
415 try(load_libraries("ggrepel"), silent = TRUE) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
416 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
417 tryCatch( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
418 opt <- check_arg(optparse::parse_args(get_args())), |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
419 error = function(e) { |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
420 if (length(grep("nextArg", e[[1]])) != 1) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
421 stop_rgcca(e[[1]], exit_code = 140) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
422 }, warning = function(w) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
423 stop_rgcca(w[[1]], exit_code = 141) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
424 ) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
425 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
426 # Load functions |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
427 all_funcs <- unclass(lsf.str(envir = asNamespace("RGCCA"), all = T)) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
428 for (i in all_funcs) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
429 eval(parse(text = paste0(i, "<-RGCCA:::", i))) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
430 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
431 # Set missing parameters by default |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
432 opt$header <- !("header" %in% names(opt)) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
433 opt$superblock <- !("superblock" %in% names(opt)) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
434 opt$scale <- !("scale" %in% names(opt)) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
435 opt$text <- !("text" %in% names(opt)) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
436 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
437 status <- 0 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
438 tryCatch({ |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
439 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
440 blocks <- load_blocks(opt$datasets, opt$names, opt$separator) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
441 group <- load_response(blocks, opt$group, opt$separator, opt$header) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
442 connection <- load_connection(file = opt$connection, separator = opt$separator) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
443 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
444 func <- quote( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
445 rgcca( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
446 blocks = blocks, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
447 connection = connection, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
448 response = opt$response, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
449 superblock = opt$superblock, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
450 ncomp = opt$ncomp, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
451 scheme = opt$scheme, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
452 scale = opt$scale, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
453 type = opt$type |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
454 ) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
455 ) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
456 if (tolower(opt$type) %in% c("sgcca", "spca", "spls")) { |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
457 func[["sparsity"]] <- opt$penalty |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
458 }else { |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
459 func[["tau"]] <- opt$penalty |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
460 } |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
461 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
462 rgcca_out <- eval(as.call(func)) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
463 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
464 opt <- post_check_arg(opt, rgcca_out) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
465 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
466 ########## Plot ########## |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
467 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
468 if (rgcca_out$call$ncomp[opt$block] == 1 && is.null(opt$block_y)) { |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
469 warning("With a number of component of 1, a second block should be chosen to perform an individual plot") |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
470 } else { |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
471 ( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
472 individual_plot <- plot_ind( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
473 rgcca_out, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
474 group, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
475 opt$compx, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
476 opt$compy, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
477 opt$block, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
478 opt$text, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
479 opt$block_y, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
480 "Response" |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
481 ) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
482 ) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
483 save_plot(opt$o1, individual_plot) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
484 } |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
485 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
486 if (rgcca_out$call$ncomp[opt$block] > 1) { |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
487 ( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
488 corcircle <- plot_var_2D( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
489 rgcca_out, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
490 opt$compx, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
491 opt$compy, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
492 opt$block, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
493 opt$text, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
494 n_mark = opt$nmark |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
495 ) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
496 ) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
497 save_plot(opt$o2, corcircle) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
498 } |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
499 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
500 top_variables <- plot_var_1D( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
501 rgcca_out, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
502 opt$compx, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
503 opt$nmark, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
504 opt$block, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
505 type = "cor" |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
506 ) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
507 save_plot(opt$o3, top_variables) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
508 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
509 # Average Variance Explained |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
510 (ave <- plot_ave(rgcca_out)) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
511 save_plot(opt$o4, ave) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
512 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
513 # Creates design scheme |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
514 design <- function() plot_network(rgcca_out) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
515 save_plot(opt$o5, design) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
516 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
517 save_ind(rgcca_out, opt$compx, opt$compy, opt$o6) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
518 save_var(rgcca_out, opt$compx, opt$compy, opt$o7) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
519 save(rgcca_out, file = opt$o8) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
520 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
521 }, error = function(e) { |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
522 if (class(e)[1] %in% c("simpleError", "error", "condition")) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
523 status <<- 1 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
524 else |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
525 status <<- class(e)[1] |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
526 message(e$message) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
527 }) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
528 quit(status = status) |