Mercurial > repos > iuc > rgcca
annotate launcher.R @ 1:4e73ea176c34 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
author | iuc |
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date | Sun, 18 Jul 2021 18:03:12 +0000 |
parents | 067d45e6caa9 |
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rev | line source |
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1
4e73ea176c34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
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1 #!/usr/bin/env Rscript |
4e73ea176c34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
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2 |
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067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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3 # Author: Etienne CAMENEN |
1
4e73ea176c34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
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4 # Date: 2021 |
4e73ea176c34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
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5 # Contact: etienne.camenen@gmail.com |
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067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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6 # Key-words: omics, RGCCA, multi-block |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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7 # 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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8 # |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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9 # 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
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10 # 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
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11 # plots). |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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12 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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13 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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14 graphics.off() |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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15 separator <- NULL |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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16 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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17 ########## Arguments ########## |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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18 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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19 # 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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20 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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21 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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22 # File parameters |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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23 make_option( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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24 opt_str = c("-d", "--datasets"), |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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25 type = "character", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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26 metavar = "path list", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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27 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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28 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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29 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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30 ), |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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31 make_option( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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32 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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33 type = "character", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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34 metavar = "path", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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35 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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36 [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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37 ), |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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38 make_option( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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39 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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40 type = "character", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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41 metavar = "path", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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42 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"
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43 plot" |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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44 ), |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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45 make_option( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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46 opt_str = c("-r", "--response"), |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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47 type = "integer", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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48 metavar = "integer", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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49 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"
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50 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"
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51 ), |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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52 make_option( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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53 opt_str = "--names", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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54 type = "character", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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55 metavar = "character list", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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56 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"
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57 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"
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58 ), |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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59 make_option( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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60 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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61 type = "logical", |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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62 action = "store_false", |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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63 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"
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64 ), |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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65 make_option( |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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66 opt_str = "--separator", |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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67 type = "integer", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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68 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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69 default = opt[1], |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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70 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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71 2: semicolon, 3: comma) [default: %default]" |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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72 ), |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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73 # Analysis parameter |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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74 make_option( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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75 opt_str = "--type", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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76 type = "character", |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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77 metavar = "character", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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78 default = opt[2], |
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4e73ea176c34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
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79 help = "Type of analysis [default: %default] (among: rgcca, sgcca, |
4e73ea176c34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
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80 pca, spca, pls, spls, cca, ifa, ra, gcca, maxvar, maxvar-b, |
4e73ea176c34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
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81 maxvar-a, mcoa,cpca-1, cpca-2, cpca-4, hpca, maxbet-b, maxbet, |
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82 maxdiff-b, maxdiff, maxvar-a, sabscor, ssqcor, ssqcov-1, ssqcov-2, |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
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0
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83 ssqcov, sumcor, sumcov-1, sumcov-2, sumcov, sabscov, sabscov-1, |
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0
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84 sabscov-2)" |
0
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85 ), |
067d45e6caa9
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86 make_option( |
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87 opt_str = "--ncomp", |
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88 type = "character", |
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89 metavar = "integer list", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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90 default = opt[3], |
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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 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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92 [default: %default]. The number should be higher than 1 and lower |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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93 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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94 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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95 ), |
067d45e6caa9
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96 make_option( |
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97 opt_str = "--penalty", |
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98 type = "character", |
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iuc
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99 metavar = "float list", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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100 default = opt[4], |
067d45e6caa9
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101 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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102 [default: %default]. Tau varies from 0 (maximizing the correlation) |
067d45e6caa9
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103 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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104 set to 1 and shrinkage parameter can be defined instead for |
067d45e6caa9
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105 automatic variable selection, varying from the square root of the |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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106 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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107 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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108 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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109 ), |
067d45e6caa9
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110 make_option( |
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111 opt_str = "--scheme", |
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112 type = "integer", |
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113 metavar = "integer", |
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114 default = opt[5], |
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115 help = "Link (i.e. scheme) function for covariance maximization |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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116 (1: x, 2: x^2, 3: |x|, 4: x^4) [default: %default]. Onnly, the x |
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117 function ('horst scheme') penalizes structural negative correlation. |
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118 The x^2 function ('factorial scheme') discriminates more strongly |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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119 the blocks than the |x| ('centroid scheme') 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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120 ), |
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121 make_option( |
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122 opt_str = "--scale", |
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123 type = "logical", |
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124 action = "store_false", |
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125 help = "DO NOT scale the blocks (i.e., a data centering step is |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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126 always performed). Otherwise, each block is normalised and divided |
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127 by the squareroot of its number of variables." |
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128 ), |
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129 make_option( |
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130 opt_str = "--superblock", |
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131 type = "logical", |
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132 action = "store_false", |
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133 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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134 blocks to visualize them all together in a consensus space). In |
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135 this case, all blocks are assumed to be connected or a connection |
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136 file could be used." |
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137 ), |
067d45e6caa9
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138 # Graphical parameters |
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139 make_option( |
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140 opt_str = "--text", |
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141 type = "logical", |
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142 action = "store_false", |
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143 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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144 plotting" |
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145 ), |
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146 make_option( |
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147 opt_str = "--block", |
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148 type = "integer", |
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149 metavar = "integer", |
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150 default = opt[6], |
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151 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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152 superblock or, if not activated, the last one, 1: the fist one, |
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153 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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154 ), |
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155 make_option( |
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156 opt_str = "--block_y", |
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157 type = "integer", |
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158 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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159 help = "Position in the path list of the plotted block for the |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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160 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"
iuc
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161 activated, the last one, 1: the fist one, 2: the 2nd, etc.) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
162 [default: the last one]" |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
163 ), |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
164 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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|
165 opt_str = "--compx", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
166 type = "integer", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
167 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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|
168 default = opt[7], |
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 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
|
170 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
|
171 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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|
172 ), |
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 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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174 opt_str = "--compy", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
175 type = "integer", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
176 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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177 default = opt[8], |
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 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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|
179 [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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|
180 components of the analysis)" |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
181 ), |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
182 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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183 opt_str = "--nmark", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
184 type = "integer", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
185 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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|
186 default = opt[9], |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
187 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
changeset
|
188 [default: %default]" |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
189 ), |
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 # 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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|
191 make_option( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
192 opt_str = "--o1", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
193 type = "character", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
194 metavar = "path", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
195 default = opt[10], |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
196 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
|
197 ), |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
198 make_option( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
199 opt_str = "--o2", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
200 type = "character", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
201 metavar = "path", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
202 default = opt[11], |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
203 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
|
204 ), |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
205 make_option( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
206 opt_str = "--o3", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
207 type = "character", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
208 metavar = "path", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
209 default = opt[12], |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
210 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
|
211 ), |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
212 make_option( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
213 opt_str = "--o4", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
214 type = "character", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
215 metavar = "path", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
216 default = opt[13], |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
217 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
|
218 ), |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
219 make_option( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
220 opt_str = "--o5", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
221 type = "character", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
222 metavar = "path", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
223 default = opt[14], |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
224 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
|
225 ), |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
226 make_option( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
227 opt_str = "--o6", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
228 type = "character", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
229 metavar = "path", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
230 default = opt[15], |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
231 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
|
232 ), |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
233 make_option( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
234 opt_str = "--o7", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
235 type = "character", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
236 metavar = "path", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
237 default = opt[16], |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
238 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
|
239 ), |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
240 make_option( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
241 opt_str = "--o8", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
242 type = "character", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
243 metavar = "path", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
244 default = opt[17], |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
245 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"
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246 ) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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247 ) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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248 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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249 } |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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250 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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251 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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252 # 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"
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253 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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254 if (is.null(opt$datasets)) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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255 stop_rgcca(paste0("datasets is required."), exit_code = 121) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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256 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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257 if (is.null(opt$scheme)) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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258 opt$scheme <- "factorial" |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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259 else if (!opt$scheme %in% seq(4)) { |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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260 stop_rgcca( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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261 paste0( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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262 "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
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263 opt$scheme, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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264 "." |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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265 ), |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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266 exit_code = 122 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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267 ) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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268 } else { |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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269 schemes <- c("horst", "factorial", "centroid") |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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270 if (opt$scheme == 4) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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271 opt$scheme <- function(x) x ^ 4 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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272 else |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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273 opt$scheme <- schemes[opt$scheme] |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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274 } |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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275 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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276 if (!opt$separator %in% seq(3)) { |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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277 stop_rgcca( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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278 paste0( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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279 "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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280 opt$separator, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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281 "." |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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282 ), |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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283 exit_code = 123 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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284 ) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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285 } else { |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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286 separators <- c("\t", ";", ",") |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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287 opt$separator <- separators[opt$separator] |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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288 } |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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289 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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290 nmark <- NULL |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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291 RGCCA:::check_integer("nmark", opt$nmark, min = 2) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
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292 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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293 for (x in c("ncomp", "penalty")) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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294 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
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295 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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296 return(opt) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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297 } |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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298 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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299 post_check_arg <- function(opt, rgcca) { |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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300 # 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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301 # 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
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302 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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303 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:
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304 if (!is.null(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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305 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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306 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:
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307 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:
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308 } |
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"
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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 if (any(opt$ncomp == 1)) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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312 opt$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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313 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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314 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:
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315 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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316 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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317 return(opt) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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318 } |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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319 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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320 ########## Main ########## |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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321 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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322 # 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:
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323 # arguments |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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324 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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325 separator = 1, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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326 type = "rgcca", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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327 ncomp = 2, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
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328 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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329 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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330 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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331 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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332 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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333 nmark = 100, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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334 o1 = "individuals.pdf", |
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 o2 = "corcircle.pdf", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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336 o3 = "top_variables.pdf", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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337 o4 = "ave.pdf", |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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338 o5 = "design.pdf", |
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 o6 = "individuals.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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340 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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341 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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342 datasets = paste0("inst/extdata/", |
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 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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344 ".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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345 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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346 ) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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347 |
1
4e73ea176c34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents:
0
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348 # Load functions |
4e73ea176c34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents:
0
diff
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349 all_funcs <- unclass(lsf.str(envir = asNamespace("RGCCA"), all = TRUE)) |
4e73ea176c34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents:
0
diff
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|
350 for (i in all_funcs) |
4e73ea176c34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents:
0
diff
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351 eval(parse(text = paste0(i, "<-RGCCA:::", i))) |
4e73ea176c34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents:
0
diff
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|
352 |
4e73ea176c34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents:
0
diff
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|
353 load_libraries(c("ggplot2", "optparse", "scales", "igraph", "MASS", "Deriv")) |
0
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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354 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:
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355 |
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 tryCatch( |
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 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
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|
358 error = function(e) { |
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 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
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|
360 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
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|
361 }, warning = function(w) |
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 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
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|
363 ) |
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 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
365 # 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
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366 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:
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367 opt$superblock <- !("superblock" %in% names(opt)) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
368 opt$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
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|
369 opt$text <- !("text" %in% names(opt)) |
1
4e73ea176c34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents:
0
diff
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|
370 cex_lab <- 20 |
4e73ea176c34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents:
0
diff
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|
371 cex_main <- 25 |
4e73ea176c34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents:
0
diff
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|
372 cex_point <- 3 |
4e73ea176c34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents:
0
diff
changeset
|
373 cex_sub <- 20 |
4e73ea176c34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents:
0
diff
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|
374 cex_axis <- 10 |
4e73ea176c34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents:
0
diff
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|
375 cex <- 1.25 |
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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|
376 |
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 status <- 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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|
378 tryCatch({ |
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 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
380 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
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|
381 group <- load_response(blocks, opt$group, opt$separator, opt$header) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
382 connection <- load_connection(file = opt$connection, separator = opt$separator) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
383 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
384 func <- quote( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
385 rgcca( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
386 blocks = blocks, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
387 connection = connection, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
388 response = opt$response, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
389 superblock = opt$superblock, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
390 ncomp = opt$ncomp, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
391 scheme = opt$scheme, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
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|
392 scale = opt$scale, |
1
4e73ea176c34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents:
0
diff
changeset
|
393 method = opt$type |
0
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
394 ) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
395 ) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
396 if (tolower(opt$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
|
397 func[["sparsity"]] <- opt$penalty |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
398 }else { |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
399 func[["tau"]] <- opt$penalty |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
400 } |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
401 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
402 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
|
403 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
404 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
|
405 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
406 ########## Plot ########## |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
407 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
408 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
|
409 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
|
410 } else { |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
411 ( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
412 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
|
413 rgcca_out, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
414 group, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
415 opt$compx, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
416 opt$compy, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
417 opt$block, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
418 opt$text, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
419 opt$block_y, |
1
4e73ea176c34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents:
0
diff
changeset
|
420 "Response", |
4e73ea176c34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents:
0
diff
changeset
|
421 cex_lab = cex_lab, |
4e73ea176c34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents:
0
diff
changeset
|
422 cex_point = cex_point, |
4e73ea176c34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents:
0
diff
changeset
|
423 cex_main = cex_main, |
4e73ea176c34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents:
0
diff
changeset
|
424 cex = cex |
0
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
425 ) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
426 ) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
427 save_plot(opt$o1, individual_plot) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
428 } |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
429 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
430 if (rgcca_out$call$ncomp[opt$block] > 1) { |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
431 ( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
432 corcircle <- plot_var_2D( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
433 rgcca_out, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
434 opt$compx, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
435 opt$compy, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
436 opt$block, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
437 opt$text, |
1
4e73ea176c34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents:
0
diff
changeset
|
438 n_mark = opt$nmark, |
4e73ea176c34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents:
0
diff
changeset
|
439 cex_lab = cex_lab, |
4e73ea176c34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents:
0
diff
changeset
|
440 cex_point = cex_point, |
4e73ea176c34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents:
0
diff
changeset
|
441 cex_main = cex_main, |
4e73ea176c34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents:
0
diff
changeset
|
442 cex = cex |
0
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 ) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
445 save_plot(opt$o2, corcircle) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
446 } |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
447 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
448 top_variables <- plot_var_1D( |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
449 rgcca_out, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
450 opt$compx, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
451 opt$nmark, |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
452 opt$block, |
1
4e73ea176c34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents:
0
diff
changeset
|
453 type = "loadings", |
4e73ea176c34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents:
0
diff
changeset
|
454 title = paste0("Variable correlations", ": ", names(rgcca_out$call$blocks)[opt$block], " with "), |
4e73ea176c34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents:
0
diff
changeset
|
455 cex_sub = cex_sub, |
4e73ea176c34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents:
0
diff
changeset
|
456 cex_main = cex_main, |
4e73ea176c34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents:
0
diff
changeset
|
457 cex_axis = cex_axis, |
4e73ea176c34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents:
0
diff
changeset
|
458 cex = cex |
0
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
459 ) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
460 save_plot(opt$o3, top_variables) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
461 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
462 # Average Variance Explained |
1
4e73ea176c34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents:
0
diff
changeset
|
463 (ave <- plot_ave( |
4e73ea176c34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents:
0
diff
changeset
|
464 rgcca_out, |
4e73ea176c34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents:
0
diff
changeset
|
465 cex_main = cex_main, |
4e73ea176c34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents:
0
diff
changeset
|
466 cex_sub = cex_sub, |
4e73ea176c34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents:
0
diff
changeset
|
467 cex_axis = cex_axis, |
4e73ea176c34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents:
0
diff
changeset
|
468 cex = cex)) |
0
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
469 save_plot(opt$o4, ave) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
470 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
471 # Creates design scheme |
1
4e73ea176c34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents:
0
diff
changeset
|
472 design <- function() plot_network( |
4e73ea176c34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents:
0
diff
changeset
|
473 rgcca_out, |
4e73ea176c34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents:
0
diff
changeset
|
474 cex_main = cex_main, |
4e73ea176c34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents:
0
diff
changeset
|
475 cex_point = cex_point, |
4e73ea176c34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents:
0
diff
changeset
|
476 cex = cex) |
0
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
477 save_plot(opt$o5, design) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
478 |
1
4e73ea176c34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents:
0
diff
changeset
|
479 save_ind(rgcca_out, opt$o6) |
4e73ea176c34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents:
0
diff
changeset
|
480 save_var(rgcca_out, opt$o7) |
0
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
481 save(rgcca_out, file = opt$o8) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
482 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
483 }, error = function(e) { |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
484 if (class(e)[1] %in% c("simpleError", "error", "condition")) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
485 status <<- 1 |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
486 else |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
487 status <<- class(e)[1] |
1
4e73ea176c34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents:
0
diff
changeset
|
488 msg <- "The design matrix C" |
4e73ea176c34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents:
0
diff
changeset
|
489 if (grepl(msg, e$message)) { |
4e73ea176c34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents:
0
diff
changeset
|
490 e$message <- gsub(msg, "The connection file", e$message) |
4e73ea176c34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents:
0
diff
changeset
|
491 } |
0
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
492 message(e$message) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
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changeset
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493 }) |
067d45e6caa9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff
changeset
|
494 quit(status = status) |