Mercurial > repos > blankenberglab > gpca

annotate r-gpca.R @ 0:ed24bacaa4d0 draft

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planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
author blankenberglab
date Mon, 19 Nov 2018 10:15:19 -0500
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children d93629e79f5e
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0
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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diff changeset
1 #!/usr/bin/env Rscript
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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2 library(optparse)
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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3 library(gPCA)
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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4
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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5
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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6 # parse options
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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7 option_list = list(
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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8 make_option(
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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9 c("--version"),
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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10 action = "store_true",
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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11 default = FALSE,
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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12 help = "Print version and exit"
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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13 ),
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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14 make_option(
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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15 c("-i", "--batch"),
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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16 action = "store",
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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17 default = NA,
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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18 type = 'character',
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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19 help = "Input batch"
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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20 ),
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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21 make_option(
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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22 c("-d", "--data"),
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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23 action = "store",
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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24 default = NA,
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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25 type = 'character',
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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26 help = "Input data"
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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27 ),
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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28 make_option(
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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29 c("-n", "--nperm"),
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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30 action = "store",
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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31 default = 1000,
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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32 type = 'numeric',
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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33 help = "Number of permutations to preform"
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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34 ),
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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35 make_option(
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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36 c("-c", "--center"),
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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37 action = "store_true",
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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38 default = FALSE,
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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39 help = "Is the input batch and data centered [default %default]"
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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40 ),
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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41 make_option(
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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42 c("-y", "--scaleY"),
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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43 action = "store_true",
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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44 default = FALSE,
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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45 help = "Scale to Y axis"
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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46 ),
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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47 make_option(
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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48 c("-f", "--filt"),
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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49 action = "store",
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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50 default = NULL,
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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51 type = 'numeric',
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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52 help = "Retain features"
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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53 ),
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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54 make_option(
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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55 c( "--npcs"),
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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56 action = "store",
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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57 default = 3,
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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58 type = 'numeric',
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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59 help = "Number of principal components to plot"
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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60 ),
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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61 make_option(
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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62 c("-p", "--path"),
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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63 action = "store",
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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64 default = '$html_outfile.extra_files_path',
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blankenberglab
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65 type = 'character',
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blankenberglab
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66 help = "File path"
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blankenberglab
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67 ),
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blankenberglab
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68 make_option(
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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69 c("-s", "--seed"),
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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70 action = "store",
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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71 default = NULL,
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blankenberglab
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72 type = 'numeric',
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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73 help = "Set a seed number"
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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74 ),
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blankenberglab
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75 make_option(
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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76 c("-x", "--numbers_outfile"),
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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77 action = "store",
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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78 default = NA,
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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79 type = 'character',
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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80 help = "Numbers output"
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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81 ),
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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82 make_option(
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83 c("-o", "--html_outfile"),
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84 action = "store",
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85 default = NA,
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86 type = 'character',
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87 help = "Output",
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88 )
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89 )
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90
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91 opt <-parse_args(OptionParser(option_list = option_list))
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92
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93 if (opt$version){
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94 # print version and exit
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95 cat(paste("gPCA version", toString(packageVersion("gPCA"))), "\n")
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96 quit()
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97 }
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98
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99 # Check parameter values
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100
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101 if ( ! file.exists(opt$batch)){
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102 stop((paste('File for batch', opt$batch, 'does not exist')))
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103 }
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104 if ( ! file.exists(opt$data)){
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105 stop((paste('File for data', opt$data, 'does not exist')))
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106 }
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107
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108 batch<-as.numeric(factor(as.matrix(read.delim(opt$batch, header=TRUE, row.names=1, sep="\t"))))
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109
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110 data<-t(as.matrix(read.delim(opt$data, row.names=1, header=TRUE, sep="\t")))
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111
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112 out<-gPCA.batchdetect(x=data, batch=batch, center=opt$center, scaleY=opt$scaleY, nperm=opt$nperm, filt=opt$filt, seed=opt$seed)
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113
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114 out$varPCg1<-((out$varPCg1-out$varPCu1)/out$varPCg1)*100
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115
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116 dir.create(opt$path);
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117
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118 write.table(data.frame(out$delta, out$p.val, out$varPCg1),file=opt$numbers_outfile, sep="\t", row.name=FALSE, quote=FALSE)
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119
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120 # General Distribution
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121 par(mai=c(0.8,0.8,0.1,0.1),cex=0.8)
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122 png(paste(opt$path,'/gDist.png', sep=""), width=1020, height=800, units='px')
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123 gDist(out)
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124 invisible(dev.off())
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125
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126
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127 # Guided/Unguided 1v2
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128 par(mai=c(0.8,0.8,0.1,0.1),cex=0.8)
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129 png(paste(opt$path,'/guided_1v2.png', sep=""), width=1020, height=800, units='px')
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130 PCplot(out,ug="unguided",type="1v2")
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131 invisible(dev.off())
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132
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133 par(mai=c(0.8,0.8,0.1,0.1),cex=0.8)
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134 png(paste(opt$path,'/unguided_1v2.png', sep=""), width=1020, height=800, units='px')
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135 PCplot(out,ug="unguided",type="1v2")
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136 invisible(dev.off())
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137
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138
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139 # Guided/Unguided comp,3
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140 par(mai=c(0.65,0.65,0.1,0.1),cex=0.8)
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141 png(paste(opt$path,'/guided_npcs.png', sep=""), width=1020, height=800, units='px')
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142 PCplot(out,ug="guided",type="comp",npcs=opt$npcs)
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143 invisible(dev.off())
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144
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145 par(mai=c(0.65,0.65,0.1,0.1),cex=0.8)
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146 png(paste(opt$path,'/unguided_npcs.png', sep=""), width=1020, height=800, units='px')
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147 PCplot(out,ug="unguided",type="comp",npcs=opt$npcs)
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148 invisible(dev.off())
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149
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150
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151 # Guided/Unguided CumlativeVarPlot
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152 par(mai=c(0.8,0.8,0.1,0.1),cex=0.8)
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153 png(paste(opt$path,'/guided_var.png', sep=""), width=1020, height=800, units='px')
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154 CumulativeVarPlot(out,ug="guided",col="blue")
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155 invisible(dev.off())
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156
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157 par(mai=c(0.8,0.8,0.1,0.1),cex=0.8)
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158 png(paste(opt$path,'/unguided_var.png', sep=""), width=1020, height=800, units='px')
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159 CumulativeVarPlot(out,ug="unguided",col="blue")
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160 invisible(dev.off())
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161
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163 write(paste('<html>
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164 <table id="r-gpca-wrap" align="center" border="1">
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165 <tr>
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166 <th>Delta</th><th>P-value</th><th>varPCg1</th>
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167 </tr>
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168 <tr>
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169 <td id=delta>',out$delta,'</td><td id=p.val>',out$p.val,'</td><td id=varPCg1>',out$varPCg1,'</td>
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170 </tr>
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171 </table>
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172
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173 <center><img src="gDist.png"/></center><br>
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174 <center><title>Guided 1v2</title><br><img src="guided_1v2.png"/></center><br>
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175 <center><title>Unguided 1v2</title><br><img src="unguided_1v2.png"/></center><br>
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176
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177 <center><title>Guided Compare to ',opt$npcs,'</title><br><img src="guided_npcs.png"/></center><br>
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178 <center><title>Unguided Compare to ',opt$npcs,'</title><br><img src="unguided_npcs.png"/></center><br>
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180 <center><title>Guided Cumulative Variance</title><br><img src="guided_var.png"/></center><br>
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181 <center><title>Unguided Cumulative Variance</title><br><img src="unguided_var.png"/></center><br>
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182
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183 </html>'
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184 ),file = opt$html_outfile)
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186 sessionInfo()