Mercurial > repos > galaxyp > msi_combine
annotate msi_combine.xml @ 2:00b6c61f5054 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
author | galaxyp |
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date | Mon, 28 May 2018 12:35:49 -0400 |
parents | f3f6c32ab690 |
children | 91bba2486773 |
rev | line source |
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1
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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1 <tool id="mass_spectrometry_imaging_combine" name="MSI combine" version="1.10.0.0"> |
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9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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2 <description> |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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3 combine several mass spectrometry imaging datasets into one |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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4 </description> |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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5 <requirements> |
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f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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6 <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement> |
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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7 <requirement type="package" version="2.2.1">r-ggplot2</requirement> |
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9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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8 </requirements> |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
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9 <command detect_errors="exit_code"> |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
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10 <![CDATA[ |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
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11 #for $i, $infile in enumerate($infiles): |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
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12 #if $infile.ext == 'imzml' |
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f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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13 ln -s '${infile.extra_files_path}/imzml' infile.imzML && |
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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14 ln -s '${infile.extra_files_path}/ibd' infile.ibd && |
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9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
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15 #elif $infile.ext == 'analyze75' |
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f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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16 ln -s '${infile.extra_files_path}/hdr' infile.hdr && |
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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17 ln -s '${infile.extra_files_path}/img' infile.img && |
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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18 ln -s '${infile.extra_files_path}/t2m' infile.t2m && |
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9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
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19 #else |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
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20 ln -s '$infile' infile_${i}.RData && |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
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21 #end if |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
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22 #end for |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
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23 cat '${msi_combine}' && |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
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24 Rscript '${msi_combine}' |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
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25 |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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26 ]]> |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
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27 </command> |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
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28 <configfiles> |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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29 <configfile name="msi_combine"><![CDATA[ |
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f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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30 #import re |
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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31 ################ load libraries, read rename and combine files ################# |
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9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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32 |
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f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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33 library(Cardinal) |
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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34 library(ggplot2) |
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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35 |
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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36 #if str( $combine_conditional.combine_method ) == 'xy_shifts': |
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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37 input_list = read.delim("$combine_conditional.coordinates_file", header = FALSE, |
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9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
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38 stringsAsFactors = FALSE) |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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39 #end if |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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40 |
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00b6c61f5054
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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41 loadRData <- function(fileName){ |
00b6c61f5054
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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42 #loads an RData file, and returns it |
00b6c61f5054
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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43 load(fileName) |
00b6c61f5054
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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44 get(ls()[ls() != "fileName"]) |
00b6c61f5054
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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45 } |
00b6c61f5054
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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46 |
0
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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47 pixel_vector = numeric() |
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f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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48 names_vector = character() |
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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49 x_shifts = 0 |
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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50 y_shifts = 0 |
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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51 max_y = numeric() |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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52 |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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53 #set $msidata = [] |
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f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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54 #set $pixelcoords = [] |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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55 #set $num_infiles = len($infiles) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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56 all_files = $num_infiles |
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f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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57 |
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9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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58 #for $i, $infile in enumerate($infiles): |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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59 |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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60 #if $infile.ext == 'imzml' |
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f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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61 msidata_$i <- readImzML('infile_${i}') |
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9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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62 #elif $infile.ext == 'analyze75' |
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f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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63 msidata_$i <- readAnalyze('infile_${i}') |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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64 #else |
00b6c61f5054
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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65 msidata_$i = loadRData('infile_${i}.RData') |
00b6c61f5054
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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66 #end if |
00b6c61f5054
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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67 |
00b6c61f5054
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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68 ########## wenn ncol msidata > 0 and nrow msidata > 0, dann alles abklappern andernfalls nicht in msiliste mitreinnehmen (unten hinter python vor end for: filenr ausprinten) |
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9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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69 sampleNames(msidata_$i) = "msidata" |
1
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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70 pixelcoords_$i = cbind(coord(msidata_$i)[,1:2], rep($i+1,ncol(msidata_$i))) |
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9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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71 |
1
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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72 #if str( $combine_conditional.combine_method ) == 'xy_shifts': |
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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73 coord(msidata_$i)\$x = coord(msidata_$i)\$x + input_list[$i+1,$combine_conditional.column_x] |
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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74 coord(msidata_$i)\$y = coord(msidata_$i)\$y + input_list[$i+1,$combine_conditional.column_y] |
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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75 pixel_vector = append(pixel_vector, rep(input_list[$i+1,$combine_conditional.column_names],times=ncol(msidata_$i))) |
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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76 |
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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77 #elif str( $combine_conditional.combine_method ) == 'automatic_combine': |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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78 #set escaped_element_identifier = re.sub('[^\w\-\s\[/]]', '_', str($infile.element_identifier)) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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79 names_vector = append(names_vector, rep(paste($i+1, "$escaped_element_identifier", sep="_"),ncol(msidata_$i))) |
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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80 coord(msidata_$i)\$x = coord(msidata_$i)\$x - (min(coord(msidata_$i)\$x-1)) + x_shifts |
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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81 coord(msidata_$i)\$y = coord(msidata_$i)\$y - (min(coord(msidata_$i)\$y-1)) + y_shifts |
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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82 x_shifts = max(coord(msidata_$i)\$x) + $combine_conditional.x_distance |
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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83 max_y = append(max_y, max(coord(msidata_$i)\$y)) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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84 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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85 all_files = $num_infiles |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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86 new_row = ($i+1)/ceiling(sqrt(all_files)) |
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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87 new_row%%1==0 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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88 if (new_row%%1==0) |
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89 {x_shifts = 0 ### x values start again at zero |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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90 y_shifts = max(max_y) + $combine_conditional.y_distance |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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91 max_y = numeric()} |
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92 |
0
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93 #end if |
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94 #silent $msidata.append('msidata_'+str($i)) |
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95 #silent $pixelcoords.append('pixelcoords_'+str($i)) |
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96 #end for |
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97 colnames(pixelcoords_$i)[3] = "file_number" |
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98 |
1
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99 ###################### automatic combination ################################### |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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100 ################################################################################ |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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101 |
1
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102 #if str( $combine_conditional.combine_method ) == 'automatic_combine': |
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103 print("automatic_combine") |
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104 msidata_combined = do.call(combine, list(#echo ','.join($msidata)#)) |
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105 print("combination successful") |
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106 sample_names = as.factor(names_vector) |
f3f6c32ab690
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107 pData(msidata_combined)\$sample = sample_names |
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108 print("names successful") |
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109 |
1
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110 ## create PDF to show pixels of each file |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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111 pdf("combining_qc.pdf", width=15, height=15) |
f3f6c32ab690
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112 position_df = cbind(coord(msidata_combined)[,1:2], pData(msidata_combined)\$sample) |
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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113 colnames(position_df)[3] = "sample_name" |
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114 print("position_df") |
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115 |
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116 combine_plot = ggplot(position_df, aes(x=x, y=y, fill=sample_name))+ |
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117 geom_tile() + |
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118 coord_fixed()+ |
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119 ggtitle("Spatial orientation of combined data")+ |
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120 theme_bw()+ |
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121 theme(text=element_text(family="ArialMT", face="bold", size=15))+ |
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122 theme(legend.position="bottom",legend.direction="vertical")+ |
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123 guides(fill=guide_legend(ncol=4,byrow=TRUE)) |
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124 |
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125 |
1
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126 coord_labels = aggregate(cbind(x,y)~sample_name, data=position_df, mean) |
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127 coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$sample_name) |
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128 for(file_count in 1:nrow(coord_labels)) |
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129 { |
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130 combine_plot = combine_plot + annotate("text",x=coord_labels[file_count,"x"],y=coord_labels[file_count,"y"],label=toString(coord_labels[file_count,4])) |
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131 } |
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132 |
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133 print(combine_plot) |
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134 dev.off() |
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135 |
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136 ## save as (.RData) |
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137 msidata = msidata_combined |
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138 save(msidata, file="$msidata_combined") |
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139 ################################## xy shifts ################################### |
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140 ################################################################################ |
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141 #elif str( $combine_conditional.combine_method ) == 'xy_shifts': |
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142 print("xy_shifts") |
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143 msidata_combined = do.call(combine, list(#echo ','.join($msidata)#)) |
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144 |
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145 ############# replace NA with 0 and rename pixels according to dataset ######### |
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146 |
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147 spectra(msidata_combined)[is.na(spectra(msidata_combined))] <- 0 |
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148 print(paste0("Number of NAs which were replaced ",sum(is.na(spectra(msidata_combined))))) |
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149 |
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150 sample_names = as.factor(pixel_vector) |
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151 pData(msidata_combined)\$sample = sample_names |
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152 |
1
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153 ###################################### outputs ################################# |
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154 ## save as (.RData) |
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155 msidata = msidata_combined |
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156 save(msidata, file="$msidata_combined") |
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157 |
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158 ## create PDF to show pixels of each file |
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159 pdf("combining_qc.pdf") |
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160 position_df = cbind(coord(msidata), pData(msidata)\$sample) |
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161 colnames(position_df)[3] = "sample_name" |
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162 |
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163 combine_plot = ggplot(position_df, aes(x=x, y=y, fill=sample_name))+ |
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164 geom_tile() + |
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165 coord_fixed()+ |
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166 ggtitle("Spatial orientation of combined data")+ |
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167 theme_bw()+ |
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168 theme(text=element_text(family="ArialMT", face="bold", size=12)) |
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169 |
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170 coord_labels = aggregate(cbind(x,y)~sample_name, data=position_df, mean) |
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171 for(file_count in 1:nrow(coord_labels)) |
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172 { |
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173 combine_plot = combine_plot + annotate("text",x=coord_labels[file_count,"x"],y=coord_labels[file_count,"y"],label=toString(coord_labels[file_count,"sample_name"])) |
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174 } |
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175 |
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176 print(combine_plot) |
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177 |
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178 dev.off() |
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179 |
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180 |
1
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181 ################################## no shifts ################################### |
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182 ################################################################################ |
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183 #elif str( $combine_conditional.combine_method ) == 'no_shifts': |
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184 print("no_shifts") |
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185 msidata_combined = do.call(combine, list(#echo ','.join($msidata)#)) |
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186 |
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187 ############# replace NA with 0 and rename pixels according to dataset ######### |
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188 |
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189 spectra(msidata_combined)[is.na(spectra(msidata_combined))] <- 0 |
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190 print(paste0("Number of NAs which were replaced ",sum(is.na(spectra(msidata_combined))))) |
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191 |
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192 ###################################### outputs ################################# |
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193 ## save as (.RData) |
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194 msidata = msidata_combined |
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195 save(msidata, file="$msidata_combined") |
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196 |
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197 ## create PDF to show pixels of each file |
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198 pdf("combining_qc.pdf") |
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199 position_df = cbind(coord(msidata), pData(msidata)\$sample) |
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200 colnames(position_df)[3] = "sample_name" |
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201 |
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202 ggplot(position_df, aes(x=x, y=y, fill=sample_name))+ |
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203 geom_tile() + |
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204 coord_fixed()+ |
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205 ggtitle("Spatial orientation of combined data")+ |
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206 theme_bw()+ |
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207 theme(text=element_text(family="ArialMT", face="bold", size=12)) |
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208 |
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209 dev.off() |
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210 |
0
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211 |
1
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212 ################################## no combination ############################## |
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213 ################################################################################ |
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214 #elif str( $combine_conditional.combine_method ) == 'no_combine': |
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215 print("no_combine") |
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216 |
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217 ## create PDF to show pixels of each file |
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218 pdf("combining_qc.pdf") |
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219 position_df = do.call(rbind, list(#echo ','.join($pixelcoords)#)) |
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220 position_df[duplicated(position_df[,1:2]),3] = 0 |
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221 position_df\$file_number = as.factor(position_df\$file_number) |
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222 |
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223 combine_plot = ggplot(position_df, aes(x=x, y=y, fill=file_number))+ |
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224 geom_tile() + |
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225 coord_fixed()+ |
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226 ggtitle("Spatial orientation before combination")+ |
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227 theme_bw()+ |
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228 theme(text=element_text(family="ArialMT", face="bold", size=12))+ |
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229 theme(panel.grid.major = element_line(colour = "black")) + |
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230 scale_x_continuous(minor_breaks = seq(min(position_df\$x-50), max(position_df\$x+50, 1))) + |
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231 scale_y_continuous(minor_breaks = seq(min(position_df\$y-50), max(position_df\$y+50, 1))) |
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232 |
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233 |
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234 coord_labels = aggregate(cbind(x,y)~file_number, data=position_df, mean) |
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235 for(file_count in 1:nrow(coord_labels)) |
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236 { |
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237 combine_plot = combine_plot + annotate("text",x=coord_labels[file_count,"x"],y=coord_labels[file_count,"y"],label=toString(coord_labels[file_count,"file_number"])) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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238 } |
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239 |
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240 print(combine_plot) |
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241 |
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242 dev.off() |
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243 #end if |
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244 |
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245 #if $output_matrix: |
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246 |
1
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247 if (length(features(msidata_combined))> 0 & length(pixels(msidata_combined)) > 0) |
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248 { |
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249 spectramatrix = spectra(msidata_combined) |
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250 rownames(spectramatrix) = mz(msidata_combined) |
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251 newmatrix = rbind(pixels(msidata_combined), spectramatrix) |
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252 write.table(newmatrix[2:nrow(newmatrix),], file="$matrixasoutput", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t") |
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253 }else{ |
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254 print("file has no features or pixels left") |
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255 } |
0
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256 #end if |
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257 |
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258 ]]></configfile> |
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259 </configfiles> |
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260 <inputs> |
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261 <param name="infiles" type="data" multiple="true" format="imzml,rdata,analyze75" |
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262 label="MSI rawdata as imzml, analyze7.5 or Cardinal MSImageSet saved as RData" |
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263 help="load imzml and ibd file by uploading composite datatype imzml"/> |
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264 <conditional name="combine_conditional"> |
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265 <param name="combine_method" type="select" label="Select the way you want to combine multiple files" help="More detailed help can be found in the help section at the bottom"> |
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266 <option value="automatic_combine" selected="True" >automatic combination</option> |
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267 <option value="no_shifts" >no coordinates shift</option> |
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268 <option value="xy_shifts">xy shifts by hand</option> |
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269 <option value="no_combine">check pixels before combination</option> |
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270 </param> |
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271 <when value="no_shifts"> |
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272 </when> |
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273 <when value="automatic_combine"> |
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274 <param name="x_distance" type="integer" value="10" label="How many pixels in x direction should be between files?"/> |
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275 <param name="y_distance" type="integer" value="10" label="How many pixels in y direction should be between files?"/> |
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276 </when> |
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277 <when value="xy_shifts"> |
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278 <param name="coordinates_file" type="data" format="tabular" label="datasetnames, X and y values to shift data before combining" |
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279 help="Tabular file with three columns: 1 for the filename, 1 for the x-coordinate shift and 1 for the y-coordinate shift"/> |
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280 <param name="column_x" data_ref="coordinates_file" label="Column with values for shift in x direction" type="data_column"/> |
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281 <param name="column_y" data_ref="coordinates_file" label="Column with values for shift in y direction" type="data_column"/> |
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282 <param name="column_names" data_ref="coordinates_file" label="Column with dataset names" type="data_column"/> |
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283 </when> |
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284 <when value="no_combine"/> |
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285 </conditional> |
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286 <param name="output_matrix" type="boolean" display="radio" label="Intensity matrix output"/> |
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287 </inputs> |
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288 <outputs> |
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289 <data format="rdata" name="msidata_combined" label="Combined MSI data"/> |
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290 <data format="pdf" name="combining_qc" from_work_dir="combining_qc.pdf" label = "Combined image of pixels"/> |
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291 <data format="tabular" name="matrixasoutput" label="Combined matrix"> |
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292 <filter>output_matrix</filter> |
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293 </data> |
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294 </outputs> |
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295 <tests> |
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296 <test expect_num_outputs="3"> |
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297 <param name="infiles" value="msidata_1.RData,msidata_2.RData,msidata_3.RData" ftype="rdata"/> |
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298 <param name="combine_method" value="xy_shifts"/> |
0
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
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299 <param name="coordinates_file" ftype="tabular" value="xy_coordinates.tabular"/> |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
parents:
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300 <param name="column_x" value="1"/> |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
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301 <param name="column_y" value="2"/> |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
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302 <param name="column_names" value="3"/> |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
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303 <param name="output_matrix" value="True"/> |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
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304 <output name="matrixasoutput" file="123_combined_matrix.tabular"/> |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
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305 <output name="msidata_combined" file="123_combined.RData" compare="sim_size" /> |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
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306 <output name="combining_qc" file="123_combined_QC.pdf" compare="sim_size" delta="20000"/> |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
parents:
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307 </test> |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
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308 <test expect_num_outputs="3"> |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
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309 <param name="infiles" value="msidata_1.RData,msidata_2.RData" ftype="rdata"/> |
1
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
galaxyp
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310 <param name="combine_method" value="no_shifts"/> |
0
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
parents:
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311 <param name="output_matrix" value="True"/> |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
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312 <output name="matrixasoutput" file="12_combined_matrix.tabular"/> |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
parents:
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313 <output name="msidata_combined" file="12_combined.RData" compare="sim_size" /> |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
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314 <output name="combining_qc" file="12_combined_QC.pdf" compare="sim_size" delta="20000"/> |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
parents:
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315 </test> |
1
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
galaxyp
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316 <test expect_num_outputs="3"> |
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
galaxyp
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317 <param name="infiles" value="msidata_1.RData,msidata_2.RData" ftype="rdata"/> |
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
galaxyp
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318 <param name="combine_method" value="automatic_combine"/> |
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
galaxyp
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319 <param name="x_distance" value="1"/> |
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
galaxyp
parents:
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320 <param name="y_distance" value="1"/> |
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
galaxyp
parents:
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diff
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321 <param name="output_matrix" value="True"/> |
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
galaxyp
parents:
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322 <output name="matrixasoutput" file="12_auto_combined_matrix.tabular"/> |
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
galaxyp
parents:
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323 <output name="msidata_combined" file="12_auto_combined.RData" compare="sim_size" /> |
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
galaxyp
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324 <output name="combining_qc" file="12_auto_combined_QC.pdf" compare="sim_size" delta="20000"/> |
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
galaxyp
parents:
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325 </test> |
0
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
parents:
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326 </tests> |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
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327 <help> |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
parents:
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328 <![CDATA[ |
1
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
galaxyp
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329 |
2
00b6c61f5054
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
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330 Cardinal is an R package that implements statistical & computational tools for analyzing mass spectrometry imaging datasets. `More information on Cardinal <http://cardinalmsi.org//>`_ |
1
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
galaxyp
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331 |
2
00b6c61f5054
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
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332 This tool uses the Cardinal combine function to combine several mass-spectrometry imaging data. |
0
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
parents:
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333 |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
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334 Input data: 3 types of input data can be used: |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
parents:
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335 |
2
00b6c61f5054
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
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336 - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/wp/imzml/>`_ |
0
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
parents:
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337 - Analyze7.5 (upload hdr, img and t2m file via the "composite" function) |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
parents:
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338 - Cardinal "MSImageSet" data (with variable name "msidata", saved as .RData) |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
parents:
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339 |
2
00b6c61f5054
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
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340 Prerequisite: |
00b6c61f5054
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
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341 |
00b6c61f5054
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
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342 - m/z values need to be the same across all datasets (before using this tool), this can be achieved with the filtering tool (use same m/z range) and the preprocessing tool (use same binning parameter) |
00b6c61f5054
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
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343 |
00b6c61f5054
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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344 Options: |
00b6c61f5054
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
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345 |
00b6c61f5054
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
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346 - "automatic combination": files are arranged in a grid with a minimal distance in x and y direction which can be given by the user, subfiles are named according to input file name |
00b6c61f5054
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
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347 - "no coordinates shift": this option can only be used if all pixels are unique across datasets, no assignment of names to the subfiles |
00b6c61f5054
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
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348 - "xy shifts by hand": each file can be moved in x and y direction according to the users need (define one tabular file in the order in which the files are loaded in the history (bottom to top) and define for each file the x and y coordinates shifts in separate columns |
00b6c61f5054
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
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349 - "check pixels before combination": no combination takes place but a pdf shows the current arrangement of the pixels |
00b6c61f5054
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
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350 |
00b6c61f5054
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
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351 Output: |
00b6c61f5054
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents:
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352 |
00b6c61f5054
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents:
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353 - imzML file containing multiple subfiles |
00b6c61f5054
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
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354 - pdf that shows the pixel positions of the combined files |
00b6c61f5054
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents:
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355 - optional: intensity matrix as tabular file (intensities for masses in rows and pixel in columns) |
00b6c61f5054
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents:
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356 |
00b6c61f5054
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents:
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357 |
0
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
parents:
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358 ]]> |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
parents:
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359 </help> |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
parents:
diff
changeset
|
360 <citations> |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
parents:
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|
361 <citation type="doi">10.1093/bioinformatics/btv146</citation> |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
parents:
diff
changeset
|
362 </citations> |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
parents:
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363 </tool> |