Mercurial > repos > galaxyp > msi_combine
annotate msi_combine.xml @ 4:d05bd881af3d draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
author | galaxyp |
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date | Tue, 19 Jun 2018 18:07:04 -0400 |
parents | 91bba2486773 |
children | ff91e78b5c5c |
rev | line source |
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4
d05bd881af3d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
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1 <tool id="mass_spectrometry_imaging_combine" name="MSI combine" version="1.10.0.2"> |
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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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2 <description> |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
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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
galaxyp
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4 </description> |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
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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
galaxyp
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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 $infile.ext == 'imzml' |
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91bba2486773
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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13 ln -s '${infile.extra_files_path}/imzml' infile_${i}.imzML && |
91bba2486773
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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14 ln -s '${infile.extra_files_path}/ibd' infile_${i}.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 $infile.ext == 'analyze75' |
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91bba2486773
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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16 ln -s '${infile.extra_files_path}/hdr' infile_${i}.hdr && |
91bba2486773
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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17 ln -s '${infile.extra_files_path}/img' infile_${i}.img && |
91bba2486773
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
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18 ln -s '${infile.extra_files_path}/t2m' infile_${i}.t2m && |
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9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
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19 #else |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
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20 ln -s '$infile' infile_${i}.RData && |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
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21 #end if |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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22 #end for |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
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23 cat '${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
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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
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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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91bba2486773
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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30 |
1
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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31 #import re |
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91bba2486773
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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32 |
91bba2486773
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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33 ################ load libraries and some preparations ################# |
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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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34 |
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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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35 library(Cardinal) |
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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36 library(ggplot2) |
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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37 |
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91bba2486773
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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38 ## read tabular file for xy_shift option |
91bba2486773
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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39 |
1
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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40 #if str( $combine_conditional.combine_method ) == 'xy_shifts': |
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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41 input_list = read.delim("$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
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42 stringsAsFactors = FALSE) |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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43 #end if |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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44 |
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91bba2486773
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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45 ## load RData and store with new variable name |
91bba2486773
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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46 |
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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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47 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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48 #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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49 load(fileName) |
00b6c61f5054
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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50 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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51 } |
00b6c61f5054
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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52 |
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91bba2486773
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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53 ## preparations for reading files one by one with for loop |
91bba2486773
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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54 |
0
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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55 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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56 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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57 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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58 max_y = numeric() |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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59 valid_dataset = logical() |
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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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60 #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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61 #set $pixelcoords = [] |
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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62 #set $num_infiles = len($infiles) |
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63 all_files = $num_infiles |
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64 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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65 |
91bba2486773
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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66 ############## reading files and changing pixel coordinates ################### |
91bba2486773
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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67 |
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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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68 #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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69 |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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70 #if $infile.ext == 'imzml' |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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71 msidata_$i <- readImzML('infile_${i}', mass.accuracy=$accuracy, units.accuracy = "$units") |
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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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72 #elif $infile.ext == 'analyze75' |
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f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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73 msidata_$i <- readAnalyze('infile_${i}') |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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74 #else |
00b6c61f5054
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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75 msidata_$i = loadRData('infile_${i}.RData') |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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76 #end if |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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77 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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78 sampleNames(msidata_$i) = "msidata" ## same name necessary to combine data in one single coordinate system |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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79 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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80 ################### preparation xy shifts ########################## |
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81 |
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82 #if str( $combine_conditional.combine_method ) == 'xy_shifts': |
3
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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83 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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84 coord(msidata_$i)\$x = coord(msidata_$i)\$x + input_list[$i+1,$combine_conditional.column_x] ## shifts x coordinates according to tabular file |
91bba2486773
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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85 coord(msidata_$i)\$y = coord(msidata_$i)\$y + input_list[$i+1,$combine_conditional.column_y] ## shifts y coordinates according to tabular file |
91bba2486773
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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86 pixel_vector = append(pixel_vector, rep(paste($i+1, input_list[$i+1,$combine_conditional.column_names], sep="_"),times=ncol(msidata_$i))) ## stores file name for each pixel |
91bba2486773
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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87 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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88 pixelcoords_$i = cbind(coord(msidata_$i)[,1:2], rep($i+1,ncol(msidata_$i))) |
91bba2486773
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89 #silent $pixelcoords.append('pixelcoords_'+str($i)) |
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90 colnames(pixelcoords_$i)[3] = "file_number" |
91bba2486773
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91 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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92 ################### preparation automatic combination ########################## |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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93 |
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94 #elif str( $combine_conditional.combine_method ) == 'automatic_combine': |
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95 names_vector = character() |
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96 #set escaped_element_identifier = re.sub('[^\w\-\s\[/]]', '_', str($infile.element_identifier)) ## use name of inputfile from Galaxy |
91bba2486773
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97 if (sum(spectra(msidata_$i))>0) ## use only valid files |
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98 { |
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99 if (is.null(levels(msidata_$i\$combined_sample))) ### if the file was not combined before use input file name, otherwise keep combined_sample name which was assigned before |
91bba2486773
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100 { |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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101 names_vector = append(names_vector, rep(paste($i+1, "$escaped_element_identifier", sep="_"),ncol(msidata_$i))) |
91bba2486773
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102 msidata_$i\$combined_sample = as.factor(names_vector) |
91bba2486773
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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103 } |
91bba2486773
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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104 } |
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105 |
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106 ## Number of input files define grid which is row-wise filled with files |
91bba2486773
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107 |
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108 coord(msidata_$i)\$x = coord(msidata_$i)\$x - (min(coord(msidata_$i)\$x-1)) + x_shifts |
f3f6c32ab690
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109 coord(msidata_$i)\$y = coord(msidata_$i)\$y - (min(coord(msidata_$i)\$y-1)) + y_shifts |
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110 x_shifts = max(coord(msidata_$i)\$x) + 5 |
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111 max_y = append(max_y, max(coord(msidata_$i)\$y)) |
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112 all_files = $num_infiles |
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113 new_row = ($i+1)/ceiling(sqrt(all_files)) |
f3f6c32ab690
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114 new_row%%1==0 |
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115 if (new_row%%1==0) |
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116 {x_shifts = 0 ### when row is filled: x values start again at zero |
91bba2486773
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117 y_shifts = max(max_y) + 5 ### when row is filled: y value increases to start a new row |
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118 max_y = numeric()} |
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119 |
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120 #end if |
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121 |
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122 ## store files to combine them later and for each file check if it is valid |
91bba2486773
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123 |
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124 #silent $msidata.append('msidata_'+str($i)) |
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125 valid_dataset = append(valid_dataset, |
91bba2486773
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126 (ncol(msidata_$i)>0 & nrow(msidata_$i)>0 & sum(spectra(msidata_$i))>0)) |
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127 |
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128 #end for |
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129 |
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130 |
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131 ###################### automatic combination ################################### |
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132 ################################################################################ |
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133 |
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134 #if str( $combine_conditional.combine_method ) == 'automatic_combine': |
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135 print("automatic_combine") |
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136 |
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137 ## combine only valid datasets |
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138 |
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139 valid_data = list(#echo ','.join($msidata)#)[valid_dataset] |
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140 msidata_combined = do.call(combine, valid_data) |
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141 print("Valid datasets in order of input bottom to top:") |
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142 print(valid_dataset) |
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143 |
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144 ## create dataframe with x,y,sample_name and show all pixels in PDF as QC |
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145 |
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146 pdf("Combined_qc.pdf", width=15, height=15) |
91bba2486773
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147 position_df = cbind(coord(msidata_combined)[,1:2], msidata_combined\$combined_sample) |
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148 colnames(position_df)[3] = "sample_name" |
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149 combine_plot = ggplot(position_df, aes(x=x, y=y, fill=sample_name))+ |
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150 geom_tile() + |
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151 coord_fixed()+ |
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152 ggtitle("Spatial orientation of combined data")+ |
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153 theme_bw()+ |
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154 theme(text=element_text(family="ArialMT", face="bold", size=15))+ |
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155 theme(legend.position="bottom",legend.direction="vertical")+ |
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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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156 guides(fill=guide_legend(ncol=4,byrow=TRUE)) |
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157 coord_labels = aggregate(cbind(x,y)~sample_name, data=position_df, mean) |
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158 coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$sample_name) |
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159 for(file_count in 1:nrow(coord_labels)) |
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160 {combine_plot = combine_plot + annotate("text",x=coord_labels[file_count,"x"], |
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161 y=coord_labels[file_count,"y"],label=toString(coord_labels[file_count,4]))} |
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162 print(combine_plot) |
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163 dev.off() |
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164 |
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165 ## save as (.RData) |
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166 |
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167 msidata = msidata_combined |
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168 save(msidata, file="$msidata_combined") |
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169 |
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170 |
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171 ################################## xy shifts ################################### |
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172 ################################################################################ |
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173 |
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174 #elif str( $combine_conditional.combine_method ) == 'xy_shifts': |
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175 print("xy_shifts") |
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176 |
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177 #if str($combine_conditional.combination_true) == "yes_combi": |
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178 print("combination with xy shifts") |
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179 |
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180 msidata_combined = do.call(combine, list(#echo ','.join($msidata)#)) |
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181 sample_names = as.factor(pixel_vector) ## the sample names are assigned to each pixel |
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182 msidata_combined\$combined_sample = sample_names ## sample names are stored in $combined_sample slot |
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183 |
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184 ## save as (.RData) |
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185 |
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186 msidata = msidata_combined |
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187 save(msidata, file="$msidata_combined") |
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188 |
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189 ## create x,y,sample_name dataframe for QC pdf |
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190 |
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191 position_df = cbind(coord(msidata), msidata\$combined_sample) |
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192 colnames(position_df)[3] = "sample_name" |
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193 |
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194 #else: |
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195 print("no combination, only testing xy shifts") |
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196 |
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197 position_df = do.call(rbind, list(#echo ','.join($pixelcoords)#)) |
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198 position_df\$sample_name = as.factor(pixel_vector) |
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199 |
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200 #end if |
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201 |
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202 ## create PDF to show all pixels in PDF as QC |
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203 |
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204 pdf("Combined_qc.pdf", width=15, height=15) |
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205 combine_plot = ggplot(position_df, aes(x=x, y=y, fill=sample_name))+ |
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206 geom_tile() + |
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207 coord_fixed()+ |
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208 ggtitle("Spatial orientation of combined data")+ |
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209 theme_bw()+ |
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210 theme(text=element_text(family="ArialMT", face="bold", size=15))+ |
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211 theme(legend.position="bottom",legend.direction="vertical")+ |
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212 theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = 6))+ |
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213 guides(fill=guide_legend(ncol=5,byrow=TRUE)) |
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214 coord_labels = aggregate(cbind(x,y)~sample_name, data=position_df, mean) |
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215 coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$sample_name) |
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216 for(file_count in 1:nrow(coord_labels)) |
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217 {combine_plot = combine_plot + annotate("text",x=coord_labels[file_count,"x"], |
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218 y=coord_labels[file_count,"y"],label=toString(coord_labels[file_count,4]))} |
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219 print(combine_plot) |
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220 dev.off() |
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221 |
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222 #end if |
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223 |
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224 ####################### optional matrix output ################################# |
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225 |
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226 #if $output_matrix: |
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227 |
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228 if (length(features(msidata_combined))> 0 & length(pixels(msidata_combined)) > 0) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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229 { |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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230 spectramatrix = spectra(msidata_combined) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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231 rownames(spectramatrix) = mz(msidata_combined) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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232 newmatrix = rbind(pixels(msidata_combined), spectramatrix) |
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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233 write.table(newmatrix[2:nrow(newmatrix),], file="$matrixasoutput", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t") |
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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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234 }else{ |
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235 print("file has no features or pixels left") |
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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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236 } |
0
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237 #end if |
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238 |
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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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239 ]]></configfile> |
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240 </configfiles> |
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241 <inputs> |
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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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242 <param name="infiles" type="data" multiple="true" format="imzml,rdata,analyze75" |
4
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243 label="MSI data as imzml, analyze7.5 or Cardinal MSImageSet saved as RData" |
0
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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244 help="load imzml and ibd file by uploading composite datatype imzml"/> |
4
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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245 <param name="accuracy" type="float" value="50" label="Only for processed imzML files: enter mass accuracy to which the m/z values will be binned" help="This should be set to the native accuracy of the mass spectrometer, if known"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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246 <param name="units" display="radio" type="select" label="Only for processed imzML files: unit of the mass accuracy" help="either m/z or ppm"> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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247 <option value="mz" >mz</option> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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248 <option value="ppm" selected="True" >ppm</option> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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249 </param> |
1
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250 <conditional name="combine_conditional"> |
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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251 <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"> |
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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252 <option value="automatic_combine" selected="True" >automatic combination</option> |
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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253 <option value="xy_shifts">xy shifts by hand</option> |
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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254 </param> |
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255 <when value="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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256 <when value="xy_shifts"> |
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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257 <param name="coordinates_file" type="data" format="tabular" label="datasetnames, X and y values to shift data before combining" |
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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258 help="Tabular file with three columns: 1 for the filename, 1 for the x-coordinate shift and 1 for the y-coordinate shift"/> |
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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259 <param name="column_x" data_ref="coordinates_file" label="Column with values for shift in x direction" type="data_column"/> |
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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260 <param name="column_y" data_ref="coordinates_file" label="Column with values for shift in y direction" type="data_column"/> |
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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261 <param name="column_names" data_ref="coordinates_file" label="Column with dataset names" type="data_column"/> |
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262 <param name="combination_true" type="boolean" display="radio" truevalue="yes_combi" falsevalue="no_combi" label="Combine datasets" help = "Combination only works if x and y-shifts lead to unique pixel positions. If this is unknown use the No option to get an idea about the pixel overlap"/> |
1
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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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263 </when> |
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264 </conditional> |
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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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265 <param name="output_matrix" type="boolean" display="radio" label="Intensity matrix output"/> |
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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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266 </inputs> |
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267 <outputs> |
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268 <data format="rdata" name="msidata_combined" label="MSI_data_combined"/> |
91bba2486773
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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269 <data format="pdf" name="combining_qc" from_work_dir="Combined_qc.pdf" label = "Combined_QC"/> |
91bba2486773
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270 <data format="tabular" name="matrixasoutput" label="Combined_matrix"> |
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271 <filter>output_matrix</filter> |
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272 </data> |
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273 </outputs> |
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274 <tests> |
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275 <test expect_num_outputs="3"> |
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276 <param name="infiles" value="msidata_1.RData,msidata_2.RData,msidata_3.RData" ftype="rdata"/> |
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277 <param name="combine_method" value="xy_shifts"/> |
0
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278 <param name="coordinates_file" ftype="tabular" value="xy_coordinates.tabular"/> |
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279 <param name="column_x" value="1"/> |
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280 <param name="column_y" value="2"/> |
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281 <param name="column_names" value="3"/> |
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282 <param name="combination_true" value="yes_combi"/> |
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283 <param name="output_matrix" value="True"/> |
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284 <output name="matrixasoutput" file="123_combined_matrix.tabular"/> |
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285 <output name="msidata_combined" file="123_combined.RData" compare="sim_size" /> |
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286 <output name="combining_qc" file="123_combined_QC.pdf" compare="sim_size" delta="20000"/> |
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287 </test> |
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288 <test expect_num_outputs="2"> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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289 <param name="infiles" value="msidata_1.RData,msidata_2.RData,msidata_3.RData" ftype="rdata"/> |
91bba2486773
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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290 <param name="combine_method" value="xy_shifts"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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291 <param name="coordinates_file" ftype="tabular" value="xy_coordinates.tabular"/> |
91bba2486773
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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292 <param name="column_x" value="1"/> |
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293 <param name="column_y" value="2"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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294 <param name="column_names" value="3"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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295 <param name="combination_true" value="no_combi"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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296 <output name="msidata_combined" file="123_no_combi.RData" compare="sim_size" /> |
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297 <output name="combining_qc" file="123_no_combi_QC.pdf" compare="sim_size" delta="20000"/> |
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298 </test> |
0
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299 <test expect_num_outputs="3"> |
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300 <param name="infiles" value="msidata_1.RData,msidata_2.RData" ftype="rdata"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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301 <param name="combine_method" value="automatic_combine"/> |
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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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302 <param name="output_matrix" value="True"/> |
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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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303 <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
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304 <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
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305 <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
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306 </test> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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307 <test expect_num_outputs="2"> |
91bba2486773
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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308 <param name="infiles" value="msidata_1.RData,123_combined.RData" ftype="rdata"/> |
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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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309 <param name="combine_method" value="automatic_combine"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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310 <param name="output_matrix" value="False"/> |
91bba2486773
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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311 <output name="msidata_combined" file="112_auto_combined.RData" compare="sim_size" /> |
91bba2486773
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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312 <output name="combining_qc" file="112_auto_combined_QC.pdf" compare="sim_size" delta="20000"/> |
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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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313 </test> |
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314 </tests> |
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315 <help> |
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316 <![CDATA[ |
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317 |
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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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318 Cardinal is an R package that implements statistical & computational tools for analyzing mass spectrometry imaging datasets. `More information on Cardinal <http://cardinalmsi.org//>`_ |
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319 |
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320 This tool uses the Cardinal combine function to combine several mass spectrometry imaging data. |
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321 |
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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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322 Input data: 3 types of input data can be used: |
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323 |
2
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324 - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/wp/imzml/>`_ |
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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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325 - Analyze7.5 (upload hdr, img and t2m file via the "composite" function) |
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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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326 - Cardinal "MSImageSet" data (with variable name "msidata", saved as .RData) |
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327 |
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328 Prerequisite: |
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329 |
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330 - 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) |
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331 |
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332 Options: |
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333 |
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334 - "automatic combination": files are automatically arranged in a grid, subfiles are named according to input file name |
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335 - "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 and the file name in a third column). To test if the pixels are correctly shifted use "combine datasets: No". |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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336 |
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337 |
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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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338 Output: |
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339 |
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340 - imzML file containing multiple subfiles |
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341 - pdf that shows the pixel positions of the combined files |
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342 - optional: intensity matrix as tabular file (intensities for m/z in rows and pixel in columns) |
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343 |
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344 |
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345 ]]> |
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346 </help> |
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347 <citations> |
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348 <citation type="doi">10.1093/bioinformatics/btv146</citation> |
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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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349 </citations> |
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350 </tool> |