Mercurial > repos > galaxyp > msi_combine
annotate msi_combine.xml @ 7:19d8eee15959 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
author | galaxyp |
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date | Wed, 22 Aug 2018 13:41:16 -0400 |
parents | f4aafc565aa3 |
children | c6564ddf0744 |
rev | line source |
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7
19d8eee15959
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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1 <tool id="mass_spectrometry_imaging_combine" name="MSI combine" version="1.10.0.5"> |
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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
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5 <requirements> |
1
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> |
7
19d8eee15959
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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7 <requirement type="package" version="3.0.0">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
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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
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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_${i}.imzML && |
91bba2486773
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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14 ln -s '${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 $infile.ext == 'analyze75' |
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91bba2486773
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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16 ln -s '${infile.extra_files_path}/hdr' infile_${i}.hdr && |
91bba2486773
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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17 ln -s '${infile.extra_files_path}/img' infile_${i}.img && |
91bba2486773
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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18 ln -s '${infile.extra_files_path}/t2m' infile_${i}.t2m && |
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9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
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19 #else |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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20 ln -s '$infile' infile_${i}.RData && |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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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 |
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f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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23 #for $i, $annotation_file in enumerate($annotation_files): |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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24 ln -s '$annotation_file' annotation_file_${i}.tabular && |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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25 #end for |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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26 |
0
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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27 cat '${msi_combine}' && |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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28 Rscript '${msi_combine}' |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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29 |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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30 ]]> |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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31 </command> |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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32 <configfiles> |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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33 <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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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 #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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36 |
91bba2486773
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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37 ################ 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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38 |
1
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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39 library(Cardinal) |
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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40 library(ggplot2) |
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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41 |
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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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42 ## 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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43 |
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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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44 #if str( $combine_conditional.combine_method ) == 'xy_shifts': |
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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45 input_list = read.delim("$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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46 stringsAsFactors = FALSE) |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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47 #end if |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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48 |
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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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49 ## 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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50 |
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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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51 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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52 #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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53 load(fileName) |
00b6c61f5054
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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54 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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55 } |
00b6c61f5054
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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56 |
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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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57 ## 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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58 |
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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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59 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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60 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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61 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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62 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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63 valid_dataset = logical() |
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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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64 #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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65 #set $pixelcoords = [] |
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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66 #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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67 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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68 |
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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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69 |
91bba2486773
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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70 ############## 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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71 |
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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 #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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73 |
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f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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74 ## read MSI data |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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75 |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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76 #if $infile.ext == 'imzml' |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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77 #if str($processed_cond.processed_file) == "processed": |
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78 msidata_$i <- readImzML('infile_${i}', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units") |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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79 #else |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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80 msidata_$i <- readImzML('infile_${i}') |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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81 #end if |
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82 #elif $infile.ext == 'analyze75' |
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83 msidata_$i <- readAnalyze('infile_${i}') |
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84 #else |
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85 msidata_$i = loadRData('infile_${i}.RData') |
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86 #end if |
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87 |
2
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88 |
6
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89 ## read annotation data, up to 5 annotations can be used for now |
f4aafc565aa3
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90 |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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91 ## read annotation tabular, set first two columns as x and y, merge with coordinates dataframe and order according to pixelorder in msidata |
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92 input_annotation = read.delim("annotation_file_${i}.tabular", header = TRUE, |
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93 stringsAsFactors = FALSE) |
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94 |
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95 if (class(input_annotation[,1]) == "character"){ |
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96 annotation_coordinates = matrix(unlist(strsplit(as.character(input_annotation[,1]), "\\,")), ncol=2, byrow=TRUE) |
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97 annotation_coordinates2 = cbind(as.numeric(substring(annotation_coordinates[,1], 5, last = 1000000L)), as.numeric(substring(annotation_coordinates[,2], 5, last = 1000000L))) |
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98 input_annotation = cbind(annotation_coordinates2, input_annotation[,-1]) |
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99 } |
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100 |
6
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101 colnames(input_annotation)[1:2] = c("x", "y") |
f4aafc565aa3
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102 msidata_coordinates = cbind(coord(msidata_$i)[,1:2], 1:ncol(msidata_$i)) |
f4aafc565aa3
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103 colnames(msidata_coordinates)[3] = "pixel_index" |
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104 ## only first 5 annotation columns are kept |
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105 if (ncol(input_annotation) > 7){ |
f4aafc565aa3
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106 input_annotation = input_annotation[,1:7]} |
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107 |
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108 annotation_df = merge(msidata_coordinates, input_annotation, by=c("x", "y"), all.x=TRUE) |
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109 annotation_df_8 = cbind(annotation_df, data.frame(matrix(NA,ncol=8-ncol(annotation_df), nrow=ncol(msidata_$i)))) |
f4aafc565aa3
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110 annotation_df_8_sorted = annotation_df_8[order(annotation_df_8\$pixel_index),]## orders pixel according to msidata |
f4aafc565aa3
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111 |
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112 ## each annotation column is assigned to the pixel in the pData slot of the MSIdata |
f4aafc565aa3
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113 msidata_$i\$column1 = annotation_df_8_sorted[,4] |
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114 msidata_$i\$column2 = annotation_df_8_sorted[,5] |
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115 msidata_$i\$column3 = annotation_df_8_sorted[,6] |
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116 msidata_$i\$column4 = annotation_df_8_sorted[,7] |
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117 msidata_$i\$column5 = annotation_df_8_sorted[,8] |
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118 |
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119 ## same name for MSI data files necessary to combine data in one single coordinate system |
f4aafc565aa3
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120 sampleNames(msidata_$i) = "msidata" |
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121 |
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122 ################### preparation xy shifts ########################## |
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123 |
1
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124 #if str( $combine_conditional.combine_method ) == 'xy_shifts': |
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125 |
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126 ## shift coordinates according to input tabular file and store file names |
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127 coord(msidata_$i)\$x = coord(msidata_$i)\$x + input_list[$i+1,$combine_conditional.column_x] ## shifts x coordinates according to tabular file |
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128 coord(msidata_$i)\$y = coord(msidata_$i)\$y + input_list[$i+1,$combine_conditional.column_y] ## shifts y coordinates according to tabular file |
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129 pixel_vector = append(pixel_vector, rep(paste($i+1, input_list[$i+1,$combine_conditional.column_names], sep="_"),times=ncol(msidata_$i))) ## stores file name for each pixel |
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130 msidata_$i\$combined_sample = rep(paste($i+1, input_list[$i+1,$combine_conditional.column_names], sep="_"),times=ncol(msidata_$i)) |
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131 pixelcoords_$i = cbind(coord(msidata_$i)[,1:2], rep($i+1,ncol(msidata_$i))) |
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132 #silent $pixelcoords.append('pixelcoords_'+str($i)) |
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133 colnames(pixelcoords_$i)[3] = "file_number" |
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134 |
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135 ################### preparation automatic combination ########################## |
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136 |
1
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137 #elif str( $combine_conditional.combine_method ) == 'automatic_combine': |
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138 names_vector = character() |
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139 #set escaped_element_identifier = re.sub('[^\w\-\s\[/]]', '_', str($infile.element_identifier)) ## use name of inputfile from Galaxy |
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140 if (sum(spectra(msidata_$i)[],na.rm=TRUE)>0) ## use only valid files |
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141 { |
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142 if (is.null(levels(msidata_$i\$combined_sample))) |
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143 { |
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144 names_vector = append(names_vector, rep(paste($i+1, "$escaped_element_identifier", sep="_"),ncol(msidata_$i))) |
91bba2486773
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145 msidata_$i\$combined_sample = as.factor(names_vector) |
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146 } |
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147 } |
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148 |
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149 ## Number of input files define grid which is row-wise filled with files |
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150 |
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151 coord(msidata_$i)\$x = coord(msidata_$i)\$x - (min(coord(msidata_$i)\$x-1)) + x_shifts |
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152 coord(msidata_$i)\$y = coord(msidata_$i)\$y - (min(coord(msidata_$i)\$y-1)) + y_shifts |
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153 x_shifts = max(coord(msidata_$i)\$x) + 5 |
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154 max_y = append(max_y, max(coord(msidata_$i)\$y)) |
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155 all_files = $num_infiles |
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156 new_row = ($i+1)/ceiling(sqrt(all_files)) |
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157 new_row%%1==0 |
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158 if (new_row%%1==0) |
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159 {x_shifts = 0 ### when row is filled: x values start again at zero |
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160 y_shifts = max(max_y) + 5 ### when row is filled: y value increases to start a new row |
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161 max_y = numeric()} |
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162 |
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163 #end if |
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164 |
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165 ## store files to combine them later and for each file check if it is valid |
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166 |
0
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167 #silent $msidata.append('msidata_'+str($i)) |
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168 valid_dataset = append(valid_dataset, |
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169 (ncol(msidata_$i)>0 & nrow(msidata_$i)>0 & sum(spectra(msidata_$i)[], na.rm=TRUE)>0)) |
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170 |
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171 #end for |
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172 |
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173 ## extract columnnames from (last) annotation tabular (for QC plot names) |
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174 annotation_colnames = colnames(input_annotation)[-c(1,2)] |
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175 |
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176 ###################### automatic combination ################################### |
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177 ################################################################################ |
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178 |
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179 #if str( $combine_conditional.combine_method ) == 'automatic_combine': |
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180 print("automatic_combine") |
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181 |
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182 ## combine only valid datasets |
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183 |
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184 valid_data = list(#echo ','.join($msidata)#)[valid_dataset] |
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185 msidata_combined = do.call(combine, valid_data) |
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186 print("Valid datasets in order of input bottom to top:") |
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187 print(valid_dataset) |
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188 |
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189 ## create dataframe with x,y,sample_name and show all pixels in PDF as QC |
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190 |
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191 pdf("Combined_qc.pdf", width=15, height=15) |
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192 position_df = cbind(coord(msidata_combined)[,1:2], msidata_combined\$combined_sample) |
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193 colnames(position_df)[3] = "sample_name" |
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194 combine_plot = ggplot(position_df, aes(x=x, y=y, fill=sample_name))+ |
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195 geom_tile() + |
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196 coord_fixed()+ |
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197 ggtitle("Spatial orientation of combined data (sample names)")+ |
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198 theme_bw()+ |
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199 theme(text=element_text(family="ArialMT", face="bold", size=15))+ |
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200 theme(legend.position="bottom",legend.direction="vertical")+ |
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201 guides(fill=guide_legend(ncol=4,byrow=TRUE)) |
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202 coord_labels = aggregate(cbind(x,y)~sample_name, data=position_df, mean, na.rm=TRUE, na.action="na.pass") |
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203 coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$sample_name) |
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204 for(file_count in 1:nrow(coord_labels)) |
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205 {combine_plot = combine_plot + annotate("text",x=coord_labels[file_count,"x"], |
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206 y=coord_labels[file_count,"y"],label=toString(coord_labels[file_count,4]))} |
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207 print(combine_plot) |
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208 dev.off() |
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209 |
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210 ## save as (.RData) |
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211 |
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212 msidata = msidata_combined |
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213 save(msidata, file="$msidata_combined") |
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214 |
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215 |
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216 ################################## xy shifts ################################### |
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217 ################################################################################ |
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218 |
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219 #elif str( $combine_conditional.combine_method ) == 'xy_shifts': |
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220 print("xy_shifts") |
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221 |
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222 ## find duplicated coordinates |
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223 all_coordinates = do.call(rbind, list(#echo ','.join($pixelcoords)#)) |
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224 duplicated_coordinates= duplicated(all_coordinates[,1:2])| duplicated(all_coordinates[,1:2], fromLast=TRUE) |
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225 print(paste0("Number of removed duplicated coordinates: ", sum(duplicated_coordinates)/2)) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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226 unique_coordinates = all_coordinates[!duplicated_coordinates,] |
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227 |
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228 ## remove duplicated coordinates |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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229 datasetlist = list() |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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230 count = 1 |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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231 for (usable_dataset in list(#echo ','.join($msidata)#)){ |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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232 pixelsofinterest = pixels(usable_dataset)[names(pixels(usable_dataset)) %in% rownames(unique_coordinates)] |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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233 filtered_dataset = usable_dataset[,pixelsofinterest] |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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234 if (ncol(filtered_dataset) > 0 ){ |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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235 datasetlist[[count]] = filtered_dataset} |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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236 count = count +1} |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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237 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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238 msidata_combined = do.call(combine, datasetlist) |
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239 |
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240 ## save as (.RData) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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241 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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242 msidata = msidata_combined |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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243 save(msidata, file="$msidata_combined") |
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244 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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245 ## create x,y,sample_name dataframe for QC pdf |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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246 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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247 position_df = cbind(coord(msidata), msidata\$combined_sample) |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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248 colnames(position_df)[3] = "sample_name" |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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249 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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250 #end if |
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251 |
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252 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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253 ################################## outputs #################################### |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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254 ################################################################################ |
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255 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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256 ########### QC with pixels and their annotations ################################ |
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257 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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258 pdf("Combined_qc.pdf", width=15, height=15) |
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259 |
6
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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260 ## combined plot |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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261 combine_plot = ggplot(position_df, aes(x=x, y=y, fill=sample_name))+ |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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262 geom_tile() + |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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263 coord_fixed()+ |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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264 ggtitle("Spatial orientation of combined data")+ |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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265 theme_bw()+ |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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266 theme(text=element_text(family="ArialMT", face="bold", size=15))+ |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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267 theme(legend.position="bottom",legend.direction="vertical")+ |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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268 guides(fill=guide_legend(ncol=5,byrow=TRUE)) |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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269 coord_labels = aggregate(cbind(x,y)~sample_name, data=position_df, mean) |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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270 coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$sample_name) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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271 for(file_count in 1:nrow(coord_labels)) |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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272 {combine_plot = combine_plot + annotate("text",x=coord_labels[file_count,"x"], |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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273 y=coord_labels[file_count,"y"],label=toString(coord_labels[file_count,4]))} |
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274 print(combine_plot) |
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275 |
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276 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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277 ## annotation plots |
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278 |
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279 ## plot 1 |
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280 |
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281 column1_df = cbind(coord(msidata), msidata\$column1) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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282 colnames(column1_df)[3] = "column1" |
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283 |
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284 if (sum(is.na(column1_df[3])) < nrow(column1_df)){ |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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285 column1_plot = ggplot(column1_df, aes(x=x, y=y, fill=column1))+ |
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286 geom_tile() + |
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287 coord_fixed()+ |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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288 ggtitle(paste0(annotation_colnames[1]))+ |
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289 theme_bw()+ |
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290 theme(text=element_text(family="ArialMT", face="bold", size=15))+ |
91bba2486773
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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291 theme(legend.position="bottom",legend.direction="vertical")+ |
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f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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292 guides(fill=guide_legend(ncol=5,byrow=TRUE, title=annotation_colnames[1])) |
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293 print(column1_plot)} |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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294 ##rename columnname for output tabular file |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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295 colnames(column1_df)[3] = annotation_colnames[1] |
f4aafc565aa3
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296 |
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297 ## plot 2 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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298 column2_df = cbind(coord(msidata), msidata\$column2) |
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299 colnames(column2_df)[3] = "column2" |
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300 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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301 if (sum(is.na(column2_df[3])) < nrow(column2_df)){ |
f4aafc565aa3
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302 column2_plot = ggplot(column2_df, aes(x=x, y=y, fill=column2))+ |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
|
303 geom_tile() + |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
|
304 coord_fixed()+ |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
|
305 ggtitle(paste0(annotation_colnames[2]))+ |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
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306 theme_bw()+ |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
|
307 theme(text=element_text(family="ArialMT", face="bold", size=15))+ |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
|
308 theme(legend.position="bottom",legend.direction="vertical")+ |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
|
309 guides(fill=guide_legend(ncol=5,byrow=TRUE, title=annotation_colnames[2])) |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
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310 print(column2_plot)} |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
|
311 ##rename columnname for output tabular file |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
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312 colnames(column2_df)[3] = annotation_colnames[2] |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
|
313 |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
|
314 ## plot 3 |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
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315 column3_df = cbind(coord(msidata), msidata\$column3) |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
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316 colnames(column3_df)[3] = "column3" |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
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317 if (sum(is.na(column3_df[3])) < nrow(column3_df)){ |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
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318 column3_plot = ggplot(column3_df, aes(x=x, y=y, fill=column3))+ |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
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319 geom_tile() + |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
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320 coord_fixed()+ |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
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321 ggtitle(paste0(annotation_colnames[3]))+ |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
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322 theme_bw()+ |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
|
323 theme(text=element_text(family="ArialMT", face="bold", size=15))+ |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
|
324 theme(legend.position="bottom",legend.direction="vertical")+ |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
|
325 guides(fill=guide_legend(ncol=5,byrow=TRUE, title=annotation_colnames[3])) |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
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326 print(column3_plot)} |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
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327 ##rename columnname for output tabular file |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
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328 colnames(column3_df)[3] = annotation_colnames[3] |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
|
329 |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
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diff
changeset
|
330 ## plot 4 |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
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331 column4_df = cbind(coord(msidata), msidata\$column4) |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
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332 colnames(column4_df)[3] = "column4" |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
|
333 |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
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334 if (sum(is.na(column4_df[3])) < nrow(column4_df)){ |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
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335 column4_plot = ggplot(column4_df, aes(x=x, y=y, fill=column4))+ |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
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336 geom_tile() + |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
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337 coord_fixed()+ |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
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338 ggtitle(paste0(annotation_colnames[4]))+ |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
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339 theme_bw()+ |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
|
340 theme(text=element_text(family="ArialMT", face="bold", size=15))+ |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
|
341 theme(legend.position="bottom",legend.direction="vertical")+ |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
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342 guides(fill=guide_legend(ncol=5,byrow=TRUE, title=annotation_colnames[4])) |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
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343 print(column4_plot)} |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
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344 ##rename columnname for output tabular file |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
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345 colnames(column4_df)[3] = annotation_colnames[4] |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
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diff
changeset
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346 |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
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diff
changeset
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347 ## plot5 |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
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diff
changeset
|
348 |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
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349 column5_df = cbind(coord(msidata), msidata\$column5) |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
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350 colnames(column5_df)[3] = "column5" |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
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351 if (sum(is.na(column5_df[3])) < nrow(column5_df)){ |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
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352 column5_plot = ggplot(column5_df, aes(x=x, y=y, fill=column5))+ |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
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353 geom_tile() + |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
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354 coord_fixed()+ |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
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355 ggtitle(paste0(annotation_colnames[5]))+ |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
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356 theme_bw()+ |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
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357 theme(text=element_text(family="ArialMT", face="bold", size=15))+ |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
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358 theme(legend.position="bottom",legend.direction="vertical")+ |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
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359 guides(fill=guide_legend(ncol=5,byrow=TRUE, title=annotation_colnames[5])) |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
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360 print(column5_plot)} |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
|
361 ##rename columnname for output tabular file |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
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362 colnames(column5_df)[3] = annotation_colnames[5] |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
|
363 |
1
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
galaxyp
parents:
0
diff
changeset
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364 dev.off() |
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
galaxyp
parents:
0
diff
changeset
|
365 |
6
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
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diff
changeset
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366 ##################### annotation tabular output ################################ |
0
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
parents:
diff
changeset
|
367 |
5
ff91e78b5c5c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents:
4
diff
changeset
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368 if (length(features(msidata))> 0 & length(pixels(msidata)) > 0){ |
6
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
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diff
changeset
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369 annotation_df_list = list(position_df, column1_df, column2_df, column3_df, column4_df, column5_df) |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
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370 combined_annotations = Reduce(function(...) merge(..., by=c("x", "y"), all=TRUE), annotation_df_list) |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
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diff
changeset
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371 write.table(combined_annotations, file="$annotation_output", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t") |
1
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
galaxyp
parents:
0
diff
changeset
|
372 }else{ |
6
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
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373 print("No annotation tabular output because file has no features or pixels left") |
1
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
galaxyp
parents:
0
diff
changeset
|
374 } |
5
ff91e78b5c5c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents:
4
diff
changeset
|
375 |
6
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
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376 ####################### optional matrix output ################################# |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
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diff
changeset
|
377 |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
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diff
changeset
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378 #if $output_matrix: |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
|
379 |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
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380 if (length(features(msidata))> 0 & length(pixels(msidata)) > 0){ |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
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diff
changeset
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381 spectramatrix = spectra(msidata)[] |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
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diff
changeset
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382 spectramatrix = cbind(mz(msidata),spectramatrix) |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
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diff
changeset
|
383 newmatrix = rbind(c("mz | spectra", names(pixels(msidata))), spectramatrix) |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
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diff
changeset
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384 write.table(newmatrix, file="$matrixasoutput", quote = FALSE, row.names = FALSE, col.names=FALSE, sep = "\t") |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
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diff
changeset
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385 }else{ |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
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diff
changeset
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386 print("No intensity matrix output because file has no features or pixels left") |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
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diff
changeset
|
387 } |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
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diff
changeset
|
388 |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
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diff
changeset
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389 #end if |
0
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
parents:
diff
changeset
|
390 |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
parents:
diff
changeset
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391 ]]></configfile> |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
parents:
diff
changeset
|
392 </configfiles> |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
parents:
diff
changeset
|
393 <inputs> |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
parents:
diff
changeset
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394 <param name="infiles" type="data" multiple="true" format="imzml,rdata,analyze75" |
4
d05bd881af3d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
3
diff
changeset
|
395 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
galaxyp
parents:
diff
changeset
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396 help="load imzml and ibd file by uploading composite datatype imzml"/> |
5
ff91e78b5c5c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents:
4
diff
changeset
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397 <conditional name="processed_cond"> |
ff91e78b5c5c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents:
4
diff
changeset
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398 <param name="processed_file" type="select" label="Is the input file a processed imzML file "> |
ff91e78b5c5c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents:
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diff
changeset
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399 <option value="no_processed" selected="True">not a processed imzML</option> |
ff91e78b5c5c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents:
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diff
changeset
|
400 <option value="processed">processed imzML</option> |
ff91e78b5c5c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents:
4
diff
changeset
|
401 </param> |
ff91e78b5c5c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents:
4
diff
changeset
|
402 <when value="no_processed"/> |
ff91e78b5c5c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents:
4
diff
changeset
|
403 <when value="processed"> |
ff91e78b5c5c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents:
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diff
changeset
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404 <param name="accuracy" type="float" value="50" label="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"/> |
ff91e78b5c5c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents:
4
diff
changeset
|
405 <param name="units" display="radio" type="select" label="Unit of the mass accuracy" help="either m/z or ppm"> |
ff91e78b5c5c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents:
4
diff
changeset
|
406 <option value="mz" >mz</option> |
ff91e78b5c5c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents:
4
diff
changeset
|
407 <option value="ppm" selected="True" >ppm</option> |
ff91e78b5c5c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents:
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diff
changeset
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408 </param> |
ff91e78b5c5c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents:
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diff
changeset
|
409 </when> |
ff91e78b5c5c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents:
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diff
changeset
|
410 </conditional> |
6
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
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diff
changeset
|
411 <param name="annotation_files" type="data" multiple="true" format="tabular" |
7
19d8eee15959
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
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diff
changeset
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412 label="Pixel annotations as tabular files, same number and order of files as input files" |
19d8eee15959
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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diff
changeset
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413 help="Coordinates in column 1 in format x = 1, y = 1 or first column x values, second column y values. Up to 5 columns with pixel annotations"/> |
1
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
galaxyp
parents:
0
diff
changeset
|
414 <conditional name="combine_conditional"> |
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
changeset
|
415 <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
galaxyp
parents:
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diff
changeset
|
416 <option value="automatic_combine" selected="True" >automatic combination</option> |
6
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
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diff
changeset
|
417 <option value="xy_shifts">shift xy coordinates with a tabular file</option> |
1
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
galaxyp
parents:
0
diff
changeset
|
418 </param> |
3
91bba2486773
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
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diff
changeset
|
419 <when value="automatic_combine"/> |
1
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
galaxyp
parents:
0
diff
changeset
|
420 <when value="xy_shifts"> |
6
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
|
421 <param name="coordinates_file" type="data" format="tabular" label="datasetnames, x and y values to shift pixel coordinates before combining" |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
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diff
changeset
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422 help="Tabular file with three columns: 1 for the filename, 1 for the x-coordinate shift and 1 for the y-coordinate shift. Pixels with the same coordinates after shifting will be deleted."/> |
1
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
galaxyp
parents:
0
diff
changeset
|
423 <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
galaxyp
parents:
0
diff
changeset
|
424 <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
galaxyp
parents:
0
diff
changeset
|
425 <param name="column_names" data_ref="coordinates_file" label="Column with dataset names" type="data_column"/> |
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
changeset
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426 </when> |
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
changeset
|
427 </conditional> |
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
galaxyp
parents:
0
diff
changeset
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428 <param name="output_matrix" type="boolean" display="radio" label="Intensity matrix output"/> |
0
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
parents:
diff
changeset
|
429 </inputs> |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
parents:
diff
changeset
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430 <outputs> |
3
91bba2486773
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
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diff
changeset
|
431 <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
galaxyp
parents:
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diff
changeset
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432 <data format="pdf" name="combining_qc" from_work_dir="Combined_qc.pdf" label = "Combined_QC"/> |
6
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
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diff
changeset
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433 <data format="tabular" name="annotation_output" label="Annotation_tabular"/> |
3
91bba2486773
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
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diff
changeset
|
434 <data format="tabular" name="matrixasoutput" label="Combined_matrix"> |
0
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
parents:
diff
changeset
|
435 <filter>output_matrix</filter> |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
parents:
diff
changeset
|
436 </data> |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
parents:
diff
changeset
|
437 </outputs> |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
parents:
diff
changeset
|
438 <tests> |
6
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
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diff
changeset
|
439 <test expect_num_outputs="4"> |
0
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
parents:
diff
changeset
|
440 <param name="infiles" value="msidata_1.RData,msidata_2.RData,msidata_3.RData" ftype="rdata"/> |
6
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
|
441 <param name="annotation_files" value="annotations_file1.tabular,annotations_file2.tabular,annotations_file3.tabular" ftype="tabular"/> |
1
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
galaxyp
parents:
0
diff
changeset
|
442 <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
parents:
diff
changeset
|
443 <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:
diff
changeset
|
444 <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
parents:
diff
changeset
|
445 <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
parents:
diff
changeset
|
446 <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
parents:
diff
changeset
|
447 <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
parents:
diff
changeset
|
448 <output name="matrixasoutput" file="123_combined_matrix.tabular"/> |
6
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
|
449 <output name="annotation_output" file="123_annotation_output.tabular"/> |
0
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
parents:
diff
changeset
|
450 <output name="msidata_combined" file="123_combined.RData" compare="sim_size" /> |
7
19d8eee15959
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
6
diff
changeset
|
451 <output name="combining_qc" file="123_combined_QC.pdf" compare="sim_size" delta="2000"/> |
0
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
parents:
diff
changeset
|
452 </test> |
6
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
|
453 <test expect_num_outputs="4"> |
0
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
parents:
diff
changeset
|
454 <param name="infiles" value="msidata_1.RData,msidata_2.RData" ftype="rdata"/> |
6
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
|
455 <param name="annotation_files" value="annotations_file1.tabular,annotations_file2.tabular" ftype="tabular"/> |
3
91bba2486773
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
2
diff
changeset
|
456 <param name="combine_method" value="automatic_combine"/> |
0
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
parents:
diff
changeset
|
457 <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
parents:
diff
changeset
|
458 <output name="matrixasoutput" file="12_combined_matrix.tabular"/> |
6
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
|
459 <output name="annotation_output" file="12_annotation_output.tabular"/> |
0
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
parents:
diff
changeset
|
460 <output name="msidata_combined" file="12_combined.RData" compare="sim_size" /> |
7
19d8eee15959
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
6
diff
changeset
|
461 <output name="combining_qc" file="12_combined_QC.pdf" compare="sim_size" delta="2000"/> |
0
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
parents:
diff
changeset
|
462 </test> |
6
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
|
463 <test expect_num_outputs="3"> |
3
91bba2486773
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
2
diff
changeset
|
464 <param name="infiles" value="msidata_1.RData,123_combined.RData" ftype="rdata"/> |
6
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
|
465 <param name="annotation_files" value="annotations_file1.tabular,123_annotation.tabular" ftype="tabular"/> |
1
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
galaxyp
parents:
0
diff
changeset
|
466 <param name="combine_method" value="automatic_combine"/> |
3
91bba2486773
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
2
diff
changeset
|
467 <param name="output_matrix" value="False"/> |
6
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
|
468 <output name="annotation_output" file="112_annotation_output.tabular"/> |
3
91bba2486773
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
2
diff
changeset
|
469 <output name="msidata_combined" file="112_auto_combined.RData" compare="sim_size" /> |
7
19d8eee15959
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
6
diff
changeset
|
470 <output name="combining_qc" file="112_auto_combined_QC.pdf" compare="sim_size" delta="2000"/> |
1
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
galaxyp
parents:
0
diff
changeset
|
471 </test> |
0
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
parents:
diff
changeset
|
472 </tests> |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
parents:
diff
changeset
|
473 <help> |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
parents:
diff
changeset
|
474 <![CDATA[ |
1
f3f6c32ab690
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
galaxyp
parents:
0
diff
changeset
|
475 |
2
00b6c61f5054
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents:
1
diff
changeset
|
476 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
parents:
0
diff
changeset
|
477 |
3
91bba2486773
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
2
diff
changeset
|
478 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:
diff
changeset
|
479 |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
parents:
diff
changeset
|
480 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:
diff
changeset
|
481 |
2
00b6c61f5054
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents:
1
diff
changeset
|
482 - 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:
diff
changeset
|
483 - 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:
diff
changeset
|
484 - 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:
diff
changeset
|
485 |
6
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
|
486 |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
|
487 Input: |
2
00b6c61f5054
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents:
1
diff
changeset
|
488 |
6
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
|
489 - MSI data files with same m/z values (to obtain same m/z values for different files: filtering tool same m/z range and preprocessing tool same binning width) |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
|
490 - Tabular files with pixel annotations need to have the x values in the first column, y values in the second column and then up to five annotations in the next columns. The order of the annotations in the columns must be the same for all files (x and y in column 1 and 2; annotation1 in column3, annotation2 in column4,...) |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
|
491 - The order and the number of MSI data files and annotation tabular files must be the same |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
|
492 - For xy shifts with tabular file: Tabular file with x and y coordinates shift and file name (see below) |
2
00b6c61f5054
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents:
1
diff
changeset
|
493 |
00b6c61f5054
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents:
1
diff
changeset
|
494 Options: |
00b6c61f5054
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents:
1
diff
changeset
|
495 |
6
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
|
496 - "automatic combination": files are automatically arranged in a grid (duplicated pixels are allowed), subfiles are named according to the input file name |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
|
497 - "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). The xy shift option combines all datasets and removes all duplicated pixels (same x and y coordinates). |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
|
498 |
2
00b6c61f5054
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents:
1
diff
changeset
|
499 |
00b6c61f5054
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents:
1
diff
changeset
|
500 Output: |
00b6c61f5054
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents:
1
diff
changeset
|
501 |
6
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
|
502 - single imzML file |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
|
503 - pdf that shows the pixel positions and annotations of the combined files |
f4aafc565aa3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents:
5
diff
changeset
|
504 - Tabular file with pixel annotations (x,y,column with input file names, up to five annotation columns) |
3
91bba2486773
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
2
diff
changeset
|
505 - optional: intensity matrix as tabular file (intensities for m/z in rows and pixel in columns) |
2
00b6c61f5054
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents:
1
diff
changeset
|
506 |
00b6c61f5054
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents:
1
diff
changeset
|
507 |
0
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
parents:
diff
changeset
|
508 ]]> |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
parents:
diff
changeset
|
509 </help> |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
parents:
diff
changeset
|
510 <citations> |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
parents:
diff
changeset
|
511 <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
|
512 </citations> |
9cbcf48bf60a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
parents:
diff
changeset
|
513 </tool> |