Mercurial > repos > galaxyp > cardinal_combine
annotate combine.xml @ 8:525f201b86c1 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
author | galaxyp |
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date | Wed, 13 May 2020 14:08:25 -0400 |
parents | 392b2dfd261d |
children | 7e18fcb92a6a |
rev | line source |
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8
525f201b86c1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
galaxyp
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1 <tool id="cardinal_combine" name="MSI combine" version="@VERSION@.1"> |
0
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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2 <description> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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3 combine several mass spectrometry imaging datasets into one |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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4 </description> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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5 <macros> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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6 <import>macros.xml</import> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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7 </macros> |
7
392b2dfd261d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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8 <expand macro="requirements"> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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9 <requirement type="package" version="3.2.1">r-ggplot2</requirement> |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
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10 <requirement type="package" version="0.12">r-maldiquantforeign</requirement> |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
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11 <requirement type="package" version="1.19.3">r-maldiquant</requirement> |
7
392b2dfd261d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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12 </expand> |
0
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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13 <command detect_errors="exit_code"> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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14 <![CDATA[ |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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15 #for $i, $infile in enumerate($infiles): |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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16 #if $infile.ext == 'imzml' |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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17 ln -s '${infile.extra_files_path}/imzml' infile_${i}.imzML && |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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18 ln -s '${infile.extra_files_path}/ibd' infile_${i}.ibd && |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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19 #elif $infile.ext == 'analyze75' |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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20 ln -s '${infile.extra_files_path}/hdr' infile_${i}.hdr && |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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21 ln -s '${infile.extra_files_path}/img' infile_${i}.img && |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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22 ln -s '${infile.extra_files_path}/t2m' infile_${i}.t2m && |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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23 #else |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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24 ln -s '$infile' infile_${i}.RData && |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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25 #end if |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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26 #end for |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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27 #if $annotation_cond.annotation_tabular == 'annotation' |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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28 #for $i, $annotation_file in enumerate($annotation_cond.annotation_files): |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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29 ln -s '$annotation_file' annotation_file_${i}.tabular && |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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30 #end for |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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31 #end if |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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32 |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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33 cat '${msi_combine}' && |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
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34 Rscript '${msi_combine}' && |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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35 mkdir $outfile_imzml.files_path && |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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36 mv ./out.imzML "${os.path.join($outfile_imzml.files_path, 'imzml')}" | true && |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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37 mv ./out.ibd "${os.path.join($outfile_imzml.files_path, 'ibd')}" | true && |
1
65245dc812c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
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38 echo "imzML file:" > $outfile_imzml && |
65245dc812c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
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39 ls -l "$outfile_imzml.files_path" >> $outfile_imzml |
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93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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40 |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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41 ]]> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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42 </command> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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43 <configfiles> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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44 <configfile name="msi_combine"><![CDATA[ |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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45 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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46 #import re |
93be1d20b5c3
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47 |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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48 ################ 1) load libraries and do preparations ################# |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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49 |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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50 library(Cardinal) |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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51 library(ggplot2) |
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b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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52 library(MALDIquantForeign) |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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53 library(MALDIquant) |
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93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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54 |
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392b2dfd261d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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55 |
0
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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56 ## read tabular file for xy_shift option |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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57 #if str( $combine_conditional.combine_method ) == 'xy_shifts': |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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58 input_list = read.delim("$combine_conditional.coordinates_file", header = $combine_conditional.xy_header, |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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59 stringsAsFactors = FALSE) |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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60 #end if |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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61 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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62 ## function to load RData and store with new variable name |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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63 loadRData <- function(fileName){ |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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64 load(fileName) |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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65 get(ls()[ls() != "fileName"]) |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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66 } |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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67 |
93be1d20b5c3
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68 ## preparations for reading files one by one with for loop |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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69 sample_names = numeric() |
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93be1d20b5c3
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70 x_shifts = 0 |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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71 y_shifts = 0 |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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72 max_y = numeric() |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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73 valid_dataset = logical() |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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74 coordinates_combined = data.frame(matrix(,ncol=2, nrow=0)) |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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75 msidata_combined = list() |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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76 #set $msidata = [] |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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77 #set $pixelcoords = [] |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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78 #set $num_infiles = len($infiles) |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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79 all_files = $num_infiles |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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80 |
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81 ###################### 2) reading MSI files #################################### |
0
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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82 |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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83 #for $i, $infile in enumerate($infiles): |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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84 |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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85 ## read and manipulate MSI data |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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86 |
7
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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87 #if $infile.ext == 'imzml' |
392b2dfd261d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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88 #if str($processed_cond.processed_file) == "processed": |
8
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
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89 msidata_$i <- readImzML('infile_${i}', resolution=$processed_cond.accuracy, units = "$processed_cond.units", attach.only=TRUE) |
525f201b86c1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
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90 msidata_$i = collect(msidata_$i, as.matrix=TRUE) ##coercion to continuous |
7
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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91 centroided(msidata_$i) = $centroids |
392b2dfd261d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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92 #else |
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93 msidata_$i <- readImzML('infile_${i}', attach.only=TRUE) |
7
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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94 centroided(msidata_$i) = $centroids |
392b2dfd261d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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95 #end if |
392b2dfd261d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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96 #elif $infile.ext == 'analyze75' |
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97 msidata_$i = readAnalyze('infile_${i}', attach.only=TRUE) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
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98 centroided(msidata_$i) = $centroids |
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99 #else |
7
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100 ## function to read RData files independent of filename |
392b2dfd261d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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101 loadRData <- function(fileName){ |
392b2dfd261d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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102 load(fileName) |
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103 get(ls()[ls() != "fileName"]) |
392b2dfd261d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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104 } |
0
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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105 msidata_$i = loadRData('infile_${i}.RData') |
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106 ## keep compatibility with old .RData files: |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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107 msidata_$i\$column1 = NULL |
b41107d8fe89
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108 msidata_$i\$column2 = NULL |
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109 msidata_$i\$column3 = NULL |
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110 msidata_$i\$column4 = NULL |
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111 msidata_$i\$column5 = NULL |
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112 msidata_$i\$combined_sample = NULL |
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113 #end if |
0
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114 |
8
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115 ## coercion into MSImageSet |
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116 msidata_$i = as(msidata_$i, "MSImageSet") |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
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117 |
0
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118 ## remove duplicated coordinates, otherwise combine will fail |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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119 print(paste0(sum(duplicated(coord(msidata_$i))), " duplicated coordinates were removed from input file")) |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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120 msidata_${i} <- msidata_${i}[,!duplicated(coord(msidata_${i}))] |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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121 |
5
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122 ## same name for MSI data files necessary to combine data into one single coordinate system |
0
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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123 sampleNames(msidata_$i) = "msidata" |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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124 |
5
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125 ############ 3) Read and process annotation tabular files ###################### |
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126 |
0
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127 #if str($annotation_cond.annotation_tabular) == 'annotation' |
93be1d20b5c3
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128 print("annotations") |
93be1d20b5c3
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129 |
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130 ## read annotation tabular, set first two columns as x and y, merge with coordinates dataframe and order according to pixelorder in msidata |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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131 input_annotation = read.delim("annotation_file_${i}.tabular", header = $annotation_cond.tabular_header, stringsAsFactors = FALSE) |
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132 colnames(input_annotation)[1:2] = c("x", "y") |
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133 |
93be1d20b5c3
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134 msidata_coordinates = cbind(coord(msidata_$i)[,1:2], 1:ncol(msidata_$i)) |
93be1d20b5c3
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135 colnames(msidata_coordinates)[3] = "pixel_index" |
93be1d20b5c3
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136 |
93be1d20b5c3
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137 annotation_df = merge(msidata_coordinates, input_annotation, by=c("x", "y"), all.x=TRUE) |
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138 annotation_df_sorted = annotation_df[order(annotation_df\$pixel_index),]## orders pixel according to msidata |
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139 annotation_df_sorted\$pixel_index = NULL |
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140 |
0
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141 ## extract columnnames from (last) annotation tabular (for QC plot names) |
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142 annotation_colnames = colnames(input_annotation) |
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143 |
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144 #end if |
93be1d20b5c3
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145 |
5
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146 ############### 4) shift coordinates with xy shifts ############################ |
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147 |
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148 #if str( $combine_conditional.combine_method ) == 'xy_shifts': |
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149 |
5
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150 ## optional: set all files to 1/1 and then add shift |
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151 #if $combine_conditional.xy_origin: |
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152 coord(msidata_$i)\$x = as.integer(coord(msidata_$i)\$x - min(coord(msidata_$i)\$x-1)) |
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153 coord(msidata_$i)\$y = as.integer(coord(msidata_$i)\$y - min(coord(msidata_$i)\$y-1)) |
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154 #end if |
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155 |
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156 ## shift coordinates according to input tabular file and store file names |
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157 coord(msidata_$i)\$x = as.integer(coord(msidata_$i)\$x + input_list[$i+1,$combine_conditional.column_x]) ## shifts x coordinates according to tabular file |
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158 coord(msidata_$i)\$y = as.integer(coord(msidata_$i)\$y + input_list[$i+1,$combine_conditional.column_y]) ## shifts y coordinates according to tabular file |
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159 sample_name = rep(paste(input_list[$i+1,$combine_conditional.column_names]),times=ncol(msidata_$i)) ## stores file name for each pixel |
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160 sample_names = append(sample_names, sample_name) |
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161 |
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162 ## store number of file to use later when removing duplicate coordinates |
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163 pixelcoords_$i = cbind(coord(msidata_$i)[,1:2], rep($i+1,ncol(msidata_$i))) |
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164 #silent $pixelcoords.append('pixelcoords_'+str($i)) |
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165 colnames(pixelcoords_$i)[3] = "file_number" |
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166 |
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167 ##################### 5) shift coordinates automatically ####################### |
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168 |
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169 #elif str( $combine_conditional.combine_method ) == 'automatic_combine': |
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170 |
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171 ## use name of Galaxy inputfile as sample annotation |
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172 sample_name = character() |
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173 #set escaped_element_identifier = re.sub('[^\w\-\s\[/]]', '_', str($infile.element_identifier)) |
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174 |
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175 if (ncol(msidata_$i)>0 & nrow(msidata_$i) >0) |
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176 { |
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177 sample_name = append(sample_name, rep(paste("$escaped_element_identifier"),ncol(msidata_$i))) |
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178 } |
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179 |
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180 ## Number of input files define grid which is row-wise filled with files |
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181 coord(msidata_$i)\$x = as.integer(coord(msidata_$i)\$x - (min(coord(msidata_$i)\$x-1)) + x_shifts) |
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182 coord(msidata_$i)\$y = as.integer(coord(msidata_$i)\$y - (min(coord(msidata_$i)\$y-1)) + y_shifts) |
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183 |
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184 x_shifts = max(coord(msidata_$i)\$x) + $combine_conditional.shift_value |
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185 max_y = append(max_y, max(coord(msidata_$i)\$y)) |
93be1d20b5c3
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186 all_files = $num_infiles |
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187 new_row = ($i+1)/ceiling(sqrt(all_files)) |
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188 new_row%%1==0 |
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189 if (new_row%%1==0) |
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190 {x_shifts = 0 ### when row is filled: x values start again at zero |
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191 y_shifts = max(max_y) + $combine_conditional.shift_value ### when row is filled: y value increases to start a new row |
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192 max_y = numeric()} |
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193 |
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194 #end if |
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195 |
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196 ############################# 6) combination of files ########################## |
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197 |
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198 ## combine shifted coordinates with sample name and annotations from input file |
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199 |
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200 #if str($annotation_cond.annotation_tabular) == 'annotation' |
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201 cardinal_coordinates_$i = data.frame(as.matrix(Cardinal::coord(msidata_$i)[,1:2]), sample_name, annotation_df_sorted[,-c(1,2)]) |
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202 #else |
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203 cardinal_coordinates_$i = data.frame(as.matrix(Cardinal::coord(msidata_$i)[,1:2]), sample_name) |
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204 #end if |
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205 |
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206 ## store files to combine them later and for each file check if it is valid |
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207 #silent $msidata.append('msidata_'+str($i)) |
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208 valid_dataset = append(valid_dataset, ncol(msidata_$i)>0 & nrow(msidata_$i)>0) |
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209 |
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210 |
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211 ######################### 6a) combination different mz axis #################### |
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212 |
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213 ## combination for files with different mz axis via MALDIquant during for loop |
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214 |
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215 #if $processed_true: |
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216 print("mz axis differ") |
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217 |
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218 cardinal_mzs_$i = Cardinal::mz(msidata_$i) |
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219 |
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220 for(number_spectra in 1:ncol(msidata_${i})){ |
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221 |
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222 if (centroided(msidata_$i) == FALSE){ |
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223 ## create mass spectrum object |
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224 maldi_data_${i} = list() |
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225 for(number_spectra in 1:ncol(msidata_$i)){ |
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226 maldi_data_${i}[[number_spectra]] = MALDIquant::createMassSpectrum(mass = cardinal_mzs_$i, intensity = Cardinal::iData(msidata_$i)[,number_spectra])} |
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227 }else{ |
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228 maldi_data_${i} = list() |
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229 for (spectra in 1:ncol(msidata_$i)) |
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230 { |
b41107d8fe89
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231 single_peaks_${i} = createMassPeaks(cardinal_mzs_$i, Cardinal::spectra(msidata_$i)[,spectra], snr=as.numeric(rep("NA", nrow(msidata_$i)))) |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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232 maldi_data_${i}[[spectra]] = single_peaks_${i} |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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233 } |
b41107d8fe89
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234 } |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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235 } |
b41107d8fe89
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236 |
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237 msidata_combined = append(msidata_combined, maldi_data_$i) |
b41107d8fe89
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238 |
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239 #end if |
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240 |
b41107d8fe89
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241 coordinates_combined = rbind(coordinates_combined, cardinal_coordinates_$i) |
0
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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242 |
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243 #end for |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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244 |
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245 |
6
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246 ######################### 6b) combination same mz axis ################### |
0
93be1d20b5c3
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247 |
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248 #if str( $combine_conditional.combine_method ) == 'automatic_combine': |
5
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249 print("automatic combine") |
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250 |
5
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251 #if not $processed_true: |
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252 ## combine only valid datasets |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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253 |
5
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254 valid_data = list(#echo ','.join($msidata)#)[valid_dataset] |
b41107d8fe89
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255 msidata = do.call(combine, valid_data) |
b41107d8fe89
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256 print("Valid datasets in order of input bottom to top:") |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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257 print(valid_dataset) |
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258 writeImzML(msidata, "out") |
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93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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259 |
5
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260 #else |
b41107d8fe89
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261 |
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262 ## save msidata as imzML file MALDIquant |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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263 MALDIquantForeign::exportImzMl(msidata_combined, file="out.imzML", processed=TRUE, coordinates=as.matrix(coordinates_combined[,1:2])) |
b41107d8fe89
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264 |
1
65245dc812c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
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265 #end if |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
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266 |
5
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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267 ########################### xy shift combination ############################### |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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268 ################################################################################ |
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269 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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270 #elif str( $combine_conditional.combine_method ) == 'xy_shifts': |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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271 print("xy_shifts") |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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272 |
5
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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273 #if not $processed_true: |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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274 |
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275 duplicated_coordinates= duplicated(coordinates_combined[,1:2])| duplicated(coordinates_combined[,1:2], fromLast=TRUE) |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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276 print(paste0("Number of removed duplicated coordinates after combination: ", sum(duplicated_coordinates))) |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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277 coordinates_combined = coordinates_combined[!duplicated_coordinates,] |
0
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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278 |
5
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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279 ## remove duplicated coordinates |
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280 datasetlist = list() |
b41107d8fe89
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281 count = 1 |
b41107d8fe89
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282 for (usable_dataset in list(#echo ','.join($msidata)#)){ |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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283 pixelsofinterest = pixels(usable_dataset)[names(pixels(usable_dataset)) %in% rownames(coordinates_combined)] |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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284 filtered_dataset = usable_dataset[,pixelsofinterest] |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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285 if (ncol(filtered_dataset) > 0 ){ |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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286 datasetlist[[count]] = filtered_dataset} |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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287 count = count +1} |
b41107d8fe89
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288 |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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289 msidata = do.call(combine, datasetlist) |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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290 writeImzML(msidata, "out") |
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93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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291 |
5
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292 #else |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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293 |
5
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294 ## in case user made mistake with xy shifts: find duplicated coordinates |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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295 duplicated_coordinates= duplicated(coordinates_combined[,1:2])| duplicated(coordinates_combined[,1:2], fromLast=TRUE) |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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296 print(paste0("Number of removed duplicated coordinates after combination: ", sum(duplicated_coordinates))) |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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297 unique_coordinates = data.frame(coordinates_combined)[!duplicated_coordinates,] |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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298 |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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299 filtered_dataset = msidata_combined [!duplicated_coordinates] |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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300 coordinates_matrix = as.matrix(unique_coordinates[,1:2]) |
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48c07268f341
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
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301 |
5
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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302 ## save msidata as imzML file MALDIquant |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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303 MALDIquantForeign::exportImzMl(filtered_dataset, file="out.imzML", processed=TRUE, coordinates=coordinates_matrix) |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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304 |
b41107d8fe89
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305 coordinates_combined = unique_coordinates |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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306 |
2
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307 #end if |
1
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308 |
0
93be1d20b5c3
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309 #end if |
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310 |
5
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
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311 ################################## outputs ##################################### |
0
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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312 ################################################################################ |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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313 |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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314 ########### QC with pixels and their annotations ################################ |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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315 |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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316 pdf("Combined_qc.pdf", width=15, height=15) |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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317 |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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318 ## combined plot |
5
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
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319 combine_plot = ggplot(coordinates_combined[,1:3], aes(x=x, y=y, fill=sample_name))+ |
0
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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320 geom_tile() + |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
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321 coord_fixed()+ |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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322 ggtitle("Spatial orientation of combined data")+ |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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323 theme_bw()+ |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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324 theme(text=element_text(family="ArialMT", face="bold", size=15))+ |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
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|
325 theme(legend.position="bottom",legend.direction="vertical")+ |
2
129cddd02600
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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1
diff
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326 guides(fill=guide_legend(ncol=4,byrow=TRUE)) |
5
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
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327 coord_labels = aggregate(cbind(x,y)~sample_name, data=coordinates_combined[,1:3], mean) |
0
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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328 coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$sample_name) |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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329 print(combine_plot) |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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330 |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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331 #if str($annotation_cond.annotation_tabular) == 'annotation' |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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332 ## annotation plots |
5
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
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333 for (inputcolumns in 4:ncol(coordinates_combined)){ |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
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334 ## plot 1 |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
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diff
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335 column1_df = coordinates_combined[,c(1,2,inputcolumns)] |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
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336 colnames(column1_df)[3] = "column1" |
0
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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337 |
5
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
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diff
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338 if (sum(is.na(column1_df[3])) < nrow(column1_df)){ |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
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diff
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339 column1_plot = ggplot(column1_df, aes(x=x, y=y, fill=column1))+ |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
4
diff
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340 geom_tile() + |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
4
diff
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|
341 coord_fixed()+ |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
4
diff
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342 ggtitle(paste0(annotation_colnames[inputcolumns-1]))+ |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
4
diff
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|
343 theme_bw()+ |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
4
diff
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344 theme(text=element_text(family="ArialMT", face="bold", size=15))+ |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
4
diff
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|
345 theme(legend.position="bottom",legend.direction="vertical")+ |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
4
diff
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|
346 guides(fill=guide_legend(ncol=4,byrow=TRUE, title=annotation_colnames[1])) |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
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4
diff
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|
347 print(column1_plot)} |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
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diff
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|
348 ##rename columnname for output tabular file |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
4
diff
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|
349 colnames(column1_df)[3] = annotation_colnames[inputcolumns-1] |
0
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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|
350 |
5
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
4
diff
changeset
|
351 } |
0
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
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|
352 |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
353 #end if |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
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|
354 dev.off() |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
355 |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
356 ##################### annotation tabular output ################################ |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
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|
357 |
5
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
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diff
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|
358 write.table(coordinates_combined, file="$pixel_annotations", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t") |
1
65245dc812c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
0
diff
changeset
|
359 |
0
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
360 ]]></configfile> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
361 </configfiles> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
362 <inputs> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
363 <param name="infiles" type="data" multiple="true" format="imzml,rdata,analyze75" |
4
48c07268f341
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents:
2
diff
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|
364 label="MSI data" |
48c07268f341
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents:
2
diff
changeset
|
365 help="Input file as imzML (composite upload), Analyze7.5 (composite upload) or Cardinal MSImageSet saved as RData (regular upload)"/> |
48c07268f341
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents:
2
diff
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|
366 <param name="centroids" type="boolean" label="Centroided input" help="Choose Yes if peak detection has already been done." truevalue="TRUE" falsevalue="FALSE"/> |
0
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
367 <conditional name="processed_cond"> |
4
48c07268f341
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents:
2
diff
changeset
|
368 <param name="processed_file" type="select" label="Processed imzML file" help="Choose no if your input is an Analyze7.5 or continuous imzML file"> |
48c07268f341
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
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diff
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|
369 <option value="no_processed" selected="True">no</option> |
48c07268f341
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
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diff
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|
370 <option value="processed">yes</option> |
0
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
371 </param> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
372 <when value="no_processed"/> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
373 <when value="processed"> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
374 <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"/> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
375 <param name="units" display="radio" type="select" label="Unit of the mass accuracy" help="either m/z or ppm"> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
376 <option value="mz" >mz</option> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
377 <option value="ppm" selected="True" >ppm</option> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
378 </param> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
379 </when> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
380 </conditional> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
381 <conditional name="annotation_cond"> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
382 <param name="annotation_tabular" type="select" label="Optional annotation of pixels with tabular files"> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
383 <option value="no_annotation" selected="True">no annotation</option> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
384 <option value="annotation">pixel annotations</option> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
385 </param> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
386 <when value="no_annotation"/> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
387 <when value="annotation"> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
388 <param name="annotation_files" type="data" multiple="true" format="tabular" |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
389 label="Pixel annotations tabular files" |
5
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
4
diff
changeset
|
390 help="Same number and order of files as input files. First column x values, second column y values, further columns with annotations"/> |
0
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
391 <param name="tabular_header" type="boolean" label="Tabular files contain a header line" truevalue="TRUE" falsevalue="FALSE"/> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
392 </when> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
393 </conditional> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
394 <conditional name="combine_conditional"> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
395 <param name="combine_method" type="select" label="Way of combining multiple files"> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
396 <option value="automatic_combine" selected="True" >automatic combination</option> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
397 <option value="xy_shifts">shift xy coordinates with a tabular file</option> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
398 </param> |
5
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
4
diff
changeset
|
399 <when value="automatic_combine"> |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
4
diff
changeset
|
400 <param name="shift_value" type="integer" value="5" label="Number of empty pixels that should separate different datasets in x and y dimension"/> |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
4
diff
changeset
|
401 </when> |
0
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
402 <when value="xy_shifts"> |
2
129cddd02600
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
403 <param name="coordinates_file" type="data" format="tabular" label="Datasetnames, x and y values to shift pixel coordinates before combining" |
0
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
404 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."/> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
405 <param name="column_x" data_ref="coordinates_file" label="Column with values for shift in x direction" type="data_column"/> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
406 <param name="column_y" data_ref="coordinates_file" label="Column with values for shift in y direction" type="data_column"/> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
407 <param name="column_names" data_ref="coordinates_file" label="Column with dataset names" type="data_column"/> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
408 <param name="xy_header" type="boolean" label="Tabular files contain a header line" truevalue="TRUE" falsevalue="FALSE"/> |
5
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
4
diff
changeset
|
409 <param name="xy_origin" type="boolean" label="Set all file coordinates to 1/1 as origin" truevalue="TRUE" falsevalue="FALSE" help="Yes: all file coordinates are shifted in order to have at least one pixel with x = 1 and one with y = 1; then coordinates shifts are added. No: the coordinate shifts are added to the current coordinates of the file"/> |
0
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
410 </when> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
411 </conditional> |
5
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
4
diff
changeset
|
412 <param name="processed_true" type="boolean" label="Do the files have different m/z axis?" help="If all m/z values of all files are exactly the same choose 'No'. If not sure choose 'Yes'." truevalue="TRUE" falsevalue="FALSE"/> |
0
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
413 </inputs> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
414 <outputs> |
5
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
4
diff
changeset
|
415 <data format="imzml" name="outfile_imzml" label="${tool.name} on ${on_string}: imzML"/> |
0
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
416 <data format="pdf" name="QC_overview" from_work_dir="Combined_qc.pdf" label = "${tool.name} on ${on_string}: QC"/> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
417 <data format="tabular" name="pixel_annotations" label="${tool.name} on ${on_string}: annotations"/> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
418 </outputs> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
419 <tests> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
420 <test> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
421 <param name="infiles" value="msidata_1.RData,msidata_2.RData,msidata_3.RData" ftype="rdata"/> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
422 <conditional name="annotation_cond"> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
423 <param name="annotation_tabular" value="annotation"/> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
424 <param name="annotation_files" value="annotations_file1.tabular,annotations_file2.tabular,annotations_file3.tabular" ftype="tabular"/> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
425 <param name="tabular_header" value="TRUE"/> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
426 </conditional> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
427 <param name="combine_method" value="xy_shifts"/> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
428 <param name="coordinates_file" ftype="tabular" value="xy_coordinates.tabular"/> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
429 <param name="column_x" value="1"/> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
430 <param name="column_y" value="2"/> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
431 <param name="column_names" value="3"/> |
5
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
4
diff
changeset
|
432 <param name="processed_true" value="FALSE"/> |
0
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
433 <output name="pixel_annotations" file="123_annotation_output.tabular"/> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
434 <output name="QC_overview" file="123_combined_QC.pdf" compare="sim_size"/> |
5
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
4
diff
changeset
|
435 <output name="outfile_imzml" ftype="imzml" file="123_combined.imzml.txt" compare="sim_size"> |
6
bb1ac6b47a6c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents:
5
diff
changeset
|
436 <extra_files type="file" file="123_combined.imzml" name="imzml" lines_diff="12"/> |
5
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
4
diff
changeset
|
437 <extra_files type="file" file="123_combined.ibd" name="ibd" compare="sim_size"/> |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
4
diff
changeset
|
438 </output> |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
4
diff
changeset
|
439 </test> |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
4
diff
changeset
|
440 <test> |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
4
diff
changeset
|
441 <param name="infiles" value="123_combined_picked.rdata,123_combined_picked2.rdata" ftype="rdata"/> |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
4
diff
changeset
|
442 <param name="centroids" value="TRUE"/> |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
4
diff
changeset
|
443 <param name="combine_method" value="xy_shifts"/> |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
4
diff
changeset
|
444 <param name="coordinates_file" ftype="tabular" value="xy_coordinates2.tabular"/> |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
4
diff
changeset
|
445 <param name="column_x" value="1"/> |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
4
diff
changeset
|
446 <param name="column_y" value="2"/> |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
4
diff
changeset
|
447 <param name="column_names" value="3"/> |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
4
diff
changeset
|
448 <param name="processed_true" value="TRUE"/> |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
4
diff
changeset
|
449 <output name="pixel_annotations" file="picked.tabular"/> |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
4
diff
changeset
|
450 <output name="QC_overview" file="picked_QC.pdf" compare="sim_size"/> |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
4
diff
changeset
|
451 <output name="outfile_imzml" ftype="imzml" file="picked.imzml.txt" compare="sim_size"> |
6
bb1ac6b47a6c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents:
5
diff
changeset
|
452 <extra_files type="file" file="picked.imzml" name="imzml" lines_diff="12"/> |
5
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
4
diff
changeset
|
453 <extra_files type="file" file="picked.ibd" name="ibd" compare="sim_size"/> |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
4
diff
changeset
|
454 </output> |
0
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
455 </test> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
456 <test> |
2
129cddd02600
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
457 <param name="infiles" value="msidata_1.RData,msidata_2.RData,msidata_3.RData" ftype="rdata"/> |
129cddd02600
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
458 <conditional name="annotation_cond"> |
129cddd02600
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
459 <param name="annotation_tabular" value="no_annotation"/> |
129cddd02600
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
460 </conditional> |
129cddd02600
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
461 <param name="combine_method" value="automatic_combine"/> |
5
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
4
diff
changeset
|
462 <param name="processed_true" value="FALSE"/> |
2
129cddd02600
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
463 <output name="QC_overview" file="123_combined_auto.pdf" compare="sim_size"/> |
129cddd02600
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
464 <output name="pixel_annotations" file="123_combined_auto.tabular"/> |
129cddd02600
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
465 <output name="outfile_imzml" ftype="imzml" file="123_combined_auto.imzml.txt" compare="sim_size"> |
6
bb1ac6b47a6c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents:
5
diff
changeset
|
466 <extra_files type="file" file="123_combined_auto.imzml" name="imzml" lines_diff="12"/> |
2
129cddd02600
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
467 <extra_files type="file" file="123_combined_auto.ibd" name="ibd" compare="sim_size"/> |
129cddd02600
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
468 </output> |
129cddd02600
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
469 </test> |
129cddd02600
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
470 <test> |
0
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
471 <param name="infiles" value="msidata_1.RData,msidata_2.RData" ftype="rdata"/> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
472 <conditional name="annotation_cond"> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
473 <param name="annotation_tabular" value="annotation"/> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
474 <param name="annotation_files" value="annotations_file1.tabular,annotations_file2.tabular" ftype="tabular"/> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
475 <param name="tabular_header" value="TRUE"/> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
476 </conditional> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
477 <param name="combine_method" value="automatic_combine"/> |
5
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
4
diff
changeset
|
478 <param name="processed_true" value="FALSE"/> |
0
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
479 <output name="pixel_annotations" file="12_annotation_output.tabular"/> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
480 <output name="QC_overview" file="12_combined_QC.pdf" compare="sim_size"/> |
5
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
4
diff
changeset
|
481 <output name="outfile_imzml" ftype="imzml" file="12_combined.imzml.txt" compare="sim_size"> |
6
bb1ac6b47a6c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents:
5
diff
changeset
|
482 <extra_files type="file" file="12_combined.imzml" name="imzml" lines_diff="12"/> |
5
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
4
diff
changeset
|
483 <extra_files type="file" file="12_combined.ibd" name="ibd" compare="sim_size"/> |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
4
diff
changeset
|
484 </output> |
0
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
485 </test> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
486 <test> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
487 <param name="infiles" value="msidata_1.RData,123_combined.RData" ftype="rdata"/> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
488 <conditional name="annotation_cond"> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
489 <param name="annotation_tabular" value="annotation"/> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
490 <param name="annotation_files" value="annotations_file1.tabular,123_annotation.tabular" ftype="tabular"/> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
491 <param name="tabular_header" value="TRUE"/> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
492 </conditional> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
493 <param name="combine_method" value="automatic_combine"/> |
5
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
4
diff
changeset
|
494 <param name="processed_true" value="FALSE"/> |
0
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
495 <output name="pixel_annotations" file="112_annotation_output.tabular"/> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
496 <output name="QC_overview" file="112_auto_combined_QC.pdf" compare="sim_size"/> |
2
129cddd02600
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
497 <output name="outfile_imzml" ftype="imzml" file="112_auto_combined.imzml.txt" compare="sim_size"> |
6
bb1ac6b47a6c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents:
5
diff
changeset
|
498 <extra_files type="file" file="112_auto_combined.imzml" name="imzml" lines_diff="12"/> |
2
129cddd02600
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
499 <extra_files type="file" file="112_auto_combined.ibd" name="ibd" compare="sim_size"/> |
129cddd02600
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
500 </output> |
0
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
501 </test> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
502 <test> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
503 <param name="infiles" value="msidata_2.RData,123_combined.RData" ftype="rdata"/> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
504 <conditional name="annotation_cond"> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
505 <param name="annotation_tabular" value="no_annotation"/> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
506 </conditional> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
507 <param name="combine_method" value="automatic_combine"/> |
5
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
4
diff
changeset
|
508 <param name="processed_true" value="FALSE"/> |
0
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
509 <output name="pixel_annotations" file="2123_annotation_output.tabular"/> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
510 <output name="QC_overview" file="2123_auto_combined_QC.pdf" compare="sim_size"/> |
5
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
4
diff
changeset
|
511 <output name="outfile_imzml" ftype="imzml" file="2123_auto_combined.imzml.txt" compare="sim_size"> |
6
bb1ac6b47a6c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents:
5
diff
changeset
|
512 <extra_files type="file" file="2123_auto_combined.imzml" name="imzml" lines_diff="12"/> |
5
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
4
diff
changeset
|
513 <extra_files type="file" file="2123_auto_combined.ibd" name="ibd" compare="sim_size"/> |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
4
diff
changeset
|
514 </output> |
0
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
515 </test> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
516 </tests> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
517 <help> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
518 <![CDATA[ |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
519 |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
520 @CARDINAL_DESCRIPTION@ |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
521 |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
522 ----- |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
523 |
5
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
4
diff
changeset
|
524 This tool combines several mass spectrometry imaging data files. |
0
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
525 |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
526 @MSIDATA_INPUT_DESCRIPTION@ |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
527 - Coordinates stored as decimals rather than integers will be rounded to obtain a regular pixel grid. This might lead to duplicated coordinates which will be automatically removed before the tools analysis starts. |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
528 @SPECTRA_TABULAR_INPUT_DESCRIPTION@ |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
529 |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
530 - For xy shifts with tabular file: Tabular file with x and y coordinates shift and file name |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
531 |
5
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
4
diff
changeset
|
532 - Each input file is renamed and shifted in x and y direction according to this tabular file. In the example the files have about the same pixel dimensions which is smaller than 510x260. |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
4
diff
changeset
|
533 - The file can have any column names as header (in this case set "Tabular file contains a header line" to "Yes") or no header at all (set "Tabular file contains a header line" to "No"). |
0
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
534 |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
535 :: |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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536 |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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537 x_shift y_shift file name |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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538 0 0 file1 |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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539 510 0 file2 |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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540 0 260 file3 |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
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541 510 260 file4 |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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542 ... |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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543 ... |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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|
544 |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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545 |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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546 |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
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547 |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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548 **Options** |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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549 |
5
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
4
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550 - "automatic combination": files are automatically arranged in a grid, subfiles are named according to the input file name |
0
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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551 - "xy shifts": 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 as shown above). The xy shift option combines all datasets and removes all duplicated pixels (same x and y coordinates). |
5
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
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552 - "Set all file coordinates to 1/1 as origin" can be choosen to override current pixel coordinates of the input file and set their minimal x and minimal y values to 1. Then the shifts from the xy shift tabular files are used to move the pixels of each dataset. |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
4
diff
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553 - In case the input files have not exactly the same m/z values set "Do the files have different m/z axis?" to "Yes". Then functionalities of the "MALDIquant" package are used to combine the datasets. |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
4
diff
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554 |
0
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
555 |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
556 **Tips** |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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557 |
5
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
4
diff
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|
558 - The combine tool puts all samples into a common x-y-grid, therefore pixel coordinates will change. In case the pixels are already annotated, the annotations should be provided as tabular files and the tool will return an annotation file with the new pixel coordinates. This annotation file can then be used together with the combined MSI data for tools in which the annotation is required (e.g. 'MSI classification') or useful (e.g. 'MSI spectra plots'). |
0
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
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|
559 |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
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|
560 |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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|
561 **Output** |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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|
562 |
6
bb1ac6b47a6c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents:
5
diff
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563 - MSI data as imzML file (in continuous format when m/z axis were the same; in processed format when m/z axis were different) |
5
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
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564 - Pdf with pixel positions and annotations of the combined files |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
4
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565 - Tabular file with pixel annotations (x,y,column with input file names and annotation columns) |
0
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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566 |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
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|
567 |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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|
568 ]]> |
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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569 </help> |
5
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
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570 <citations> |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
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571 <citation type="doi">10.1093/bioinformatics/btv146</citation> |
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
4
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572 <citation type="doi">10.1007/978-3-319-45809-0_6</citation> |
7
392b2dfd261d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
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573 <citation type="doi">10.1093/gigascience/giz143</citation> |
5
b41107d8fe89
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents:
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574 </citations> |
0
93be1d20b5c3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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575 </tool> |