Mercurial > repos > galaxyp > cardinal_filtering

annotate macros.xml @ 7:1d4a6fe69a40 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
author galaxyp
date Thu, 23 Apr 2020 08:10:44 -0400
parents d2ccd8348018
children a8157342d9a3
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d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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1 <macros>
7
1d4a6fe69a40 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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2 <token name="@VERSION@">2.4.0</token>
6
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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3
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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4 <xml name="requirements">
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5 <requirements>
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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6 <requirement type="package" version="@VERSION@">bioconductor-cardinal</requirement>
7
1d4a6fe69a40 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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7 <requirement type="package" version="3.6.1">r-base</requirement>
6
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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8 <yield/>
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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9 </requirements>
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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10 </xml>
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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12 <xml name="print_version">
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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13 <version_command><![CDATA[
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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14 echo $(R --version | grep version | grep -v GNU)", Cardinal version" $(R --vanilla --slave -e "library(Cardinal); cat(sessionInfo()\$otherPkgs\$Cardinal\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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15 ]]></version_command>
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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16 </xml>
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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18 <token name="@INPUT_LINKING@"><![CDATA[
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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19 #if $infile.ext == 'imzml'
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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20 ln -s '${infile.extra_files_path}/imzml' infile.imzML &&
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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21 ln -s '${infile.extra_files_path}/ibd' infile.ibd &&
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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22 #elif $infile.ext == 'analyze75'
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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23 ln -s '${infile.extra_files_path}/hdr' infile.hdr &&
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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24 ln -s '${infile.extra_files_path}/img' infile.img &&
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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25 ln -s '${infile.extra_files_path}/t2m' infile.t2m &&
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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26 #else
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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27 ln -s $infile infile.RData &&
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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28 #end if
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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29 ]]></token>
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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30
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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32 <token name="@READING_MSIDATA@"><![CDATA[
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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33 ## importing MSI data files
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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34
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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35 #if $infile.ext == 'imzml'
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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36 #if str($processed_cond.processed_file) == "processed":
7
1d4a6fe69a40 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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37 msidata <- readImzML('infile', resolution=$processed_cond.accuracy, attach.only=TRUE, units = "$processed_cond.units")
1d4a6fe69a40 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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38 msidata = collect(msidata, as.matrix=TRUE) ##coercion to continuous
6
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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39 centroided(msidata) = $centroids
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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40 #else
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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41 msidata <- readImzML('infile', attach.only=TRUE)
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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42 centroided(msidata) = $centroids
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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43 #end if
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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44 #elif $infile.ext == 'analyze75'
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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45 msidata = readAnalyze('infile', attach.only=TRUE)
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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46 centroided(msidata) = $centroids
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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47 #else
7
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48 ## function to read RData files independent of filename
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49 loadRData <- function(fileName){
1d4a6fe69a40 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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50 load(fileName)
1d4a6fe69a40 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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51 get(ls()[ls() != "fileName"])
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52 }
6
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53 msidata = loadRData('infile.RData')
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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54 #end if
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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55
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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56 ]]></token>
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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57
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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58 <token name="@DATA_PROPERTIES@"><![CDATA[
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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59 ## Number of features (mz)
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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60 maxfeatures = length(features(msidata))
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61 ## Range mz
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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62 minmz = round(min(mz(msidata)), digits=2)
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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63 maxmz = round(max(mz(msidata)), digits=2)
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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64 ## Number of spectra (pixels)
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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65 pixelcount = length(pixels(msidata))
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66 ## Range x coordinates
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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67 minimumx = min(coord(msidata)[,1])
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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68 maximumx = max(coord(msidata)[,1])
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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69 ## Range y coordinates
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70 minimumy = min(coord(msidata)[,2])
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71 maximumy = max(coord(msidata)[,2])
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72
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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73
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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74 properties = c("Number of m/z features",
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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75 "Range of m/z values",
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76 "Number of pixels",
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77 "Range of x coordinates",
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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78 "Range of y coordinates")
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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79
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80 values = c(paste0(maxfeatures),
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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81 paste0(minmz, " - ", maxmz),
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82 paste0(pixelcount),
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83 paste0(minimumx, " - ", maximumx),
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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84 paste0(minimumy, " - ", maximumy))
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85
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86 property_df = data.frame(properties, values)
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87 ]]></token>
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88
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89 <token name="@READING_MSIDATA_FULLY_COMPATIBLE@"><![CDATA[
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90 ## importing MSI data files
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91
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92 #if $infile.ext == 'imzml'
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93 #if str($processed_cond.processed_file) == "processed":
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94 msidata <- readImzML('infile', resolution=$processed_cond.accuracy, units = "$processed_cond.units", attach.only=TRUE)
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95 centroided(msidata) = $centroids
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96 #else
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97 msidata <- readImzML('infile', attach.only=TRUE)
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98 centroided(msidata) = $centroids
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99 #end if
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100 #elif $infile.ext == 'analyze75'
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101 msidata = readAnalyze('infile', attach.only=TRUE)
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102 centroided(msidata) = $centroids
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103 #else
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104 ## function to read RData files independent of filename
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105 loadRData <- function(fileName){
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106 load(fileName)
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107 get(ls()[ls() != "fileName"])
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108 }
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109 msidata = loadRData('infile.RData')
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110 msidata = as(msidata, "MSImagingExperiment")
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111 run(msidata) = "infile"
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112 #end if
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113
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114 ]]></token>
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115
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116 <token name="@DATA_PROPERTIES_INRAM@"><![CDATA[
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117 ########################### QC numbers ########################
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118 ## including intensity calculations which need data in RAM
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119 ## Number of features (mz)
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120 maxfeatures = length(features(msidata))
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121 ## Range mz
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122 minmz = round(min(mz(msidata)), digits=2)
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123 maxmz = round(max(mz(msidata)), digits=2)
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124 ## Number of spectra (pixels)
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125 pixelcount = length(pixels(msidata))
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126 ## Range x coordinates
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127 minimumx = min(coord(msidata)[,1])
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128 maximumx = max(coord(msidata)[,1])
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129 ## Range y coordinates
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130 minimumy = min(coord(msidata)[,2])
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131 maximumy = max(coord(msidata)[,2])
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132 ## Range of intensities
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133 minint = round(min(as.matrix(spectra(msidata)), na.rm=TRUE), digits=2)
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134 maxint = round(max(as.matrix(spectra(msidata)), na.rm=TRUE), digits=2)
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135 ## Number of intensities > 0, for if conditions
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136 npeaks= sum(as.matrix(spectra(msidata))>0, na.rm=TRUE)
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137 ## Number of NA in spectra matrix
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138 NAcount = sum(is.na(spectra(msidata)))
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139 ## Number of NA in spectra matrix
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140 infcount = sum(is.infinite(as.matrix(spectra(msidata))))
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141 ## Number of duplicated coordinates
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142 dupl_coord = sum(duplicated(coord(msidata)))
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143 properties = c("Number of m/z features",
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144 "Range of m/z values",
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145 "Number of pixels",
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146 "Range of x coordinates",
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147 "Range of y coordinates",
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148 "Range of intensities",
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149 "Number of NA intensities",
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150 "Number of Inf intensities",
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151 "Number of duplicated coordinates")
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152
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153 values = c(paste0(maxfeatures),
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154 paste0(minmz, " - ", maxmz),
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155 paste0(pixelcount),
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156 paste0(minimumx, " - ", maximumx),
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157 paste0(minimumy, " - ", maximumy),
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158 paste0(minint, " - ", maxint),
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159 paste0(NAcount),
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160 paste0(infcount),
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161 paste0(dupl_coord))
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162
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163 property_df = data.frame(properties, values)
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164 ]]></token>
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165
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166 <token name="@CARDINAL_DESCRIPTION@"><![CDATA[
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167 Cardinal is an R package that implements statistical & computational tools for analyzing mass spectrometry imaging datasets.
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168 `More information on Cardinal <http://cardinalmsi.org/>`_
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169 ]]></token>
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170 <token name="@MSIDATA_INPUT_DESCRIPTION@"><![CDATA[
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171 **Input data**
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172
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173 - MSI data: 3 types of input data can be used:
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
174
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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diff changeset
175 - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/wp/imzml/>`_
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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176 - Analyze7.5 (upload hdr, img and t2m file via the "composite" function)
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
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diff changeset
177 - Cardinal "MSImageSet" data saved as .RData
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
178 ]]></token>
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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179 <token name="@MZ_TABULAR_INPUT_DESCRIPTION@"><![CDATA[
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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diff changeset
180 - Optional tabular file with m/z values:
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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181
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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182 - One column with numeric m/z values (without empty fields or letters)
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
183 - The file is allowed to have any column names as header (in this case set "Tabular file contains a header line" to yes)
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
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diff changeset
184 - m/z features outside the m/z range of the input file are ignored
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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diff changeset
185
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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diff changeset
186
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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diff changeset
187 ::
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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diff changeset
188
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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diff changeset
189 m/z
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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190 100.0
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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diff changeset
191 100.01
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
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diff changeset
192 100.02
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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193 ...
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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194 ...
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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diff changeset
195
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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diff changeset
196 ]]></token>
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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197 <token name="@MZ_2COLS_TABULAR_INPUT_DESCRIPTION@"><![CDATA[
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
198 - Tabular file with m/z values:
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
199
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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200 - One column with numeric m/z values (without empty fields or letters), another column with names for the m/z (m/z column can also be used as name)
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
201 - The file is allowed to have any column names as header (in this case set "Tabular file contains a header line" to yes)
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
202 - m/z features outside the m/z range of the input file are ignored
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
203
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
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diff changeset
204
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
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205 ::
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 4
diff changeset
206
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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diff changeset
207 m/z name
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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208 100.0 analyte1
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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209 100.01 analyte2
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
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diff changeset
210 100.02 analyte3
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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211 ...
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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212 ...
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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213
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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214 ]]></token>
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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215 <token name="@SPECTRA_TABULAR_INPUT_DESCRIPTION@"><![CDATA[
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
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diff changeset
216 - Optional file with pixel coordinates and annotation:
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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217
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
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218 - Tabular file: One column with x values, one column with y values and one column with annotations
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
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diff changeset
219 - The file is allowed to have any column names as header (in this case set "Tabular file contains a header line" to yes)
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
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220 - Pixel with coordinates outside the coordinates of the input file are ignored
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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221
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
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222 ::
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
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223
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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224 x_coord y_coord annotation
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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diff changeset
225 1 1 healthy
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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226 2 1 healthy
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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227 3 1 disease
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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228 ...
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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229 ...
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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230
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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231 ]]></token>
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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232
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
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233 <xml name="reading_msidata">
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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234 <param name="infile" type="data" format="imzml,rdata,analyze75"
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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235 label="MSI data"
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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236 help="Input file as imzML (composite upload), Analyze7.5 (composite upload) or Cardinal MSImageSet saved as RData (regular upload)"/>
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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237 <param name="centroids" type="boolean" label="Centroided input" help="Choose Yes if peak detection has already been done." truevalue="TRUE" falsevalue="FALSE"/>
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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238 <conditional name="processed_cond">
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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239 <param name="processed_file" type="select" label="Processed imzML file" help="Choose no if your input is an Analyze7.5 or continuous imzML file">
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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240 <option value="no_processed" selected="True">no</option>
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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241 <option value="processed">yes</option>
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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242 </param>
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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243 <when value="no_processed"/>
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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244 <when value="processed">
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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245 <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"/>
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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246 <param name="units" display="radio" type="select" label="Unit of the mass accuracy" help="either m/z or ppm">
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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247 <option value="mz" >mz</option>
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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248 <option value="ppm" selected="True" >ppm</option>
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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249 </param>
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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250 </when>
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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251 </conditional>
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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252 </xml>
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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253
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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254 <xml name="pdf_filename">
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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255 <param name="filename" type="text" value="" label="Title" help="Will appear in the pdf output, if nothing given it will take the dataset name">
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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diff changeset
256 <sanitizer invalid_char="">
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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257 <valid initial="string.ascii_letters,string.digits">
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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258 <add value="_"/>
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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259 <add value=" "/>
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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260 </valid>
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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261 </sanitizer>
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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262 </param>
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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263 </xml>
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264
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265 <xml name="sanitizer_multiple_digits">
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266 <sanitizer invalid_char="">
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267 <valid initial="string.digits">
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268 <add value=":" />
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269 <add value="," />
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270 </valid>
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271 </sanitizer>
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272 </xml>
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273
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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274 <xml name="reading_1_column_mz_tabular" token_label="Tabular file with m/z features">
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275 <param name="mz_tabular" type="data" format="tabular" label="@LABEL@" help="Only numeric m/z values are allowed"/>
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276 <param name="feature_column" data_ref="mz_tabular" label="Column with features" type="data_column"/>
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277 <param name="feature_header" type="boolean" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/>
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278 </xml>
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279
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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280 <xml name="reading_2_column_mz_tabular" token_optional="false">
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281 <param name="calibrant_file" type="data" optional="@OPTIONAL@" format="tabular"
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282 label="m/z of interest (e.g. internal Calibrants)" help="one column with m/z values, optional second column with names (m/z values can also be selected as name)"/>
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283 <param name="mz_column" data_ref="calibrant_file" optional="@OPTIONAL@" label="Column with m/z values" type="data_column"/>
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284 <param name="name_column" data_ref="calibrant_file" optional="@OPTIONAL@" label="Column with name of m/z values" type="data_column"/>
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285 <param name="calibrant_header" type="boolean" optional="@OPTIONAL@" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/>
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286 </xml>
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287
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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288 <xml name="reading_pixel_annotations">
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289 <param name="annotation_file" type="data" format="tabular" label="Tabular file with pixel coordinates and annotation"
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290 help="Tabular file with three columns: x values, y values and pixel annotations"/>
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291 <param name="column_x" data_ref="annotation_file" label="Column with x values" type="data_column"/>
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292 <param name="column_y" data_ref="annotation_file" label="Column with y values" type="data_column"/>
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293 <param name="column_names" data_ref="annotation_file" label="Column with pixel annotations" type="data_column"/>
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294 <param name="tabular_header" type="boolean" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/>
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295 </xml>
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296
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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297 <xml name="citations">
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298 <citations>
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299 <citation type="doi">10.1093/bioinformatics/btv146</citation>
7
1d4a6fe69a40 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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300 <citation type="doi">10.1093/gigascience/giz143</citation>
6
d2ccd8348018 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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301 </citations>
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302 </xml>
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303 <xml name="infile_analyze75">
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304 <param name="infile" value="" ftype="analyze75">
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305 <composite_data value="Analyze75.hdr"/>
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306 <composite_data value="Analyze75.img"/>
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307 <composite_data value="Analyze75.t2m"/>
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308 </param>
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309 </xml>
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310 <xml name="infile_imzml">
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311 <param name="infile" value="" ftype="imzml">
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312 <composite_data value="Example_Continuous.imzML"/>
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313 <composite_data value="Example_Continuous.ibd"/>
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314 </param>
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315 </xml>
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316 <xml name="processed_infile_imzml">
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317 <param name="infile" value="" ftype="imzml">
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318 <composite_data value="Example_Processed.imzML"/>
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319 <composite_data value="Example_Processed.ibd"/>
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320 </param>
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321 </xml>
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322 </macros>