Mercurial > repos > galaxyp > mass_spectrometry_imaging_segmentations

annotate segmentation_tool.xml @ 4:aec189b0c64d draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
author galaxyp
date Mon, 28 May 2018 12:39:28 -0400
parents 830c6df59603
children cee9cf693709
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aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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1 <tool id="mass_spectrometry_imaging_segmentations" name="MSI segmentation" version="1.10.0.0">
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2 <description>tool for spatial clustering</description>
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3 <requirements>
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4 <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement>
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5 <requirement type="package" version="2.2.1">r-gridextra</requirement>
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6 <requirement type="package" version="0.20-35">r-lattice</requirement>
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7 </requirements>
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8 <command detect_errors="exit_code">
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9 <![CDATA[
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11 #if $infile.ext == 'imzml'
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12 ln -s '${infile.extra_files_path}/imzml' infile.imzML &&
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13 ln -s '${infile.extra_files_path}/ibd' infile.ibd &&
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14 #elif $infile.ext == 'analyze75'
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15 ln -s '${infile.extra_files_path}/hdr' infile.hdr &&
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16 ln -s '${infile.extra_files_path}/img' infile.img &&
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17 ln -s '${infile.extra_files_path}/t2m' infile.t2m &&
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18 #else
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19 ln -s $infile infile.RData &&
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20 #end if
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21 cat '${MSI_segmentation}' &&
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22 echo ${MSI_segmentation} &&
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23 Rscript '${MSI_segmentation}'
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25 ]]>
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26 </command>
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27 <configfiles>
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28 <configfile name="MSI_segmentation"><![CDATA[
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31 ################################# load libraries and read file #########################
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34 library(Cardinal)
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35 library(gridExtra)
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36 library(lattice)
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38 ## Read MALDI Imaging dataset
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39
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40 #if $infile.ext == 'imzml'
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41 msidata = readImzML('infile')
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42 #elif $infile.ext == 'analyze75'
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43 msidata = readAnalyze('infile')
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44 #else
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45 load('infile.RData')
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46 #end if
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47
4
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48 ###################################### file properties in numbers ##############
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49
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50 ## Number of features (mz)
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51 maxfeatures = length(features(msidata))
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52 ## Range mz
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53 minmz = round(min(mz(msidata)), digits=2)
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54 maxmz = round(max(mz(msidata)), digits=2)
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55 ## Number of spectra (pixels)
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56 pixelcount = length(pixels(msidata))
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57 ## Range x coordinates
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58 minimumx = min(coord(msidata)[,1])
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59 maximumx = max(coord(msidata)[,1])
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60 ## Range y coordinates
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61 minimumy = min(coord(msidata)[,2])
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62 maximumy = max(coord(msidata)[,2])
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63 ## Range of intensities
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64 minint = round(min(spectra(msidata)[]), digits=2)
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65 maxint = round(max(spectra(msidata)[]), digits=2)
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66 medint = round(median(spectra(msidata)[]), digits=2)
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67 ## Number of intensities > 0
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68 npeaks= sum(spectra(msidata)[]>0)
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69 ## Spectra multiplied with mz (potential number of peaks)
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70 numpeaks = ncol(spectra(msidata)[])*nrow(spectra(msidata)[])
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71 ## Percentage of intensities > 0
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72 percpeaks = round(npeaks/numpeaks*100, digits=2)
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73 ## Number of empty TICs
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74 TICs = colSums(spectra(msidata)[])
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75 NumemptyTIC = sum(TICs == 0)
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78 ## Processing informations
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79 processinginfo = processingData(msidata)
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80 centroidedinfo = processinginfo@centroided # TRUE or FALSE
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81
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82 ## if TRUE write processinginfo if no write FALSE
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83
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
diff changeset
84 ## normalization
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
diff changeset
85 if (length(processinginfo@normalization) == 0) {
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
diff changeset
86 normalizationinfo='FALSE'
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
diff changeset
87 } else {
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
diff changeset
88 normalizationinfo=processinginfo@normalization
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
diff changeset
89 }
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
diff changeset
90 ## smoothing
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
diff changeset
91 if (length(processinginfo@smoothing) == 0) {
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
diff changeset
92 smoothinginfo='FALSE'
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
diff changeset
93 } else {
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
diff changeset
94 smoothinginfo=processinginfo@smoothing
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
diff changeset
95 }
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
diff changeset
96 ## baseline
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
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97 if (length(processinginfo@baselineReduction) == 0) {
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
diff changeset
98 baselinereductioninfo='FALSE'
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
diff changeset
99 } else {
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
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100 baselinereductioninfo=processinginfo@baselineReduction
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
diff changeset
101 }
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
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102 ## peak picking
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
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103 if (length(processinginfo@peakPicking) == 0) {
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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104 peakpickinginfo='FALSE'
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
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105 } else {
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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106 peakpickinginfo=processinginfo@peakPicking
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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107 }
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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108
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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109 #############################################################################
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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110
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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111 properties = c("Number of mz features",
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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112 "Range of mz values [Da]",
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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113 "Number of pixels",
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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114 "Range of x coordinates",
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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115 "Range of y coordinates",
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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116 "Range of intensities",
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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117 "Median of intensities",
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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118 "Intensities > 0",
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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119 "Number of zero TICs",
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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120 "Preprocessing",
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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121 "Normalization",
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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122 "Smoothing",
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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123 "Baseline reduction",
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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124 "Peak picking",
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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125 "Centroided")
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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126
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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127 values = c(paste0(maxfeatures),
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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128 paste0(minmz, " - ", maxmz),
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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129 paste0(pixelcount),
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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130 paste0(minimumx, " - ", maximumx),
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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131 paste0(minimumy, " - ", maximumy),
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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132 paste0(minint, " - ", maxint),
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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133 paste0(medint),
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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134 paste0(percpeaks, " %"),
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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135 paste0(NumemptyTIC),
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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diff changeset
136 paste0(" "),
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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137 paste0(normalizationinfo),
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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138 paste0(smoothinginfo),
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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139 paste0(baselinereductioninfo),
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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140 paste0(peakpickinginfo),
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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diff changeset
141 paste0(centroidedinfo))
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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142
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143 property_df = data.frame(properties, values)
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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144
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145
4
aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 3
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146 ######################################## PDF ###################################
aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
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147 ################################################################################
aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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148 ################################################################################
0
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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149
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150
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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151 pdf("segmentationpdf.pdf", fonts = "Times", pointsize = 12)
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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152 plot(0,type='n',axes=FALSE,ann=FALSE)
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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153
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154 title(main=paste0("Spatial segmentation for file: \n\n", "$infile.display_name"))
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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155
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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156
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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157 ############################# I) numbers ####################################
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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158 #############################################################################
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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159 grid.table(property_df, rows= NULL)
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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160
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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161 if (npeaks > 0)
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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162 {
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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163
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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164
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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165 ######################## II) segmentation tools #############################
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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166 #############################################################################
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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167 #set $color_string = ','.join(['"%s"' % $color.feature_color for $color in $colours])
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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168 colourvector = c($color_string)
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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169
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170
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171 #if str( $segm_cond.segmentationtool ) == 'pca':
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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172 print('pca')
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173 ##pca
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174
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175 component_vector = character()
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176 for (numberofcomponents in 1:$segm_cond.pca_ncomp)
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177 {component_vector[numberofcomponents]= paste0("PC", numberofcomponents)}
1
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178 pca = PCA(msidata, ncomp=$segm_cond.pca_ncomp, column = component_vector, superpose = FALSE,
0
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179 method = "$segm_cond.pca_method", scale = $segm_cond.pca_scale, layout = c(ncomp, 1))
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180
4
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181 print(image(pca, main="PCA image", lattice=TRUE, strip = strip.custom(bg="lightgrey", par.strip.text=list(col="black", cex=.9)), col=colourvector))
0
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182 print(plot(pca, main="PCA plot", lattice=TRUE, col= colourvector, strip = strip.custom(bg="lightgrey", par.strip.text=list(col="black", cex=.9))))
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183
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184
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185 pcaloadings = (pca@resultData\$ncomp\$loadings) ### loading for each mz value
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186 pcascores = (pca@resultData\$ncomp\$scores) ### scores for each pixel
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187
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188 write.table(pcaloadings, file="$mzfeatures", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t")
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189 write.table(pcascores, file="$pixeloutput", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t")
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190
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191 #elif str( $segm_cond.segmentationtool ) == 'kmeans':
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192 print('kmeans')
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193 ##k-means
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194
2
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195 skm = spatialKMeans(msidata, r=c($segm_cond.kmeans_r), k=c($segm_cond.kmeans_k), method="$segm_cond.kmeans_method")
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196 print(image(skm, key=TRUE, main="K-means clustering", lattice=TRUE, strip = strip.custom(bg="lightgrey", par.strip.text=list(col="black", cex=.9)), col= colourvector, layout=c(1,1)))
2
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197
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198 print(plot(skm, main="K-means plot", lattice=TRUE, col= colourvector, strip = strip.custom(bg="lightgrey", par.strip.text=list(col="black", cex=.9)), layout=c($segm_cond.kmeans_layout)))
0
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199
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200
2
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201 skm_clusters = data.frame(matrix(NA, nrow = pixelcount, ncol = 0))
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202 for (iteration in 1:length(skm@resultData)){
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203 skm_cluster = ((skm@resultData)[[iteration]]\$cluster)
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204 skm_clusters = cbind(skm_clusters, skm_cluster) }
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205 colnames(skm_clusters) = names((skm@resultData))
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206
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207 skm_toplabels = topLabels(skm, n=$segm_cond.kmeans_toplabels)
0
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208
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209 write.table(skm_toplabels, file="$mzfeatures", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t")
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210 write.table(skm_clusters, file="$pixeloutput", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t")
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211
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212
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213 #elif str( $segm_cond.segmentationtool ) == 'centroids':
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214 print('centroids')
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215 ##centroids
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216
2
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217 ssc = spatialShrunkenCentroids(msidata, r=c($segm_cond.centroids_r), k=c($segm_cond.centroids_k), s=c($segm_cond.centroids_s), method="$segm_cond.centroids_method")
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218 print(image(ssc, key=TRUE, main="Spatial shrunken centroids", lattice=TRUE, strip = strip.custom(bg="lightgrey", par.strip.text=list(col="black", cex=.9)), col= colourvector,layout=c(1,1)))
2
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219 print(plot(ssc, main="Spatial shrunken centroids plot", lattice=TRUE, col= colourvector, strip = strip.custom(bg="lightgrey", par.strip.text=list(col="black", cex=.9)),layout=c($segm_cond.centroids_layout)))
0
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220
2
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221 ssc_classes = data.frame(matrix(NA, nrow = pixelcount, ncol = 0))
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222 for (iteration in 1:length(ssc@resultData)){
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223 ssc_class = ((ssc@resultData)[[iteration]]\$classes)
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224 ssc_classes = cbind(ssc_classes, ssc_class) }
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225 colnames(ssc_classes) = names((ssc@resultData))
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226
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227 ssc_toplabels = topLabels(ssc, n=$segm_cond.centroids_toplabels)
0
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228
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229 write.table(ssc_toplabels, file="$mzfeatures", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t")
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230 write.table(ssc_classes, file="$pixeloutput", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t")
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231
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232
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233 #end if
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234
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235 dev.off()
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236
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237 }else{
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238 print("Inputfile has no intensities > 0")
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239 dev.off()
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240 }
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241
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242 ]]></configfile>
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243 </configfiles>
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244 <inputs>
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245 <param name="infile" type="data" format="imzml, rdata, analyze75"
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246 label="Inputfile as imzML, Analyze7.5 or Cardinal MSImageSet saved as RData"
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247 help="Upload composite datatype imzml (ibd+imzML) or analyze75 (hdr+img+t2m) or regular upload .RData (Cardinal MSImageSet)"/>
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248 <conditional name="segm_cond">
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249 <param name="segmentationtool" type="select" label="Select the tool for spatial clustering">
0
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250 <option value="pca" selected="True">pca</option>
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251 <option value="kmeans">k-means</option>
4
aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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parents: 3
diff changeset
252 <option value="centroids">spatial shrunken centroids</option>
0
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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253 </param>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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254 <when value="pca">
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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255 <param name="pca_ncomp" type="integer" value="2"
4
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galaxyp
parents: 3
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256 label="The number of principal components to calculate"/>
0
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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257 <param name="pca_method" type="select"
4
aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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parents: 3
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258 label="The function used to calculate the singular value decomposition">
0
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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259 <option value="irlba" selected="True">irlba</option>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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260 <option value="svd">svd</option>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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261 </param>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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262 <param name="pca_scale" type="select" display="radio" optional="False"
4
aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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parents: 3
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263 label="Scaling of data before analysis">
0
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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264 <option value="TRUE">yes</option>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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265 <option value="FALSE" selected="True">no</option>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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266 </param>
4
aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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parents: 3
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267 </when>
0
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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268
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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269 <when value="kmeans">
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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270 <param name="kmeans_r" type="text" value="2"
4
aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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parents: 3
diff changeset
271 label="The spatial neighborhood radius of nearby pixels to consider (r)" help="Multiple values are allowed (e.g. 1,2,3 or 2:5)"/>
0
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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272 <param name="kmeans_k" type="text" value="3"
4
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parents: 3
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273 label="The number of clusters (k)" help="Multiple values are allowed (e.g. 1,2,3 or 2:5)"/>
0
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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274 <param name="kmeans_method" type="select" display="radio"
4
aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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275 label="The method to use to calculate the spatial smoothing kernels for the embedding. The 'gaussian' method refers to spatially-aware (SA) clustering, and 'adaptive' refers to spatially-aware structurally-adaptive (SASA) clustering">
0
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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276 <option value="gaussian">gaussian</option>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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277 <option value="adaptive" selected="True">adaptive</option>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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278 </param>
2
f66c5789deac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit ed7d3e6f1a09c78c8f71cc1bdc1a20249767f646
galaxyp
parents: 1
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279 <param name="kmeans_toplabels" type="integer" value="500"
f66c5789deac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit ed7d3e6f1a09c78c8f71cc1bdc1a20249767f646
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parents: 1
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280 label="Number of toplabels (masses) which should be written in tabular output"/>
f66c5789deac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit ed7d3e6f1a09c78c8f71cc1bdc1a20249767f646
galaxyp
parents: 1
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281 <param name="kmeans_layout" type="text" value="1,1"
f66c5789deac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit ed7d3e6f1a09c78c8f71cc1bdc1a20249767f646
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parents: 1
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282 label="Number of rows and columns to plot pictures in pdf output" help="e.g. 1,1 means 1 plot per page; 2,3 means 2 rows with 3 plots each = 6 plots per page"/>
f66c5789deac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit ed7d3e6f1a09c78c8f71cc1bdc1a20249767f646
galaxyp
parents: 1
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283 </when>
0
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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diff changeset
284
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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285 <when value="centroids">
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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286 <param name="centroids_r" type="text" value="2"
4
aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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parents: 3
diff changeset
287 label="The spatial neighborhood radius of nearby pixels to consider (r)" help="Multiple values are allowed (e.g. 1,2,3 or 2:5)"/>
0
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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288 <param name="centroids_k" type="text" value="5"
4
aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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parents: 3
diff changeset
289 label="The initial number of clusters (k)" help="Multiple values are allowed (e.g. 1,2,3 or 2:5)"/>
2
f66c5789deac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit ed7d3e6f1a09c78c8f71cc1bdc1a20249767f646
galaxyp
parents: 1
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290 <param name="centroids_s" type="text" value="2"
4
aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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parents: 3
diff changeset
291 label="The sparsity thresholding parameter by which to shrink the t-statistics (s)"
aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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292 help="As s increases, fewer mass features (m/z values) will be used in the spatial segmentation, and only the informative mass features will be retained. Multiple values are allowed (e.g. 1,2,3 or 2:5)"/>
aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 3
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293 <param name="centroids_method" type="select" display="radio" label = "The method to use to calculate the spatial smoothing kernels for the embedding. The 'gaussian' method refers to spatially-aware (SA) weights, and 'adaptive' refers to spatially-aware structurally-adaptive (SASA) weights">
0
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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294 <option value="gaussian" selected="True">gaussian</option>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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295 <option value="adaptive">adaptive</option>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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296 </param>
2
f66c5789deac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit ed7d3e6f1a09c78c8f71cc1bdc1a20249767f646
galaxyp
parents: 1
diff changeset
297 <param name="centroids_toplabels" type="integer" value="500"
f66c5789deac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit ed7d3e6f1a09c78c8f71cc1bdc1a20249767f646
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parents: 1
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298 label="Number of toplabels (masses) which should be written in tabular output"/>
f66c5789deac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit ed7d3e6f1a09c78c8f71cc1bdc1a20249767f646
galaxyp
parents: 1
diff changeset
299 <param name="centroids_layout" type="text" value="1,1"
f66c5789deac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit ed7d3e6f1a09c78c8f71cc1bdc1a20249767f646
galaxyp
parents: 1
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300 label="Number of rows and columns to plot pictures in pdf output" help="e.g. 1,1 means 1 plot per page; 2,3 means 2 rows with 3 plots each = 6 plots per page"/>
0
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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301 </when>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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302 </conditional>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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303 <repeat name="colours" title="Colours for the plots" min="1" max="50">
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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304 <param name="feature_color" type="color" label="Colours" value="#ff00ff" help="Numbers of columns should be the same as number of components">
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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305 <sanitizer>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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306 <valid initial="string.letters,string.digits">
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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307 <add value="#" />
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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308 </valid>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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309 </sanitizer>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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310 </param>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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311 </repeat>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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312 </inputs>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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313 <outputs>
3
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parents: 2
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314 <data format="pdf" name="segmentationimages" from_work_dir="segmentationpdf.pdf" label = "${tool.name} ${on_string}"/>
830c6df59603 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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315 <data format="tabular" name="mzfeatures" label="Mz features ${on_string}"/>
830c6df59603 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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316 <data format="tabular" name="pixeloutput" label="Pixels ${on_string}"/>
0
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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317 </outputs>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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318 <tests>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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319 <test>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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320 <param name="infile" value="" ftype="imzml">
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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321 <composite_data value="Example_Continuous.imzML"/>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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322 <composite_data value="Example_Continuous.ibd"/>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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323 </param>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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324 <param name="segmentationtool" value="pca"/>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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325 <repeat name="colours">
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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326 <param name="feature_color" value="#ff00ff"/>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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327 </repeat>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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328 <repeat name="colours">
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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329 <param name="feature_color" value="#0000FF"/>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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330 </repeat>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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331 <output name="segmentationimages" file="pca_imzml.pdf" compare="sim_size" delta="20000"/>
1
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parents: 0
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332 <output name="mzfeatures" file="loadings_pca.tabular" compare="sim_size"/>
d4158c9955ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents: 0
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333 <output name="pixeloutput" file="scores_pca.tabular" compare="sim_size"/>
0
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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334 </test>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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335 <test>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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336 <param name="infile" value="" ftype="analyze75">
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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337 <composite_data value="Analyze75.hdr" />
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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338 <composite_data value="Analyze75.img" />
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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diff changeset
339 <composite_data value="Analyze75.t2m" />
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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340 </param>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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341 <param name="segmentationtool" value="kmeans"/>
2
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parents: 1
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342 <param name="kmeans_r" value="1:3"/>
f66c5789deac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit ed7d3e6f1a09c78c8f71cc1bdc1a20249767f646
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parents: 1
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343 <param name="kmeans_k" value="2,3"/>
4
aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
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344 <param name="kmeans_toplabels" value="20"/>
0
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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345 <repeat name="colours">
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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346 <param name="feature_color" value="#ff00ff"/>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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347 </repeat>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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348 <repeat name="colours">
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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349 <param name="feature_color" value="#0000FF"/>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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350 </repeat>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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diff changeset
351 <repeat name="colours">
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
diff changeset
352 <param name="feature_color" value="#00C957"/>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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353 </repeat>
4
aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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parents: 3
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354 <output name="segmentationimages" file="kmeans_analyze.pdf" compare="sim_size" delta="20000"/>
1
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parents: 0
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355 <output name="mzfeatures" file="toplabels_skm.tabular" compare="sim_size"/>
d4158c9955ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
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parents: 0
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356 <output name="pixeloutput" file="cluster_skm.tabular" compare="sim_size"/>
0
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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357 </test>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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358 <test>
4
aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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359 <param name="infile" value="preprocessed.RData" ftype="rdata"/>
0
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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360 <param name="segmentationtool" value="centroids"/>
4
aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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361 <param name="centroids_r" value="1,2"/>
aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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parents: 3
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362 <param name="centroids_k" value="5"/>
aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 3
diff changeset
363 <param name="centroids_toplabels" value="50"/>
0
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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364 <repeat name="colours">
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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diff changeset
365 <param name="feature_color" value="#0000FF"/>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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366 </repeat>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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diff changeset
367 <repeat name="colours">
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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368 <param name="feature_color" value="#00C957"/>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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369 </repeat>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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diff changeset
370 <repeat name="colours">
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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diff changeset
371 <param name="feature_color" value="#B0171F"/>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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diff changeset
372 </repeat>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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diff changeset
373 <repeat name="colours">
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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diff changeset
374 <param name="feature_color" value="#FFD700"/>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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375 </repeat>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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diff changeset
376 <repeat name="colours">
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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diff changeset
377 <param name="feature_color" value="#848484"/>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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378 </repeat>
4
aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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diff changeset
379 <output name="segmentationimages" file="centroids_rdata.pdf" compare="sim_size" delta="20000"/>
1
d4158c9955ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents: 0
diff changeset
380 <output name="mzfeatures" file="toplabels_ssc.tabular" compare="sim_size"/>
d4158c9955ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents: 0
diff changeset
381 <output name="pixeloutput" file="classes_ssc.tabular" compare="sim_size"/>
0
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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382 </test>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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383 </tests>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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384 <help>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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diff changeset
385 <![CDATA[
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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386
4
aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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387 Cardinal is an R package that implements statistical & computational tools for analyzing mass spectrometry imaging datasets. `More information on Cardinal <http://cardinalmsi.org//>`_
aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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diff changeset
388
aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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389 This tool provides three different Cardinal functions for unsupervised clustering/spatial segmentation of mass-spectrometry imaging data.
0
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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diff changeset
390
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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391 Input data: 3 types of input data can be used:
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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392
4
aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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393 - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/wp/imzml/>`_
0
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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394 - Analyze7.5 (upload hdr, img and t2m file via the "composite" function)
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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395 - Cardinal "MSImageSet" data (with variable name "msidata", saved as .RData)
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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diff changeset
396
4
aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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diff changeset
397 Options:
aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 3
diff changeset
398
aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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399 - PCA: principal component analysis
aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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400 - k-means: patially-aware k-means clustering
aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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401 - spatial shrunken centroids: Allows the number of segments to decrease according to the data. This allows automatic selection of the number of clusters
aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 3
diff changeset
402
aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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diff changeset
403 Output:
aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 3
diff changeset
404
aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 3
diff changeset
405 - Pdf with the heatmaps and plots for the segmentation
aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
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406 - Tabular file with information on masses and pixels: loadings/scores (PCA), toplabels/clusters (k-means), toplabels/classes (spatial shrunken centroids)
aec189b0c64d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 3
diff changeset
407
0
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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408 ]]>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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409 </help>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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410 <citations>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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411 <citation type="doi">10.1093/bioinformatics/btv146</citation>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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412 </citations>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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413 </tool>