Mercurial > repos > galaxyp > mass_spectrometry_imaging_segmentations

annotate segmentation_tool.xml @ 0:0c1a9b68f436 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
author galaxyp
date Sat, 24 Feb 2018 13:51:32 -0500
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0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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1 <tool id="mass_spectrometry_imaging_segmentations" name="MSI segmentation" version="1.7.0">
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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="1.7.0">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="2.23-15">r-kernsmooth</requirement>
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7 <requirement type="package" version="0.20-35">r-lattice</requirement>
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8 </requirements>
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9 <command detect_errors="exit_code">
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10 <![CDATA[
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11
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12 #if $infile.ext == 'imzml'
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13 cp '${infile.extra_files_path}/imzml' infile.imzML &&
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14 cp '${infile.extra_files_path}/ibd' infile.ibd &&
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15 #elif $infile.ext == 'analyze75'
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16 cp '${infile.extra_files_path}/hdr' infile.hdr &&
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17 cp '${infile.extra_files_path}/img' infile.img &&
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18 cp '${infile.extra_files_path}/t2m' infile.t2m &&
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19 #else
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20 ln -s $infile infile.RData &&
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21 #end if
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22 cat '${MSI_segmentation}' &&
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23 echo ${MSI_segmentation} &&
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24 Rscript '${MSI_segmentation}'
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25
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26 ]]>
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27 </command>
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28 <configfiles>
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29 <configfile name="MSI_segmentation"><![CDATA[
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30
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31
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32 ################################# load libraries and read file #########################
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33
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34
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35 library(Cardinal)
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36 library(gridExtra)
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37 library(KernSmooth)
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38 library(lattice)
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39
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40 ## Read MALDI Imaging dataset
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41
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42 #if $infile.ext == 'imzml'
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43 msidata <- readMSIData('infile.imzML')
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44 #elif $infile.ext == 'analyze75'
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45 msidata <- readMSIData('infile.hdr')
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46 #else
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47 load('infile.RData')
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48 #end if
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49
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50 ###################################### file properties in numbers ######################
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51
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52 ## Number of features (mz)
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53 maxfeatures = length(features(msidata))
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54 ## Range mz
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55 minmz = round(min(mz(msidata)), digits=2)
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56 maxmz = round(max(mz(msidata)), digits=2)
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57 ## Number of spectra (pixels)
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58 pixelcount = length(pixels(msidata))
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59 ## Range x coordinates
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60 minimumx = min(coord(msidata)[,1])
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61 maximumx = max(coord(msidata)[,1])
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62 ## Range y coordinates
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63 minimumy = min(coord(msidata)[,2])
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64 maximumy = max(coord(msidata)[,2])
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65 ## Range of intensities
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66 minint = round(min(spectra(msidata)[]), digits=2)
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67 maxint = round(max(spectra(msidata)[]), digits=2)
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68 medint = round(median(spectra(msidata)[]), digits=2)
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69 ## Number of intensities > 0
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70 npeaks= sum(spectra(msidata)[]>0)
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71 ## Spectra multiplied with mz (potential number of peaks)
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72 numpeaks = ncol(spectra(msidata)[])*nrow(spectra(msidata)[])
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73 ## Percentage of intensities > 0
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74 percpeaks = round(npeaks/numpeaks*100, digits=2)
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75 ## Number of empty TICs
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76 TICs = colSums(spectra(msidata)[])
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77 NumemptyTIC = sum(TICs == 0)
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78
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79
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80 ## Processing informations
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81 processinginfo = processingData(msidata)
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82 centroidedinfo = processinginfo@centroided # TRUE or FALSE
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83
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84 ## if TRUE write processinginfo if no write FALSE
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
diff changeset
85
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
diff changeset
86 ## normalization
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
87 if (length(processinginfo@normalization) == 0) {
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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88 normalizationinfo='FALSE'
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
89 } else {
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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90 normalizationinfo=processinginfo@normalization
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
91 }
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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92 ## smoothing
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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93 if (length(processinginfo@smoothing) == 0) {
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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94 smoothinginfo='FALSE'
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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95 } else {
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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96 smoothinginfo=processinginfo@smoothing
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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97 }
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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98 ## baseline
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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99 if (length(processinginfo@baselineReduction) == 0) {
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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100 baselinereductioninfo='FALSE'
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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101 } else {
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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102 baselinereductioninfo=processinginfo@baselineReduction
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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103 }
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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104 ## peak picking
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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105 if (length(processinginfo@peakPicking) == 0) {
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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106 peakpickinginfo='FALSE'
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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107 } else {
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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108 peakpickinginfo=processinginfo@peakPicking
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109 }
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110
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111 #############################################################################
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112
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113 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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114 "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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115 "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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116 "Range of x coordinates",
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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117 "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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118 "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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119 "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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120 "Intensities > 0",
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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121 "Number of zero TICs",
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122 "Preprocessing",
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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123 "Normalization",
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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124 "Smoothing",
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125 "Baseline reduction",
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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126 "Peak picking",
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127 "Centroided")
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128
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129 values = c(paste0(maxfeatures),
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130 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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131 paste0(pixelcount),
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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132 paste0(minimumx, " - ", maximumx),
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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133 paste0(minimumy, " - ", maximumy),
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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134 paste0(minint, " - ", maxint),
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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135 paste0(medint),
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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136 paste0(percpeaks, " %"),
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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137 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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138 paste0(" "),
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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139 paste0(normalizationinfo),
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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140 paste0(smoothinginfo),
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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141 paste0(baselinereductioninfo),
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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142 paste0(peakpickinginfo),
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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143 paste0(centroidedinfo))
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 property_df = data.frame(properties, values)
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146
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147
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148 ######################################## PDF #############################################
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 ##########################################################################################
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151
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152
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153 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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154 plot(0,type='n',axes=FALSE,ann=FALSE)
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155
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156 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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157
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158
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159 ############################# I) numbers ####################################
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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160 #############################################################################
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161 grid.table(property_df, rows= NULL)
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162
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163 if (npeaks > 0)
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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
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166
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167 ######################## 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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168 #############################################################################
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169 #set $color_string = ','.join(['"%s"' % $color.feature_color for $color in $colours])
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170 colourvector = c($color_string)
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171
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172
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173 #if str( $segm_cond.segmentationtool ) == 'pca':
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174 print('pca')
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175 ##pca
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176
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177 component_vector = character()
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178 for (numberofcomponents in 1:$segm_cond.pca_ncomp)
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179 {component_vector[numberofcomponents]= paste0("PC", numberofcomponents)}
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180 pca <- PCA(msidata, ncomp=$segm_cond.pca_ncomp, column = component_vector, superpose = FALSE,
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181 method = "$segm_cond.pca_method", scale = $segm_cond.pca_scale, layout = c(ncomp, 1))
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182
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183 print(image(pca, main="PCA image", lattice=TRUE, strip = strip.custom(bg="lightgrey", par.strip.text=list(col="black", cex=.9)), contrast.enhance = "$segm_cond.pca_imagecontrast", smooth.image = "$segm_cond.pca_imagesmoothing", col=colourvector))
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184 print(plot(pca, main="PCA plot", lattice=TRUE, col= colourvector, strip = strip.custom(bg="lightgrey", par.strip.text=list(col="black", cex=.9))))
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185
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186
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187 pcaloadings = (pca@resultData\$ncomp\$loadings) ### loading for each mz value
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188 pcascores = (pca@resultData\$ncomp\$scores) ### scores for each pixel
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189
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190 write.table(pcaloadings, file="$mzfeatures", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t")
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191 write.table(pcascores, file="$pixeloutput", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t")
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192
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193 #elif str( $segm_cond.segmentationtool ) == 'kmeans':
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194 print('kmeans')
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195 ##k-means
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196
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197 skm <- spatialKMeans(msidata, r=$segm_cond.kmeans_r, k=$segm_cond.kmeans_k, method="$segm_cond.kmeans_method")
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198 print(image(skm, key=TRUE, main="K-means clustering", lattice=TRUE, strip = strip.custom(bg="lightgrey", par.strip.text=list(col="black", cex=.9)), contrast.enhance = "$segm_cond.kmeans_imagecontrast", col= colourvector, smooth.image = "$segm_cond.kmeans_imagesmoothing"))
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199 print(plot(skm, main="K-means plot", lattice=TRUE, col= colourvector, strip = strip.custom(bg="lightgrey", par.strip.text=list(col="black", cex=.9))))
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200
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201
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202 skm_clusters = (skm@resultData\$r\$cluster)
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203 skm_toplabels = topLabels(skm, n=500)
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204
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205 write.table(skm_toplabels, file="$mzfeatures", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t")
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206 write.table(skm_clusters, file="$pixeloutput", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t")
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207
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208
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209 #elif str( $segm_cond.segmentationtool ) == 'centroids':
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210 print('centroids')
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211 ##centroids
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212
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213 ssc <- spatialShrunkenCentroids(msidata, r=$segm_cond.centroids_r, k=$segm_cond.centroids_k, s=$segm_cond.centroids_s, method="$segm_cond.centroids_method")
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214 print(image(ssc, key=TRUE, main="Spatial shrunken centroids", lattice=TRUE, strip = strip.custom(bg="lightgrey", par.strip.text=list(col="black", cex=.9)), contrast.enhance = "$segm_cond.centroids_imagecontrast", col= colourvector, smooth.image = "$segm_cond.centroids_imagesmoothing"))
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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215 print(plot(ssc, main="Spatial shrunken centroids plot", lattice=TRUE, col= colourvector, strip = strip.custom(bg="lightgrey", par.strip.text=list(col="black", cex=.9))))
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216
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217 ssc_classes = (ssc@resultData\$r\$classes)
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218 ssc_toplabels = topLabels(ssc, n=500)
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219
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220 write.table(ssc_toplabels, file="$mzfeatures", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t")
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221 write.table(ssc_classes, file="$pixeloutput", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t")
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222
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223
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224 #end if
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225
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226 dev.off()
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227
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228 }else{
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229 print("Inputfile has no intensities > 0")
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230 dev.off()
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231 }
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232
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233 ]]></configfile>
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234 </configfiles>
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235 <inputs>
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236 <param name="infile" type="data" format="imzml, rdata, analyze75"
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237 label="Inputfile as imzML, Analyze7.5 or Cardinal MSImageSet saved as RData"
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238 help="Upload composite datatype imzml (ibd+imzML) or analyze75 (hdr+img+t2m) or regular upload .RData (Cardinal MSImageSet)"/>
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239 <conditional name="segm_cond">
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240 <param name="segmentationtool" type="select" label="Select the tool for spatial clustering.">
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241 <option value="pca" selected="True">pca</option>
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242 <option value="kmeans">k-means</option>
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243 <option value="centroids">shrunken centroids</option>
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244 </param>
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245 <when value="pca">
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246 <param name="pca_ncomp" type="integer" value="2"
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247 label="The number of principal components to calculate."/>
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248 <param name="pca_method" type="select"
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249 label="The function used to calculate the singular value decomposition.">
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250 <option value="irlba" selected="True">irlba</option>
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251 <option value="svd">svd</option>
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252 </param>
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253 <param name="pca_scale" type="select" display="radio" optional="False"
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
diff changeset
254 label="Shoud the data be scaled first?">
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
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255 <option value="TRUE">yes</option>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
diff changeset
256 <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
galaxyp
parents:
diff changeset
257 </param>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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258 <param name="pca_imagecontrast" type="select" label="Select a contrast enhancement function." help="The 'histogram' equalization method flatterns the distribution of intensities. The hotspot 'suppression' method uses thresholding to reduce the intensities of hotspots">
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
diff changeset
259 <option value="none" selected="True">none</option>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
diff changeset
260 <option value="suppression">suppression</option>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
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261 <option value="histogram">histogram</option>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
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262 </param>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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263 <param name="pca_imagesmoothing" type="select" label="Select an image smoothing function." help="The 'gaussian' smoothing method smooths images with a simple gaussian kernel. The 'adaptive' method uses bilateral filtering to preserve edges.">
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
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264 <option value="none" selected="True">none</option>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
diff changeset
265 <option value="gaussian">gaussian</option>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
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266 <option value="adaptive">adaptive</option>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
diff changeset
267 </param>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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268 </when>
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
269
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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270 <when value="kmeans">
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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271 <param name="kmeans_r" type="text" value="2"
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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272 label="The spatial neighborhood radius of nearby pixels to consider (r)."/>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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273 <param name="kmeans_k" type="text" value="3"
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
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274 label="The number of clusters (k)."/>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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275 <param name="kmeans_method" type="select" display="radio"
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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276 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.">
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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277 <option value="gaussian">gaussian</option>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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278 <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
galaxyp
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diff changeset
279 </param>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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280 <param name="kmeans_imagecontrast" type="select" label="Select a contrast enhancement function." help="The 'histogram' equalization method flatterns the distribution of intensities. The hotspot 'suppression' method uses thresholding to reduce the intensities of hotspots">
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
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281 <option value="none" selected="True">none</option>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
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282 <option value="suppression">suppression</option>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
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283 <option value="histogram">histogram</option>
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 </param>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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285 <param name="kmeans_imagesmoothing" type="select" label="Select an image smoothing function." help="The 'gaussian' smoothing method smooths images with a simple gaussian kernel. The 'adaptive' method uses bilateral filtering to preserve edges.">
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
diff changeset
286 <option value="none" selected="True">none</option>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
diff changeset
287 <option value="gaussian">gaussian</option>
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
288 <option value="adaptive">adaptive</option>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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289 </param>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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290 </when>
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
291
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
292 <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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293 <param name="centroids_r" type="text" value="2"
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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294 label="The spatial neighborhood radius of nearby pixels to consider (r)."/>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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295 <param name="centroids_k" type="text" value="5"
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
296 label="The initial number of clusters (k)."/>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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297 <param name="centroids_s" type="integer" value="2"
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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298 label="The sparsity thresholding parameter by which to shrink the t-statistics (s)."
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
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299 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."/>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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300 <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.">
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
diff changeset
301 <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
galaxyp
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diff changeset
302 <option value="adaptive">adaptive</option>
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
303 </param>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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304 <param name="centroids_imagecontrast" type="select" label="Select a contrast enhancement function." help="The 'histogram' equalization method flatterns the distribution of intensities. The hotspot 'suppression' method uses thresholding to reduce the intensities of hotspots">
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
diff changeset
305 <option value="none" selected="True">none</option>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
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306 <option value="suppression">suppression</option>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
diff changeset
307 <option value="histogram">histogram</option>
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
308 </param>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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309 <param name="centroids_imagesmoothing" type="select" label="Select an image smoothing function." help="The 'gaussian' smoothing method smooths images with a simple gaussian kernel. The 'adaptive' method uses bilateral filtering to preserve edges.">
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
diff changeset
310 <option value="none" selected="True">none</option>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
diff changeset
311 <option value="gaussian">gaussian</option>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
diff changeset
312 <option value="adaptive">adaptive</option>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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313 </param>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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314 </when>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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315 </conditional>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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316 <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
galaxyp
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317 <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
galaxyp
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318 <sanitizer>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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319 <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
parents:
diff changeset
320 <add value="#" />
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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321 </valid>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
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322 </sanitizer>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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323 </param>
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
324 </repeat>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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325 </inputs>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
diff changeset
326 <outputs>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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327 <data format="pdf" name="segmentationimages" from_work_dir="segmentationpdf.pdf" label = "${tool.name} on $infile.display_name"/>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
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328 <data format="tabular" name="mzfeatures" label="mzfeatures ${tool.name} on $infile.display_name"/>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
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329 <data format="tabular" name="pixeloutput" label="pixels ${tool.name} on $infile.display_name"/>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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330 </outputs>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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331 <tests>
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
332 <test>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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333 <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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diff changeset
334 <composite_data value="Example_Continuous.imzML"/>
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
335 <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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336 </param>
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
337 <param name="segmentationtool" value="pca"/>
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
338 <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
339 <param name="feature_color" value="#ff00ff"/>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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340 </repeat>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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341 <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
342 <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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343 </repeat>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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344 <output name="segmentationimages" file="pca_imzml.pdf" compare="sim_size" delta="20000"/>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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345 <output name="mzfeatures" file="pcaloadings_results1.txt" compare="sim_size"/>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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346 <output name="pixeloutput" file="pcascores_results1.txt" compare="sim_size"/>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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347 </test>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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348 <test>
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="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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350 <composite_data value="Analyze75.hdr" />
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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351 <composite_data value="Analyze75.img" />
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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352 <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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353 </param>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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354 <param name="segmentationtool" value="kmeans"/>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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355 <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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356 <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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357 </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
358 <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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diff changeset
359 <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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360 </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
361 <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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diff changeset
362 <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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363 </repeat>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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364 <output name="segmentationimages" file="kmeans_imzml.pdf" compare="sim_size" delta="20000"/>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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365 <output name="mzfeatures" file="toplabels_results1.txt" compare="sim_size"/>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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366 <output name="pixeloutput" file="cluster_results1.txt" compare="sim_size"/>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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367 </test>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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368 <test>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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369 <param name="infile" value="preprocessing_results1.RData" ftype="rdata"/>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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370 <param name="segmentationtool" 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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diff changeset
371 <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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diff changeset
372 <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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373 </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
374 <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
375 <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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diff changeset
376 </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
377 <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
378 <param name="feature_color" value="#B0171F"/>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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379 </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
380 <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
381 <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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diff changeset
382 </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
383 <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
384 <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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385 </repeat>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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386 <output name="segmentationimages" file="centroids_imzml.pdf" compare="sim_size" delta="20000"/>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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387 <output name="mzfeatures" file="toplabels_results1.txt" compare="sim_size"/>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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388 <output name="pixeloutput" file="classes_results1.txt" compare="sim_size"/>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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389 </test>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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390 </tests>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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391 <help>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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392 <![CDATA[
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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393
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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394 Spatially aware segmentation of mass-spectrometry imaging data by unsupervised clustering algorithms. Underlying structures can be identified with the following tools: pca, k-means clustering and spatial shrunken centroids. The spatialShrunkenCentroids method allows the number of segments to decrease according to the data. This allows automatic selection of the number
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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395 of clusters.
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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396
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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397 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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diff changeset
398
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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399 - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <http://ms-imaging.org/wp/introduction/>`_
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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400 - 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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401 - 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
galaxyp
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diff changeset
402
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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403 The output of this tool contains a pdf with plots from the segmentation tools.
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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404 ]]>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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diff changeset
405 </help>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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406 <citations>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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diff changeset
407 <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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408 </citations>
0c1a9b68f436 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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409 </tool>