Mercurial > repos > galaxyp > mass_spectrometry_imaging_segmentations

annotate segmentation_tool.xml @ 7:791aedb1b8ea draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
author galaxyp
date Fri, 06 Jul 2018 14:12:15 -0400
parents b3c8c831e51a
children fa8b6f0f68d4
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1 <tool id="mass_spectrometry_imaging_segmentations" name="MSI segmentation" version="1.10.0.3">
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2 <description>mass spectrometry imaging 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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33 library(Cardinal)
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34 library(gridExtra)
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35 library(lattice)
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37 ## Read MALDI Imaging dataset
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38
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39 #if $infile.ext == 'imzml'
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40 #if str($processed_cond.processed_file) == "processed":
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41 msidata <- readImzML('infile', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units")
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42 #else
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43 msidata <- readImzML('infile')
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44 #end if
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45 #elif $infile.ext == 'analyze75'
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46 msidata = readAnalyze('infile')
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47 #else
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48 load('infile.RData')
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49 #end if
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50
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52 ## create full matrix to make processed imzML files compatible with segmentation
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53 iData(msidata) <- iData(msidata)[]
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54 ###################################### file properties in numbers ##############
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55
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56 ## Number of features (m/z)
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57 maxfeatures = length(features(msidata))
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58 ## Range m/z
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59 minmz = round(min(mz(msidata)), digits=2)
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60 maxmz = round(max(mz(msidata)), digits=2)
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61 ## Number of spectra (pixels)
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62 pixelcount = length(pixels(msidata))
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63 ## Range x coordinates
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64 minimumx = min(coord(msidata)[,1])
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65 maximumx = max(coord(msidata)[,1])
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66 ## Range y coordinates
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67 minimumy = min(coord(msidata)[,2])
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68 maximumy = max(coord(msidata)[,2])
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69 ## Range of intensities
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70 minint = round(min(spectra(msidata)[],na.rm=TRUE), digits=2)
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71 maxint = round(max(spectra(msidata)[],na.rm=TRUE), digits=2)
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72 medint = round(median(spectra(msidata)[]), digits=2)
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73 ## Number of intensities > 0
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74 npeaks= sum(spectra(msidata)[]>0, na.rm=TRUE)
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75 ## Spectra multiplied with m/z (potential number of peaks)
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76 numpeaks = ncol(spectra(msidata)[])*nrow(spectra(msidata)[])
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77 ## Percentage of intensities > 0
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78 percpeaks = round(npeaks/numpeaks*100, digits=2)
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79 ## Number of empty TICs
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80 TICs = colSums(spectra(msidata)[], na.rm=TRUE)
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81 NumemptyTIC = sum(TICs == 0)
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82
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83
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84
0
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85 ## Processing informations
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86 processinginfo = processingData(msidata)
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87 centroidedinfo = processinginfo@centroided # TRUE or FALSE
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88
5
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89 ## if TRUE write processinginfo if FALSE write FALSE
0
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90
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91 ## normalization
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92 if (length(processinginfo@normalization) == 0) {
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93 normalizationinfo='FALSE'
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94 } else {
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95 normalizationinfo=processinginfo@normalization
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96 }
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97 ## smoothing
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98 if (length(processinginfo@smoothing) == 0) {
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99 smoothinginfo='FALSE'
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100 } else {
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101 smoothinginfo=processinginfo@smoothing
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102 }
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103 ## baseline
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104 if (length(processinginfo@baselineReduction) == 0) {
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105 baselinereductioninfo='FALSE'
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106 } else {
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107 baselinereductioninfo=processinginfo@baselineReduction
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108 }
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109 ## peak picking
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110 if (length(processinginfo@peakPicking) == 0) {
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111 peakpickinginfo='FALSE'
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112 } else {
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113 peakpickinginfo=processinginfo@peakPicking
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114 }
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115
5
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116 properties = c("Number of m/z features",
6
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117 "Range of m/z values",
0
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118 "Number of pixels",
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119 "Range of x coordinates",
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120 "Range of y coordinates",
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121 "Range of intensities",
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122 "Median of intensities",
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123 "Intensities > 0",
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124 "Number of zero TICs",
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125 "Preprocessing",
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126 "Normalization",
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127 "Smoothing",
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128 "Baseline reduction",
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129 "Peak picking",
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130 "Centroided")
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131
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132 values = c(paste0(maxfeatures),
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133 paste0(minmz, " - ", maxmz),
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134 paste0(pixelcount),
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135 paste0(minimumx, " - ", maximumx),
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136 paste0(minimumy, " - ", maximumy),
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137 paste0(minint, " - ", maxint),
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138 paste0(medint),
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139 paste0(percpeaks, " %"),
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140 paste0(NumemptyTIC),
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141 paste0(" "),
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142 paste0(normalizationinfo),
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143 paste0(smoothinginfo),
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144 paste0(baselinereductioninfo),
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145 paste0(peakpickinginfo),
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146 paste0(centroidedinfo))
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147
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148 property_df = data.frame(properties, values)
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149
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150
4
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151 ######################################## PDF ###################################
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152 ################################################################################
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153 ################################################################################
0
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154
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155
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156 pdf("segmentationpdf.pdf", fonts = "Times", pointsize = 12)
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157 plot(0,type='n',axes=FALSE,ann=FALSE)
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158
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159 title(main=paste0("Spatial segmentation for file: \n\n", "$infile.display_name"))
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160
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161
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162 ############################# I) numbers ####################################
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163 #############################################################################
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164 grid.table(property_df, rows= NULL)
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165
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166 if (npeaks > 0)
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167 {
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168
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169 ######################## II) segmentation tools #############################
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170 #############################################################################
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171 #set $color_string = ','.join(['"%s"' % $color.feature_color for $color in $colours])
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172 colourvector = c($color_string)
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173
5
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174 ### preparation for images and plots:
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175 #if str($image_cond.image_type) == "standard_image":
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176 print("standard image")
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177
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178 strip_input = TRUE
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179 lattice_input = FALSE
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180
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181 #elif str($image_cond.image_type) == "lattice_image":
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182 print("lattice image")
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183
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184 strip_input = strip.custom(bg="lightgrey", par.strip.text=list(col="black", cex=.9))
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185 lattice_input = TRUE
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186
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187 #end if
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188
0
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189
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190 #if str( $segm_cond.segmentationtool ) == 'pca':
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191 print('pca')
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192 ##pca
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193
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194 component_vector = character()
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195 for (numberofcomponents in 1:$segm_cond.pca_ncomp)
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196 {component_vector[numberofcomponents]= paste0("PC", numberofcomponents)}
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197 pca_result = PCA(msidata, ncomp=$segm_cond.pca_ncomp, column = component_vector, superpose = FALSE,
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198 method = "$segm_cond.pca_method", scale = $segm_cond.pca_scale, layout = c(ncomp, 1))
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199
6
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200 ### images in pdf file
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201 print(image(pca_result, main="PCA image", lattice=lattice_input, strip = strip_input, col=colourvector))
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202 for (PCs in 1:$segm_cond.pca_ncomp){
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203 print(image(pca_result, column = c(paste0("PC",PCs)), lattice=lattice_input, superpose = FALSE, col.regions = risk.colors(100)))}
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204 ### plots in pdf file
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205 print(plot(pca_result, main="PCA plot", lattice=lattice_input, col= colourvector, strip = strip_input))
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206 for (PCs in 1:$segm_cond.pca_ncomp){
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207 print(plot(pca_result, column = c(paste0("PC",PCs)),superpose = FALSE))}
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208
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209 ### values in tabular files
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210 pcaloadings = (pca_result@resultData\$ncomp\$loadings) ### loading for each m/z value
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211 pcascores = (pca_result@resultData\$ncomp\$scores) ### scores for each pixel
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212
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213 write.table(pcaloadings, file="$mzfeatures", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t")
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214 write.table(pcascores, file="$pixeloutput", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t")
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215
5
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216 ## optional output as .RData
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217 #if $output_rdata:
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218 ## save as (.RData)
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219 save(pca, file="$segmentation_rdata")
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220
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221 #end if
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222
0
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223 #elif str( $segm_cond.segmentationtool ) == 'kmeans':
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224 print('kmeans')
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225 ##k-means
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226
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227 skm = spatialKMeans(msidata, r=c($segm_cond.kmeans_r), k=c($segm_cond.kmeans_k), method="$segm_cond.kmeans_method")
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228 print(image(skm, key=TRUE, main="K-means clustering", lattice=lattice_input, strip=strip_input, col= colourvector, layout=c(1,1)))
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229
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230 print(plot(skm, main="K-means plot", lattice=lattice_input, col= colourvector, strip=strip_input, layout=c($segm_cond.kmeans_layout)))
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231
2
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232 skm_clusters = data.frame(matrix(NA, nrow = pixelcount, ncol = 0))
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233 for (iteration in 1:length(skm@resultData)){
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234 skm_cluster = ((skm@resultData)[[iteration]]\$cluster)
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235 skm_clusters = cbind(skm_clusters, skm_cluster) }
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236 colnames(skm_clusters) = names((skm@resultData))
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237
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238 skm_toplabels = topLabels(skm, n=$segm_cond.kmeans_toplabels)
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239
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240 write.table(skm_toplabels, file="$mzfeatures", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t")
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241 write.table(skm_clusters, file="$pixeloutput", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t")
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242
5
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243 ## optional output as .RData
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244 #if $output_rdata:
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245
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246 ## save as (.RData)
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247 save(skm, file="$segmentation_rdata")
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248
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249 #end if
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250
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251 #elif str( $segm_cond.segmentationtool ) == 'centroids':
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252 print('centroids')
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253 ##centroids
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254
2
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255 ssc = spatialShrunkenCentroids(msidata, r=c($segm_cond.centroids_r), k=c($segm_cond.centroids_k), s=c($segm_cond.centroids_s), method="$segm_cond.centroids_method")
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256 print(image(ssc, key=TRUE, main="Spatial shrunken centroids", lattice=lattice_input, strip = strip_input, col= colourvector,layout=c(1,1)))
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257 print(plot(ssc, main="Spatial shrunken centroids plot", lattice=lattice_input, col= colourvector, strip = strip_input,layout=c($segm_cond.centroids_layout)))
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258 print(plot(ssc, mode = "tstatistics",key = TRUE, lattice=lattice_input, layout = c($segm_cond.centroids_layout), main="t-statistics", col=colourvector))
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259 plot(summary(ssc), main = "Number of segments")
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260
2
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261 ssc_classes = data.frame(matrix(NA, nrow = pixelcount, ncol = 0))
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262 for (iteration in 1:length(ssc@resultData)){
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263 ssc_class = ((ssc@resultData)[[iteration]]\$classes)
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264 ssc_classes = cbind(ssc_classes, ssc_class) }
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265 colnames(ssc_classes) = names((ssc@resultData))
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266
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267 ssc_toplabels = topLabels(ssc, n=$segm_cond.centroids_toplabels)
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268
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269 write.table(ssc_toplabels, file="$mzfeatures", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t")
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270 write.table(ssc_classes, file="$pixeloutput", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t")
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271
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272 ## optional output as .RData
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273 #if $output_rdata:
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274
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275 ## save as (.RData)
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276 save(ssc, file="$segmentation_rdata")
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277
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278 #end if
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279
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280 #end if
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281
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282 dev.off()
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283
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284 }else{
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285 print("Inputfile has no intensities > 0")
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286 dev.off()
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287 }
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288
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289 ]]></configfile>
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290 </configfiles>
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291 <inputs>
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292 <param name="infile" type="data" format="imzml,rdata,analyze75"
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293 label="Inputfile as imzML, Analyze7.5 or Cardinal MSImageSet saved as RData"
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294 help="Upload composite datatype imzml (ibd+imzML) or analyze75 (hdr+img+t2m) or regular upload .RData (Cardinal MSImageSet)"/>
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295 <conditional name="processed_cond">
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296 <param name="processed_file" type="select" label="Is the input file a processed imzML file ">
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297 <option value="no_processed" selected="True">not a processed imzML</option>
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298 <option value="processed">processed imzML</option>
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299 </param>
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300 <when value="no_processed"/>
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301 <when value="processed">
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302 <param name="accuracy" type="float" value="50" label="Mass accuracy to which the m/z values will be binned" help="This should be set to the native accuracy of the mass spectrometer, if known"/>
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303 <param name="units" display="radio" type="select" label="Unit of the mass accuracy" help="either m/z or ppm">
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304 <option value="mz" >mz</option>
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305 <option value="ppm" selected="True" >ppm</option>
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306 </param>
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307 </when>
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308 </conditional>
0
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309 <conditional name="segm_cond">
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310 <param name="segmentationtool" type="select" label="Select the tool for spatial clustering">
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311 <option value="pca" selected="True">pca</option>
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312 <option value="kmeans">k-means</option>
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313 <option value="centroids">spatial shrunken centroids</option>
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314 </param>
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315 <when value="pca">
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316 <param name="pca_ncomp" type="integer" value="2"
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317 label="The number of principal components to calculate"/>
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318 <param name="pca_method" type="select"
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319 label="The function used to calculate the singular value decomposition">
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320 <option value="irlba" selected="True">irlba</option>
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321 <option value="svd">svd</option>
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322 </param>
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323 <param name="pca_scale" type="select" display="radio" optional="False"
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324 label="Scaling of data before analysis">
0
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325 <option value="TRUE">yes</option>
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326 <option value="FALSE" selected="True">no</option>
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327 </param>
4
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328 </when>
0
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329
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330 <when value="kmeans">
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331 <param name="kmeans_r" type="text" value="2"
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332 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
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333 <param name="kmeans_k" type="text" value="3"
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334 label="The number of clusters (k)" help="Multiple values are allowed (e.g. 1,2,3 or 2:5)"/>
0
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335 <param name="kmeans_method" type="select" display="radio"
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336 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
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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337 <option value="gaussian">gaussian</option>
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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338 <option value="adaptive" selected="True">adaptive</option>
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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339 </param>
2
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parents: 1
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340 <param name="kmeans_toplabels" type="integer" value="500"
5
25e1e84cfe1b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7
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parents: 4
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341 label="Number of toplabels (m/z) which should be written in tabular output"/>
2
76d0244b1bbc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit ed7d3e6f1a09c78c8f71cc1bdc1a20249767f646
galaxyp
parents: 1
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342 <param name="kmeans_layout" type="text" value="1,1"
76d0244b1bbc 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 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"/>
76d0244b1bbc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit ed7d3e6f1a09c78c8f71cc1bdc1a20249767f646
galaxyp
parents: 1
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344 </when>
0
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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345
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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346 <when value="centroids">
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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347 <param name="centroids_r" type="text" value="2"
4
38afc994e3cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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348 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
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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349 <param name="centroids_k" type="text" value="5"
4
38afc994e3cc 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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350 label="The initial number of clusters (k)" help="Multiple values are allowed (e.g. 1,2,3 or 2:5)"/>
2
76d0244b1bbc 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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351 <param name="centroids_s" type="text" value="2"
4
38afc994e3cc 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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352 label="The sparsity thresholding parameter by which to shrink the t-statistics (s)"
5
25e1e84cfe1b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7
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parents: 4
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353 help="As s increases, fewer m/z features (m/z values) will be used in the spatial segmentation, and only the informative m/z features will be retained. Multiple values are allowed (e.g. 1,2,3 or 2:5)"/>
4
38afc994e3cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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354 <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">
6
b3c8c831e51a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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parents: 5
diff changeset
355 <option value="gaussian">gaussian</option>
b3c8c831e51a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 5
diff changeset
356 <option value="adaptive" selected="True">adaptive</option>
0
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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diff changeset
357 </param>
2
76d0244b1bbc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit ed7d3e6f1a09c78c8f71cc1bdc1a20249767f646
galaxyp
parents: 1
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358 <param name="centroids_toplabels" type="integer" value="500"
5
25e1e84cfe1b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 4
diff changeset
359 label="Number of toplabels (m/z) which should be written in tabular output"/>
2
76d0244b1bbc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit ed7d3e6f1a09c78c8f71cc1bdc1a20249767f646
galaxyp
parents: 1
diff changeset
360 <param name="centroids_layout" type="text" value="1,1"
76d0244b1bbc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit ed7d3e6f1a09c78c8f71cc1bdc1a20249767f646
galaxyp
parents: 1
diff changeset
361 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
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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diff changeset
362 </when>
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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diff changeset
363 </conditional>
5
25e1e84cfe1b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 4
diff changeset
364 <conditional name="image_cond">
25e1e84cfe1b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 4
diff changeset
365 <param name="image_type" type="select" label="Select the image type">
25e1e84cfe1b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 4
diff changeset
366 <option value="standard_image" selected="True">standard</option>
25e1e84cfe1b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 4
diff changeset
367 <option value="lattice_image">lattice</option>
25e1e84cfe1b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 4
diff changeset
368 </param>
25e1e84cfe1b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 4
diff changeset
369 <when value="standard_image"/>
25e1e84cfe1b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 4
diff changeset
370 <when value="lattice_image"/>
25e1e84cfe1b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 4
diff changeset
371 </conditional>
0
71eaa6d9d057 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 name="colours" title="Colours for the plots" min="1" max="50">
71eaa6d9d057 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 <param name="feature_color" type="color" label="Colours" value="#ff00ff" help="Numbers of columns should be the same as number of components">
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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diff changeset
374 <sanitizer>
71eaa6d9d057 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 <valid initial="string.letters,string.digits">
71eaa6d9d057 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 <add value="#" />
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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377 </valid>
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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diff changeset
378 </sanitizer>
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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379 </param>
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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diff changeset
380 </repeat>
5
25e1e84cfe1b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7
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diff changeset
381 <param name="output_rdata" type="boolean" display="radio" label="Results as .RData output"/>
0
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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diff changeset
382 </inputs>
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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diff changeset
383 <outputs>
5
25e1e84cfe1b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7
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diff changeset
384 <data format="pdf" name="segmentationimages" from_work_dir="segmentationpdf.pdf" label = "$infile.display_name segmentation"/>
25e1e84cfe1b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7
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diff changeset
385 <data format="tabular" name="mzfeatures" label="$infile.display_name m/z features"/>
25e1e84cfe1b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7
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diff changeset
386 <data format="tabular" name="pixeloutput" label="$infile.display_name pixels"/>
25e1e84cfe1b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 4
diff changeset
387 <data format="rdata" name="segmentation_rdata" label="$infile.display_name segmentation">
25e1e84cfe1b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7
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diff changeset
388 <filter>output_rdata</filter>
25e1e84cfe1b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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diff changeset
389 </data>
0
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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diff changeset
390 </outputs>
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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diff changeset
391 <tests>
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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diff changeset
392 <test>
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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diff changeset
393 <param name="infile" value="" ftype="imzml">
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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diff changeset
394 <composite_data value="Example_Continuous.imzML"/>
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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diff changeset
395 <composite_data value="Example_Continuous.ibd"/>
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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396 </param>
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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397 <param name="segmentationtool" value="pca"/>
5
25e1e84cfe1b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 4
diff changeset
398 <param name="image_type" value="lattice_image"/>
0
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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diff changeset
399 <repeat name="colours">
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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diff changeset
400 <param name="feature_color" value="#ff00ff"/>
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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diff changeset
401 </repeat>
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
diff changeset
402 <repeat name="colours">
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
diff changeset
403 <param name="feature_color" value="#0000FF"/>
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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404 </repeat>
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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405 <output name="segmentationimages" file="pca_imzml.pdf" compare="sim_size" delta="20000"/>
1
942c11934f50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents: 0
diff changeset
406 <output name="mzfeatures" file="loadings_pca.tabular" compare="sim_size"/>
942c11934f50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents: 0
diff changeset
407 <output name="pixeloutput" file="scores_pca.tabular" compare="sim_size"/>
0
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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408 </test>
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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diff changeset
409 <test>
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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diff changeset
410 <param name="infile" value="" ftype="analyze75">
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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diff changeset
411 <composite_data value="Analyze75.hdr" />
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
diff changeset
412 <composite_data value="Analyze75.img" />
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
parents:
diff changeset
413 <composite_data value="Analyze75.t2m" />
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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414 </param>
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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415 <param name="segmentationtool" value="kmeans"/>
2
76d0244b1bbc 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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416 <param name="kmeans_r" value="1:3"/>
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417 <param name="kmeans_k" value="2,3"/>
4
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418 <param name="kmeans_toplabels" value="20"/>
0
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galaxyp
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419 <repeat name="colours">
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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420 <param name="feature_color" value="#ff00ff"/>
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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421 </repeat>
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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422 <repeat name="colours">
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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423 <param name="feature_color" value="#0000FF"/>
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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424 </repeat>
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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425 <repeat name="colours">
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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426 <param name="feature_color" value="#00C957"/>
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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427 </repeat>
5
25e1e84cfe1b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7
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428 <param name="output_rdata" value="True"/>
4
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429 <output name="segmentationimages" file="kmeans_analyze.pdf" compare="sim_size" delta="20000"/>
1
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430 <output name="mzfeatures" file="toplabels_skm.tabular" compare="sim_size"/>
942c11934f50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
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431 <output name="pixeloutput" file="cluster_skm.tabular" compare="sim_size"/>
5
25e1e84cfe1b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7
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432 <output name="pixeloutput" file="cluster_skm.tabular" compare="sim_size"/>
25e1e84cfe1b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7
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433 <output name="segmentation_rdata" file="cluster_skm.RData" compare="sim_size"/>
0
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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434 </test>
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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435 <test>
4
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436 <param name="infile" value="preprocessed.RData" ftype="rdata"/>
0
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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437 <param name="segmentationtool" value="centroids"/>
4
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438 <param name="centroids_r" value="1,2"/>
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439 <param name="centroids_k" value="3"/>
4
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440 <param name="centroids_toplabels" value="50"/>
0
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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441 <repeat name="colours">
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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442 <param name="feature_color" value="#0000FF"/>
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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443 </repeat>
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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444 <repeat name="colours">
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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445 <param name="feature_color" value="#00C957"/>
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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446 </repeat>
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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447 <repeat name="colours">
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
galaxyp
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448 <param name="feature_color" value="#B0171F"/>
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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449 </repeat>
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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450 <repeat name="colours">
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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451 <param name="feature_color" value="#FFD700"/>
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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452 </repeat>
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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453 <repeat name="colours">
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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454 <param name="feature_color" value="#848484"/>
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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455 </repeat>
4
38afc994e3cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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456 <output name="segmentationimages" file="centroids_rdata.pdf" compare="sim_size" delta="20000"/>
1
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parents: 0
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457 <output name="mzfeatures" file="toplabels_ssc.tabular" compare="sim_size"/>
942c11934f50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
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diff changeset
458 <output name="pixeloutput" file="classes_ssc.tabular" compare="sim_size"/>
0
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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459 </test>
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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460 </tests>
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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461 <help>
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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462 <![CDATA[
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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463
4
38afc994e3cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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diff changeset
464 Cardinal is an R package that implements statistical & computational tools for analyzing mass spectrometry imaging datasets. `More information on Cardinal <http://cardinalmsi.org//>`_
38afc994e3cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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diff changeset
465
5
25e1e84cfe1b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7
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466 This tool provides three different Cardinal functions for unsupervised clustering/spatial segmentation of mass spectrometry imaging data.
0
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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diff changeset
467
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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468 Input data: 3 types of input data can be used:
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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469
4
38afc994e3cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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470 - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/wp/imzml/>`_
0
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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471 - Analyze7.5 (upload hdr, img and t2m file via the "composite" function)
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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472 - Cardinal "MSImageSet" data (with variable name "msidata", saved as .RData)
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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473
4
38afc994e3cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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diff changeset
474 Options:
38afc994e3cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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475
38afc994e3cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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476 - PCA: principal component analysis
6
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477 - k-means: spatially-aware k-means clustering
4
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478 - spatial shrunken centroids: Allows the number of segments to decrease according to the data. This allows automatic selection of the number of clusters
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diff changeset
479
38afc994e3cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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480 Output:
38afc994e3cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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481
38afc994e3cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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482 - Pdf with the heatmaps and plots for the segmentation
5
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483 - Tabular file with information on m/z and pixels: loadings/scores (PCA), toplabels/clusters (k-means), toplabels/classes (spatial shrunken centroids)
25e1e84cfe1b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit a7be47698f53eb4f00961192327d93e8989276a7
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484 - Optional .RData file which contains the segmentation results and can be used for further exploration in R
4
38afc994e3cc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_segmentation commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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485
0
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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486 ]]>
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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487 </help>
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488 <citations>
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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489 <citation type="doi">10.1093/bioinformatics/btv146</citation>
71eaa6d9d057 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
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490 </citations>
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491 </tool>