Mercurial > repos > galaxyp > cardinal_segmentations

annotate segmentation.xml @ 7:5e73ae48d674 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
author galaxyp
date Thu, 23 Apr 2020 11:59:49 +0000
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children 64d0651a9f76
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1 <tool id="cardinal_segmentations" name="MSI segmentation" version="@VERSION@.0">
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2 <description>mass spectrometry imaging spatial clustering</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements">
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7 <requirement type="package" version="2.3">r-gridextra</requirement>
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8 </expand>
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9 <command detect_errors="exit_code">
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10 <![CDATA[
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12 @INPUT_LINKING@
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13 cat '${MSI_segmentation}' &&
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14 Rscript '${MSI_segmentation}'
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16 ]]>
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17 </command>
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18 <configfiles>
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19 <configfile name="MSI_segmentation"><![CDATA[
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21 ################################# load libraries and read file #################
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23 library(Cardinal)
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24 library(gridExtra)
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26 @READING_MSIDATA@
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28 msidata = as(msidata, "MSImageSet") ##coercion to MSImageSet
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30 ## remove duplicated coordinates
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31 msidata <- msidata[,!duplicated(coord(msidata))]
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34 @DATA_PROPERTIES_INRAM@
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35
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37 ######################################## PDF ###################################
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38 ################################################################################
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39 ################################################################################
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42 pdf("segmentationpdf.pdf", fonts = "Times", pointsize = 12)
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43 plot(0,type='n',axes=FALSE,ann=FALSE)
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45 title(main=paste0("Spatial segmentation for file: \n\n", "$infile.display_name"))
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48 ############################# I) numbers ####################################
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49 #############################################################################
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50 grid.table(property_df, rows= NULL)
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52 if (npeaks > 0 && sum(is.na(spectra(msidata)))==0)
0
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53 {
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55 ######################## II) segmentation tools #############################
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56 #############################################################################
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57 #set $color_string = ','.join(['"%s"' % $color.feature_color for $color in $colours])
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58 colourvector = c($color_string)
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60 ## set seed to make analysis reproducible
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61 set.seed($setseed)
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62
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63 #if str( $segm_cond.segmentationtool ) == 'pca':
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64 print('pca')
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65 ##pca
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66
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67 component_vector = character()
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68 for (numberofcomponents in 1:$segm_cond.pca_ncomp)
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69 {component_vector[numberofcomponents]= paste0("PC", numberofcomponents)}
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70
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71 pca_result = PCA(msidata, ncomp=$segm_cond.pca_ncomp, column = component_vector, superpose = FALSE,
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72 method = "$segm_cond.pca_method", scale = $segm_cond.pca_scale, layout = c(ncomp, 1))
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73
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74 ## remove msidata to clean up RAM space
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75 rm(msidata)
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76 gc()
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78 ### table in pdf file
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79 plot(0,type='n',axes=FALSE,ann=FALSE)
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80 sd_table = as.data.frame(round(pca_result@resultData\$ncomp\$sdev, digits=2))
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81 colnames(sd_table) = "Standard deviation"
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82 PC_vector = character()
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83 for (PCs in 1:$segm_cond.pca_ncomp){
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84 PC_vector[[PCs]] = c(paste0("PC",PCs))}
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85 sd_table = cbind(PC_vector, sd_table)
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86 colnames(sd_table)[1] = "Principal components"
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87 grid.table(sd_table, rows=NULL)
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88 ### images in pdf file
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89 print(image(pca_result, main="PCA image", strip = FALSE, col=colourvector, ylim=c(maximumy+2, minimumy-2)))
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90 for (PCs in 1:$segm_cond.pca_ncomp){
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91 print(image(pca_result, column = c(paste0("PC",PCs)),strip = FALSE, superpose = FALSE, main=paste0("PC", PCs), col.regions = risk.colors(100), ylim=c(maximumy+2, minimumy-2)))}
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92 ### plots in pdf file
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93 print(plot(pca_result, main="PCA plot", col= colourvector, strip = FALSE))
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94 for (PCs in 1:$segm_cond.pca_ncomp){
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95 print(plot(pca_result, column = c(paste0("PC",PCs)),main=paste0("PC", PCs),strip = FALSE,superpose = FALSE))}
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96
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97 ### values in tabular files
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98 pcaloadings = formatC(pca_result@resultData\$ncomp\$loadings, format = "e", digits = 6)### loading for each m/z value
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99 pcaloadings2 = cbind(matrix(unlist(strsplit(rownames(pcaloadings), " = ")), ncol=2, byrow=TRUE)[,2], pcaloadings)
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100 colnames(pcaloadings2) = c("mz", colnames(pcaloadings))
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101 pcascores = round(pca_result@resultData\$ncomp\$scores, digits=6) ### scores for each pixel
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102
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103 ## pixel names and coordinates
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104 ## to remove potential sample names and z dimension, split at comma and take only x and y
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105 x_coords = unlist(lapply(strsplit(rownames(pcascores), ","), `[[`, 1))
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106 y_coords = unlist(lapply(strsplit(rownames(pcascores), ","), `[[`, 2))
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107 x_coordinates = gsub("x = ","",x_coords)
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108 y_coordinates = gsub(" y = ","",y_coords)
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109
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110 pixel_names = paste0("xy_", x_coordinates, "_", y_coordinates)
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111 pcascores2 = data.frame(pixel_names, x_coordinates, y_coordinates, pcascores)
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112 colnames(pcascores2) = c("pixel names", "x", "y", colnames(pcascores))
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113 write.table(pcaloadings2, file="$mzfeatures", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
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114 write.table(pcascores2, file="$pixeloutput", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
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115
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116 ## optional output as .RData
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117 #if $output_rdata:
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118 ## save as (.RData)
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119 save(pca, file="$segmentation_rdata")
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120
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121 #end if
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122
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123 #elif str( $segm_cond.segmentationtool ) == 'kmeans':
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124 print('kmeans')
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125 ##k-means
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126
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127 skm = spatialKMeans(msidata, r=c($segm_cond.kmeans_r), k=c($segm_cond.kmeans_k), method="$segm_cond.kmeans_method")
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128
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129 ## remove msidata to clean up RAM space
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130 rm(msidata)
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131 gc()
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132
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133 print(image(skm, key=TRUE, main="K-means clustering", strip=FALSE, col= colourvector, layout=c(1,1), ylim=c(maximumy+2, minimumy-2)))
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134 print(plot(skm, main="K-means plot", col= colourvector, strip=FALSE, layout=c(1,1)))
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135
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136 skm_clusters = data.frame(matrix(NA, nrow = pixelcount, ncol = 0))
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137 for (iteration in 1:length(skm@resultData)){
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138 skm_cluster = ((skm@resultData)[[iteration]]\$cluster)
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139 skm_clusters = cbind(skm_clusters, skm_cluster) }
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140
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141 ## pixel names and coordinates
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142 ## to remove potential sample names and z dimension, split at comma and take only x and y
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143 x_coords = unlist(lapply(strsplit(rownames(skm_clusters), ","), `[[`, 1))
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144 y_coords = unlist(lapply(strsplit(rownames(skm_clusters), ","), `[[`, 2))
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145 x_coordinates = gsub("x = ","",x_coords)
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146 y_coordinates = gsub(" y = ","",y_coords)
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147 pixel_names = paste0("xy_", x_coordinates, "_", y_coordinates)
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148 skm_clusters2 = data.frame(pixel_names, x_coordinates, y_coordinates, skm_clusters)
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149 colnames(skm_clusters2) = c("pixel names", "x", "y",names(skm@resultData))
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150
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151 skm_toplabels = topFeatures(skm, n=$segm_cond.kmeans_toplabels)
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152
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153 write.table(skm_toplabels, file="$mzfeatures", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
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154 write.table(skm_clusters2, file="$pixeloutput", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
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155
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156 ## optional output as .RData
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157 #if $output_rdata:
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158
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159 ## save as (.RData)
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160 save(skm, file="$segmentation_rdata")
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161
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162 #end if
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163
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164 #elif str( $segm_cond.segmentationtool ) == 'centroids':
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165 print('centroids')
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166 ##centroids
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167
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168 ssc = spatialShrunkenCentroids(msidata, r=c($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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169 ## remove msidata to clean up RAM space
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170 rm(msidata)
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171 gc()
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172 print(image(ssc, key=TRUE, main="Spatial shrunken centroids", strip = TRUE, col= colourvector,layout=c(1,1), ylim=c(maximumy+2, minimumy-2)))
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173 print(plot(ssc, main="Spatial shrunken centroids plot", col= colourvector, strip = TRUE,layout=c(1,1)))
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174 print(plot(ssc, mode = "tstatistics",key = TRUE, layout = c(1,1), main="t-statistics", col=colourvector))
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175
0
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176 plot(summary(ssc), main = "Number of segments")
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177
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178 ssc_classes = data.frame(matrix(NA, nrow = pixelcount, ncol = 0))
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179 for (iteration in 1:length(ssc@resultData)){
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180 ssc_class = ((ssc@resultData)[[iteration]]\$classes)
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181 ssc_classes = cbind(ssc_classes, ssc_class) }
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182
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183 ## pixel names and coordinates
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184 ## to remove potential sample names and z dimension, split at comma and take only x and y
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185 x_coords = unlist(lapply(strsplit(rownames(ssc_classes), ","), `[[`, 1))
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186 y_coords = unlist(lapply(strsplit(rownames(ssc_classes), ","), `[[`, 2))
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187 x_coordinates = gsub("x = ","",x_coords)
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188 y_coordinates = gsub(" y = ","",y_coords)
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189 pixel_names = paste0("xy_", x_coordinates, "_", y_coordinates)
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190 ssc_classes2 = data.frame(pixel_names, x_coordinates, y_coordinates, ssc_classes)
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191 colnames(ssc_classes2) = c("pixel names", "x", "y", names(ssc@resultData))
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192
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193 ssc_toplabels = topFeatures(ssc, n=$segm_cond.centroids_toplabels)
0
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194
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195 write.table(ssc_toplabels, file="$mzfeatures", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
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196 write.table(ssc_classes2, file="$pixeloutput", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
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197
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198 ## optional output as .RData
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199 #if $output_rdata:
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200
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201 ## save as (.RData)
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202 save(ssc, file="$segmentation_rdata")
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203
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204 #end if
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205
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206 #end if
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207
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208 dev.off()
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209
4
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210 ## optional svg output with original coordinates
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211 #if $svg_pixelimage:
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212 print("svg image")
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213 ## reverse y axis for svg output = correct order and nice svg image
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214
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215
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216 svg(file="svg_pixel_output.svg", width=maximumx, height=maximumy)
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217 par(mar=c(0,0,0,0))
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218 #if str( $segm_cond.segmentationtool ) == 'pca':
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219 coord(pca_result)\$y <- max(coord(pca_result)\$y) - coord(pca_result)\$y + 1
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220 image(pca_result, strip = FALSE, colorkey=FALSE, axes=FALSE, xlab=NA, ylab=NA, col=colourvector)
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221 #elif str( $segm_cond.segmentationtool ) == 'kmeans':
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222 coord(skm)\$y <- max(coord(skm)\$y) - coord(skm)\$y + 1
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223 image(skm, key=FALSE, strip=FALSE, col= colourvector)
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224 #elif str( $segm_cond.segmentationtool ) == 'centroids':
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225 coord(ssc)\$y <- max(coord(ssc)\$y) - coord(ssc)\$y + 1
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226 image(ssc, key=FALSE, strip = FALSE, col= colourvector)
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227 #end if
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228 dev.off()
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229 #end if
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230
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231
0
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232 }else{
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233 print("Inputfile has no intensities > 0")
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234 dev.off()
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235 }
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236
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237 ]]></configfile>
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238 </configfiles>
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239 <inputs>
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240 <expand macro="reading_msidata"/>
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241 <conditional name="segm_cond">
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242 <param name="segmentationtool" type="select" label="Select the tool for spatial clustering">
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243 <option value="pca" selected="True">pca</option>
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244 <option value="kmeans">k-means</option>
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245 <option value="centroids">spatial shrunken centroids</option>
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246 </param>
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247 <when value="pca">
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248 <param name="pca_ncomp" type="integer" value="2"
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249 label="The number of principal components to calculate"/>
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250 <param name="pca_method" type="select"
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251 label="The function used to calculate the singular value decomposition">
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252 <option value="irlba" selected="True">irlba</option>
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253 <option value="svd">svd</option>
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254 </param>
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255 <param name="pca_scale" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Scaling of data before analysis"/>
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256 </when>
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257 <when value="kmeans">
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258 <param name="kmeans_r" type="text" value="2"
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259 label="The spatial neighborhood radius of nearby pixels to consider (r)" help="Multiple values are allowed (e.g. 1,2,3 or 2:5)">
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260 <expand macro="sanitizer_multiple_digits"/>
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261 </param>
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262 <param name="kmeans_k" type="text" value="3"
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263 label="The number of clusters (k)" help="Multiple values are allowed (e.g. 1,2,3 or 2:5)">
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264 <expand macro="sanitizer_multiple_digits"/>
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265 </param>
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266 <param name="kmeans_method" type="select" display="radio"
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267 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">
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268 <option value="gaussian">gaussian</option>
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269 <option value="adaptive" selected="True">adaptive</option>
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270 </param>
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271 <param name="kmeans_toplabels" type="integer" value="500"
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272 label="Number of toplabels (m/z) which should be written in tabular output"/>
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273 </when>
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274
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275 <when value="centroids">
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276 <param name="centroids_r" type="text" value="2"
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277 label="The spatial neighborhood radius of nearby pixels to consider (r)" help="Multiple values are allowed (e.g. 1,2,3 or 2:5)">
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278 <expand macro="sanitizer_multiple_digits"/>
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279 </param>
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280 <param name="centroids_k" type="text" value="5"
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281 label="The initial number of clusters (k)" help="Multiple values are allowed (e.g. 1,2,3 or 2:5)">
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282 <expand macro="sanitizer_multiple_digits"/>
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283 </param>
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284 <param name="centroids_s" type="text" value="2"
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285 label="The sparsity thresholding parameter by which to shrink the t-statistics (s)"
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286 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)">
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287 <expand macro="sanitizer_multiple_digits"/>
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288 </param>
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289 <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">
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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290 <option value="gaussian">gaussian</option>
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291 <option value="adaptive" selected="True">adaptive</option>
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292 </param>
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293 <param name="centroids_toplabels" type="integer" value="500"
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294 label="Number of toplabels (m/z) which should be written in tabular output"/>
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295 </when>
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296 </conditional>
4
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297 <param name="svg_pixelimage" type="boolean" label="Export first segmentation image as svg"/>
0
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298 <repeat name="colours" title="Colours for the plots" min="1" max="50">
2
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299 <param name="feature_color" type="color" label="Colours" value="#ff00ff" help="Numbers of colours should be the same as number of components">
0
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300 <sanitizer>
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301 <valid initial="string.letters,string.digits">
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302 <add value="#" />
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303 </valid>
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304 </sanitizer>
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305 </param>
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306 </repeat>
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307 <param name="output_rdata" type="boolean" label="Results as .RData output"/>
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308 <param name="setseed" type="integer" value="1" label="set seed" help="Use same value to reproduce previous results"/>
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309 </inputs>
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310 <outputs>
2
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311 <data format="pdf" name="segmentationimages" from_work_dir="segmentationpdf.pdf" label = "${tool.name} on ${on_string}: results"/>
0
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312 <data format="tabular" name="mzfeatures" label="${tool.name} on ${on_string}: features"/>
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313 <data format="tabular" name="pixeloutput" label="${tool.name} on ${on_string}: pixels"/>
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314 <data format="rdata" name="segmentation_rdata" label="${tool.name} on ${on_string}: results.RData">
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315 <filter>output_rdata</filter>
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316 </data>
4
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317 <data format="svg" name="svg_output" from_work_dir="svg_pixel_output.svg" label="${tool.name} on ${on_string}: image.svg">
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318 <filter>svg_pixelimage</filter>
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319 </data>
0
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320 </outputs>
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321 <tests>
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322 <test>
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323 <expand macro="infile_imzml"/>
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324 <param name="segmentationtool" value="pca"/>
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325 <repeat name="colours">
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326 <param name="feature_color" value="#ff00ff"/>
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327 </repeat>
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328 <repeat name="colours">
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329 <param name="feature_color" value="#0000FF"/>
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330 </repeat>
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331 <output name="segmentationimages" file="pca_imzml.pdf" compare="sim_size"/>
2
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332 <output name="mzfeatures">
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333 <assert_contents>
7
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334 <has_text text="300.1667" />
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335 <has_text text="300.25" />
2
4ba8fcfef86f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
336 <has_text text="-4.234458e-04" />
4ba8fcfef86f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
337 <has_text text="3.878545e-10" />
4ba8fcfef86f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
338 <has_n_columns n="3" />
4ba8fcfef86f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
339 </assert_contents>
4ba8fcfef86f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
340 </output>
0
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
341 <output name="pixeloutput" file="scores_pca.tabular"/>
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
342 </test>
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
343 <test>
7
5e73ae48d674 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
344 <expand macro="infile_imzml"/>
0
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
345 <param name="segmentationtool" value="kmeans"/>
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
346 <param name="kmeans_r" value="1:3"/>
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
347 <param name="kmeans_k" value="2,3"/>
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
348 <param name="kmeans_toplabels" value="20"/>
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
349 <repeat name="colours">
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
350 <param name="feature_color" value="#ff00ff"/>
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
351 </repeat>
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
352 <repeat name="colours">
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
353 <param name="feature_color" value="#0000FF"/>
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
354 </repeat>
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
355 <repeat name="colours">
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
356 <param name="feature_color" value="#00C957"/>
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
357 </repeat>
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
358 <param name="output_rdata" value="True"/>
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
359 <output name="segmentationimages" file="kmeans_analyze.pdf" compare="sim_size"/>
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
360 <output name="mzfeatures" file="toplabels_skm.tabular"/>
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
361 <output name="pixeloutput" file="cluster_skm.tabular"/>
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
362 <output name="segmentation_rdata" file="cluster_skm.RData" compare="sim_size"/>
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
363 </test>
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
364 <test>
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
365 <param name="infile" value="preprocessed.RData" ftype="rdata"/>
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
366 <param name="segmentationtool" value="centroids"/>
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
367 <param name="centroids_r" value="1,2"/>
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
368 <param name="centroids_k" value="3"/>
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
369 <param name="centroids_toplabels" value="50"/>
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
370 <repeat name="colours">
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
371 <param name="feature_color" value="#0000FF"/>
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
372 </repeat>
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
373 <repeat name="colours">
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
374 <param name="feature_color" value="#00C957"/>
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
375 </repeat>
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
376 <repeat name="colours">
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
377 <param name="feature_color" value="#B0171F"/>
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
378 </repeat>
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
379 <output name="segmentationimages" file="centroids_rdata.pdf" compare="sim_size"/>
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
380 <output name="mzfeatures" file="toplabels_ssc.tabular"/>
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
381 <output name="pixeloutput" file="classes_ssc.tabular"/>
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
382 </test>
7
5e73ae48d674 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
383 <test>
5e73ae48d674 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
384 <param name="infile" value="" ftype="imzml">
5e73ae48d674 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
385 <composite_data value="preprocessing_results3.imzml"/>
5e73ae48d674 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
386 <composite_data value="preprocessing_results3.ibd"/>
5e73ae48d674 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
387 </param>
5e73ae48d674 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
388 <conditional name="processed_cond">
5e73ae48d674 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
389 <param name="processed_file" value="processed"/>
5e73ae48d674 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
390 <param name="accuracy" value="1"/>
5e73ae48d674 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
391 <param name="units" value="mz"/>
5e73ae48d674 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
392 </conditional>
5e73ae48d674 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
393 <param name="segmentationtool" value="centroids"/>
5e73ae48d674 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
394 <param name="centroids_r" value="1"/>
5e73ae48d674 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
395 <param name="centroids_k" value="2,3"/>
5e73ae48d674 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
396 <param name="centroids_s" value="0,3"/>
5e73ae48d674 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
397 <param name="centroids_toplabels" value="100"/>
5e73ae48d674 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
398 <repeat name="colours">
5e73ae48d674 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
399 <param name="feature_color" value="#0000FF"/>
5e73ae48d674 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
400 </repeat>
5e73ae48d674 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
401 <repeat name="colours">
5e73ae48d674 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
402 <param name="feature_color" value="#00C957"/>
5e73ae48d674 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
403 </repeat>
5e73ae48d674 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
404 <repeat name="colours">
5e73ae48d674 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
405 <param name="feature_color" value="#B0171F"/>
5e73ae48d674 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
406 </repeat>
5e73ae48d674 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
407 <output name="segmentationimages" file="centroids_proc.pdf" compare="sim_size"/>
5e73ae48d674 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
408 <output name="mzfeatures" file="toplabels_proc.tabular"/>
5e73ae48d674 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
409 <output name="pixeloutput" file="classes_proc.tabular"/>
5e73ae48d674 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
410 </test>
0
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
411 </tests>
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
412 <help>
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
413 <![CDATA[
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
414
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
415 @CARDINAL_DESCRIPTION@
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
416
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
417 -----
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
418
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
419 This tool provides three different Cardinal functions for unsupervised clustering/spatial segmentation of mass spectrometry imaging data.
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
420
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
421 @MSIDATA_INPUT_DESCRIPTION@
4
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422 - NA intensities are not allowed
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423 - duplicated coordinates will be removed
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424
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425
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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426 **Options**
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427
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428 - PCA: principal component analysis
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429 - k-means: spatially-aware k-means clustering (adopted from `Alexandrov and Kobarg <https://doi.org/10.1093/bioinformatics/btr246>`_)
43049941e1ab planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
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430 - spatial shrunken centroids: Allows the number of segments to decrease according to the data. This allows selection of the number of clusters (more details in `Bemis et al. <https://doi.org/10.1074/mcp.O115.053918>`_)
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431
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432 **Output**
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433
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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434 - Pdf with the heatmaps and plots for the segmentation
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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435 - Tabular file with information on m/z and pixels: loadings/scores (PCA), toplabels/clusters (k-means), toplabels/classes (spatial shrunken centroids)
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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436 - Optional .RData file which contains the segmentation results and can be used for further exploration in R using the Cardinal package
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437 - Optional: svg file with the first segmentation image
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438
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439 ]]>
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440 </help>
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441 <expand macro="citations"/>
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442 </tool>