Mercurial > repos > galaxyp > cardinal_segmentations

annotate segmentation.xml @ 5:b16b64ca7b7c draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
author galaxyp
date Fri, 13 Dec 2019 13:52:13 -0500
parents 9f7d1ec01767
children 4a2ac25d1063
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1 <tool id="cardinal_segmentations" name="MSI segmentation" version="@VERSION@.3">
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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 <requirement type="package" version="0.20_35">r-lattice</requirement>
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9 </expand>
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10 <command detect_errors="exit_code">
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11 <![CDATA[
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13 @INPUT_LINKING@
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14 cat '${MSI_segmentation}' &&
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15 Rscript '${MSI_segmentation}'
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17 ]]>
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18 </command>
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19 <configfiles>
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20 <configfile name="MSI_segmentation"><![CDATA[
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23 ################################# load libraries and read file #################
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25 library(Cardinal)
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26 library(gridExtra)
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27 library(lattice)
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31 @READING_MSIDATA_INRAM@
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34 ## remove duplicated coordinates
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35 msidata <- msidata[,!duplicated(coord(msidata))]
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38 @DATA_PROPERTIES_INRAM@
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41 ######################################## PDF ###################################
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42 ################################################################################
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43 ################################################################################
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46 pdf("segmentationpdf.pdf", fonts = "Times", pointsize = 12)
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47 plot(0,type='n',axes=FALSE,ann=FALSE)
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49 title(main=paste0("Spatial segmentation for file: \n\n", "$infile.display_name"))
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52 ############################# I) numbers ####################################
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53 #############################################################################
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54 grid.table(property_df, rows= NULL)
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56 if (npeaks > 0 && sum(is.na(spectra(msidata)))==0)
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57 {
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59 ######################## II) segmentation tools #############################
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60 #############################################################################
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61 #set $color_string = ','.join(['"%s"' % $color.feature_color for $color in $colours])
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62 colourvector = c($color_string)
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64 ### preparation for images and plots:
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65 #if str($image_type) == "standard_image":
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66 print("standard image")
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67
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68 strip_input = FALSE
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69 lattice_input = FALSE
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70
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71 #elif str($image_type) == "lattice_image":
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72 print("lattice image")
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74 strip_input = strip.custom(bg="lightgrey", par.strip.text=list(col="black", cex=.9))
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75 lattice_input = TRUE
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77 #end if
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79 ## set seed to make analysis reproducible
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80 set.seed($setseed)
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82 #if str( $segm_cond.segmentationtool ) == 'pca':
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83 print('pca')
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84 ##pca
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85
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86 component_vector = character()
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87 for (numberofcomponents in 1:$segm_cond.pca_ncomp)
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88 {component_vector[numberofcomponents]= paste0("PC", numberofcomponents)}
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89
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90 pca_result = PCA(msidata, ncomp=$segm_cond.pca_ncomp, column = component_vector, superpose = FALSE,
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91 method = "$segm_cond.pca_method", scale = $segm_cond.pca_scale, layout = c(ncomp, 1))
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92
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93 ## remove msidata to clean up RAM space
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94 rm(msidata)
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95 gc()
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96
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97 ### table in pdf file
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98 plot(0,type='n',axes=FALSE,ann=FALSE)
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99 sd_table = as.data.frame(round(pca_result@resultData\$ncomp\$sdev, digits=2))
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100 colnames(sd_table) = "Standard deviation"
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101 PC_vector = character()
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102 for (PCs in 1:$segm_cond.pca_ncomp){
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103 PC_vector[[PCs]] = c(paste0("PC",PCs))}
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104 sd_table = cbind(PC_vector, sd_table)
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105 colnames(sd_table)[1] = "Principal components"
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106 grid.table(sd_table, rows=NULL)
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107 ### images in pdf file
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108 print(image(pca_result, main="PCA image", lattice=lattice_input, strip = strip_input, col=colourvector, ylim=c(maximumy+2, minimumy-2)))
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109 for (PCs in 1:$segm_cond.pca_ncomp){
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110 print(image(pca_result, column = c(paste0("PC",PCs)), lattice=lattice_input,strip = strip_input, superpose = FALSE, main=paste0("PC", PCs), col.regions = risk.colors(100), ylim=c(maximumy+2, minimumy-2)))}
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111 ### plots in pdf file
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112 print(plot(pca_result, main="PCA plot", lattice=lattice_input, col= colourvector, strip = strip_input))
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113 for (PCs in 1:$segm_cond.pca_ncomp){
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114 print(plot(pca_result, column = c(paste0("PC",PCs)),main=paste0("PC", PCs),strip = FALSE,superpose = FALSE))}
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115
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116 ### values in tabular files
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117 pcaloadings = formatC(pca_result@resultData\$ncomp\$loadings, format = "e", digits = 6)### loading for each m/z value
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118 pcaloadings2 = cbind(matrix(unlist(strsplit(rownames(pcaloadings), " = ")), ncol=2, byrow=TRUE)[,2], pcaloadings)
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119 colnames(pcaloadings2) = c("mz", colnames(pcaloadings))
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120 pcascores = round(pca_result@resultData\$ncomp\$scores, digits=6) ### scores for each pixel
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121
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122 ## pixel names and coordinates
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123 ## to remove potential sample names and z dimension, split at comma and take only x and y
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124 x_coords = unlist(lapply(strsplit(rownames(pcascores), ","), `[[`, 1))
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125 y_coords = unlist(lapply(strsplit(rownames(pcascores), ","), `[[`, 2))
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126 x_coordinates = gsub("x = ","",x_coords)
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127 y_coordinates = gsub(" y = ","",y_coords)
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128
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129 pixel_names = paste0("xy_", x_coordinates, "_", y_coordinates)
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130 pcascores2 = data.frame(pixel_names, x_coordinates, y_coordinates, pcascores)
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131 colnames(pcascores2) = c("pixel names", "x", "y", colnames(pcascores))
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132 write.table(pcaloadings2, file="$mzfeatures", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
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133 write.table(pcascores2, file="$pixeloutput", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
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134
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135 ## optional output as .RData
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136 #if $output_rdata:
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137 ## save as (.RData)
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138 save(pca, file="$segmentation_rdata")
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139
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140 #end if
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141
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142 #elif str( $segm_cond.segmentationtool ) == 'kmeans':
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143 print('kmeans')
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144 ##k-means
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145
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146 skm = spatialKMeans(msidata, r=c($segm_cond.kmeans_r), k=c($segm_cond.kmeans_k), method="$segm_cond.kmeans_method")
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147
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148 ## remove msidata to clean up RAM space
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149 rm(msidata)
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150 gc()
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151
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152 print(image(skm, key=TRUE, main="K-means clustering", lattice=lattice_input, strip=strip_input, col= colourvector, layout=c(1,1), ylim=c(maximumy+2, minimumy-2)))
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153 print(plot(skm, main="K-means plot", lattice=lattice_input, col= colourvector, strip=strip_input, layout=c(1,1)))
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154
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155 skm_clusters = data.frame(matrix(NA, nrow = pixelcount, ncol = 0))
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156 for (iteration in 1:length(skm@resultData)){
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157 skm_cluster = ((skm@resultData)[[iteration]]\$cluster)
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158 skm_clusters = cbind(skm_clusters, skm_cluster) }
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159
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160 ## pixel names and coordinates
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161 ## to remove potential sample names and z dimension, split at comma and take only x and y
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162 x_coords = unlist(lapply(strsplit(rownames(skm_clusters), ","), `[[`, 1))
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163 y_coords = unlist(lapply(strsplit(rownames(skm_clusters), ","), `[[`, 2))
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164 x_coordinates = gsub("x = ","",x_coords)
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165 y_coordinates = gsub(" y = ","",y_coords)
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166 pixel_names = paste0("xy_", x_coordinates, "_", y_coordinates)
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167 skm_clusters2 = data.frame(pixel_names, x_coordinates, y_coordinates, skm_clusters)
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168 colnames(skm_clusters2) = c("pixel names", "x", "y",names(skm@resultData))
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169
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170 skm_toplabels = topLabels(skm, n=$segm_cond.kmeans_toplabels)
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171
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172 write.table(skm_toplabels, file="$mzfeatures", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
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173 write.table(skm_clusters2, file="$pixeloutput", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
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174
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175 ## optional output as .RData
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176 #if $output_rdata:
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177
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178 ## save as (.RData)
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179 save(skm, file="$segmentation_rdata")
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180
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181 #end if
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182
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183 #elif str( $segm_cond.segmentationtool ) == 'centroids':
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184 print('centroids')
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185 ##centroids
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186
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187 ssc = spatialShrunkenCentroids(msidata, r=c($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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188 ## remove msidata to clean up RAM space
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189 rm(msidata)
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190 gc()
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191 print(image(ssc, key=TRUE, main="Spatial shrunken centroids", lattice=lattice_input, strip = TRUE, col= colourvector,layout=c(1,1), ylim=c(maximumy+2, minimumy-2)))
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192 print(plot(ssc, main="Spatial shrunken centroids plot", lattice=lattice_input, col= colourvector, strip = TRUE,layout=c(1,1)))
0
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193 print(plot(ssc, mode = "tstatistics",key = TRUE, lattice=lattice_input, layout = c(1,1), main="t-statistics", col=colourvector))
4
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194
0
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195 plot(summary(ssc), main = "Number of segments")
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196
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197 ssc_classes = data.frame(matrix(NA, nrow = pixelcount, ncol = 0))
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198 for (iteration in 1:length(ssc@resultData)){
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199 ssc_class = ((ssc@resultData)[[iteration]]\$classes)
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200 ssc_classes = cbind(ssc_classes, ssc_class) }
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201
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202 ## pixel names and coordinates
1
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203 ## to remove potential sample names and z dimension, split at comma and take only x and y
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204 x_coords = unlist(lapply(strsplit(rownames(ssc_classes), ","), `[[`, 1))
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205 y_coords = unlist(lapply(strsplit(rownames(ssc_classes), ","), `[[`, 2))
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206 x_coordinates = gsub("x = ","",x_coords)
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207 y_coordinates = gsub(" y = ","",y_coords)
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208 pixel_names = paste0("xy_", x_coordinates, "_", y_coordinates)
0
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209 ssc_classes2 = data.frame(pixel_names, x_coordinates, y_coordinates, ssc_classes)
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210 colnames(ssc_classes2) = c("pixel names", "x", "y", names(ssc@resultData))
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211
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212 ssc_toplabels = topLabels(ssc, n=$segm_cond.centroids_toplabels)
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213
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214 write.table(ssc_toplabels, file="$mzfeatures", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
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215 write.table(ssc_classes2, file="$pixeloutput", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
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216
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217 ## optional output as .RData
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218 #if $output_rdata:
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219
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220 ## save as (.RData)
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221 save(ssc, file="$segmentation_rdata")
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222
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223 #end if
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224
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225 #end if
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226
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227 dev.off()
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228
4
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229 ## optional svg output with original coordinates
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230 #if $svg_pixelimage:
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231 print("svg image")
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232 ## reverse y axis for svg output = correct order and nice svg image
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233
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234
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235 svg(file="svg_pixel_output.svg", width=maximumx, height=maximumy)
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236 par(mar=c(0,0,0,0))
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237 #if str( $segm_cond.segmentationtool ) == 'pca':
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238 coord(pca_result)\$y <- max(coord(pca_result)\$y) - coord(pca_result)\$y + 1
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239 image(pca_result, strip = FALSE, colorkey=FALSE, axes=FALSE, xlab=NA, ylab=NA, col=colourvector)
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240 #elif str( $segm_cond.segmentationtool ) == 'kmeans':
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241 coord(skm)\$y <- max(coord(skm)\$y) - coord(skm)\$y + 1
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242 image(skm, key=FALSE, strip=FALSE, col= colourvector)
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243 #elif str( $segm_cond.segmentationtool ) == 'centroids':
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244 coord(ssc)\$y <- max(coord(ssc)\$y) - coord(ssc)\$y + 1
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245 image(ssc, key=FALSE, strip = FALSE, col= colourvector)
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246 #end if
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247 dev.off()
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248 #end if
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249
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250
0
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251 }else{
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252 print("Inputfile has no intensities > 0")
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253 dev.off()
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254 }
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255
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256 ]]></configfile>
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257 </configfiles>
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258 <inputs>
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259 <expand macro="reading_msidata"/>
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260 <conditional name="segm_cond">
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261 <param name="segmentationtool" type="select" label="Select the tool for spatial clustering">
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262 <option value="pca" selected="True">pca</option>
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263 <option value="kmeans">k-means</option>
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264 <option value="centroids">spatial shrunken centroids</option>
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265 </param>
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266 <when value="pca">
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267 <param name="pca_ncomp" type="integer" value="2"
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268 label="The number of principal components to calculate"/>
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269 <param name="pca_method" type="select"
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270 label="The function used to calculate the singular value decomposition">
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271 <option value="irlba" selected="True">irlba</option>
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272 <option value="svd">svd</option>
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273 </param>
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274 <param name="pca_scale" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Scaling of data before analysis"/>
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275 </when>
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276 <when value="kmeans">
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277 <param name="kmeans_r" type="text" value="2"
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278 label="The spatial neighborhood radius of nearby pixels to consider (r)" help="Multiple values are allowed (e.g. 1,2,3 or 2:5)">
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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279 <expand macro="sanitizer_multiple_digits"/>
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280 </param>
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281 <param name="kmeans_k" type="text" value="3"
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282 label="The number of clusters (k)" help="Multiple values are allowed (e.g. 1,2,3 or 2:5)">
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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283 <expand macro="sanitizer_multiple_digits"/>
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284 </param>
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285 <param name="kmeans_method" type="select" display="radio"
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286 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">
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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287 <option value="gaussian">gaussian</option>
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288 <option value="adaptive" selected="True">adaptive</option>
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289 </param>
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290 <param name="kmeans_toplabels" type="integer" value="500"
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291 label="Number of toplabels (m/z) which should be written in tabular output"/>
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292 </when>
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293
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294 <when value="centroids">
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295 <param name="centroids_r" type="text" value="2"
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296 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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297 <expand macro="sanitizer_multiple_digits"/>
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298 </param>
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299 <param name="centroids_k" type="text" value="5"
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300 label="The initial number of clusters (k)" help="Multiple values are allowed (e.g. 1,2,3 or 2:5)">
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301 <expand macro="sanitizer_multiple_digits"/>
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302 </param>
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303 <param name="centroids_s" type="text" value="2"
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304 label="The sparsity thresholding parameter by which to shrink the t-statistics (s)"
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305 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)">
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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306 <expand macro="sanitizer_multiple_digits"/>
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307 </param>
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308 <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">
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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309 <option value="gaussian">gaussian</option>
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310 <option value="adaptive" selected="True">adaptive</option>
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311 </param>
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312 <param name="centroids_toplabels" type="integer" value="500"
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313 label="Number of toplabels (m/z) which should be written in tabular output"/>
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314 </when>
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315 </conditional>
4
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316 <param name="image_type" type="boolean" checked="True" truevalue="standard_image" falsevalue="lattice_image"
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317 label="Standard image" help="No: lattice function is used to display image"/>
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318 <param name="svg_pixelimage" type="boolean" label="Export first segmentation image as svg"/>
0
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319 <repeat name="colours" title="Colours for the plots" min="1" max="50">
2
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320 <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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321 <sanitizer>
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322 <valid initial="string.letters,string.digits">
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323 <add value="#" />
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324 </valid>
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325 </sanitizer>
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326 </param>
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327 </repeat>
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328 <param name="output_rdata" type="boolean" label="Results as .RData output"/>
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329 <param name="setseed" type="integer" value="1" label="set seed" help="Use same value to reproduce previous results"/>
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330 </inputs>
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331 <outputs>
2
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332 <data format="pdf" name="segmentationimages" from_work_dir="segmentationpdf.pdf" label = "${tool.name} on ${on_string}: results"/>
0
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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333 <data format="tabular" name="mzfeatures" label="${tool.name} on ${on_string}: features"/>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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334 <data format="tabular" name="pixeloutput" label="${tool.name} on ${on_string}: pixels"/>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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335 <data format="rdata" name="segmentation_rdata" label="${tool.name} on ${on_string}: results.RData">
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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336 <filter>output_rdata</filter>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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337 </data>
4
9f7d1ec01767 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
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diff changeset
338 <data format="svg" name="svg_output" from_work_dir="svg_pixel_output.svg" label="${tool.name} on ${on_string}: image.svg">
9f7d1ec01767 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
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339 <filter>svg_pixelimage</filter>
9f7d1ec01767 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
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340 </data>
0
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
341 </outputs>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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342 <tests>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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343 <test>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
344 <expand macro="infile_imzml"/>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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345 <param name="segmentationtool" value="pca"/>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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346 <param name="image_type" value="lattice_image"/>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
347 <repeat name="colours">
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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348 <param name="feature_color" value="#ff00ff"/>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
349 </repeat>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
350 <repeat name="colours">
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
351 <param name="feature_color" value="#0000FF"/>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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352 </repeat>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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353 <output name="segmentationimages" file="pca_imzml.pdf" compare="sim_size"/>
2
034885df9b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
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354 <output name="mzfeatures">
034885df9b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
355 <assert_contents>
034885df9b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
356 <has_text text="300.17" />
034885df9b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
357 <has_text text="-4.234458e-04" />
034885df9b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
358 <has_text text="3.878545e-10" />
034885df9b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
359 <has_n_columns n="3" />
034885df9b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
360 </assert_contents>
034885df9b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
361 </output>
0
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
362 <output name="pixeloutput" file="scores_pca.tabular"/>
e56a955cd1c0 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>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
364 <test>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
365 <expand macro="infile_analyze75"/>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
366 <param name="segmentationtool" value="kmeans"/>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
367 <param name="kmeans_r" value="1:3"/>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
368 <param name="kmeans_k" value="2,3"/>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
369 <param name="kmeans_toplabels" value="20"/>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
370 <repeat name="colours">
e56a955cd1c0 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="#ff00ff"/>
e56a955cd1c0 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>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
373 <repeat name="colours">
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
374 <param name="feature_color" value="#0000FF"/>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
375 </repeat>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
376 <repeat name="colours">
e56a955cd1c0 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="#00C957"/>
e56a955cd1c0 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>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
379 <param name="output_rdata" value="True"/>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
380 <output name="segmentationimages" file="kmeans_analyze.pdf" compare="sim_size"/>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
381 <output name="mzfeatures" file="toplabels_skm.tabular"/>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
382 <output name="pixeloutput" file="cluster_skm.tabular"/>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
383 <output name="segmentation_rdata" file="cluster_skm.RData" compare="sim_size"/>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
384 </test>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
385 <test>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
386 <param name="infile" value="preprocessed.RData" ftype="rdata"/>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
387 <param name="segmentationtool" value="centroids"/>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
388 <param name="centroids_r" value="1,2"/>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
389 <param name="centroids_k" value="3"/>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
390 <param name="centroids_toplabels" value="50"/>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
391 <repeat name="colours">
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
392 <param name="feature_color" value="#0000FF"/>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
393 </repeat>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
394 <repeat name="colours">
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
395 <param name="feature_color" value="#00C957"/>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
396 </repeat>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
397 <repeat name="colours">
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
398 <param name="feature_color" value="#B0171F"/>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
399 </repeat>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
400 <repeat name="colours">
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
401 <param name="feature_color" value="#FFD700"/>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
402 </repeat>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
403 <repeat name="colours">
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
404 <param name="feature_color" value="#848484"/>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
405 </repeat>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
406 <output name="segmentationimages" file="centroids_rdata.pdf" compare="sim_size"/>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
407 <output name="mzfeatures" file="toplabels_ssc.tabular"/>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
408 <output name="pixeloutput" file="classes_ssc.tabular"/>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
409 </test>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
410 </tests>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
411 <help>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
412 <![CDATA[
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
413
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
414 @CARDINAL_DESCRIPTION@
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
415
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
416 -----
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
417
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
418 This tool provides three different Cardinal functions for unsupervised clustering/spatial segmentation of mass spectrometry imaging data.
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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419
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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420 @MSIDATA_INPUT_DESCRIPTION@
4
9f7d1ec01767 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
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421 - NA intensities are not allowed
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422 - duplicated coordinates will be removed
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423
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424
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425 **Options**
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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426
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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427 - PCA: principal component analysis
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9f7d1ec01767 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
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428 - k-means: spatially-aware k-means clustering (adopted from `Alexandrov and Kobarg <https://doi.org/10.1093/bioinformatics/btr246>`_)
9f7d1ec01767 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
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429 - 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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e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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430
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431 **Output**
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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432
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433 - Pdf with the heatmaps and plots for the segmentation
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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434 - Tabular file with information on m/z and pixels: loadings/scores (PCA), toplabels/clusters (k-means), toplabels/classes (spatial shrunken centroids)
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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435 - 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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436 - Optional: svg file with the first segmentation image
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437
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438 ]]>
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439 </help>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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440 <expand macro="citations"/>
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441 </tool>