Mercurial > repos > galaxyp > cardinal_segmentations

annotate segmentation.xml @ 13:199ae8af4d0d draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c
author galaxyp
date Thu, 04 Jul 2024 13:22:00 +0000
parents 46d53f24c81c
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1 <tool id="cardinal_segmentations" name="MSI segmentation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
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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 <command detect_errors="exit_code">
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8 <![CDATA[
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10 @INPUT_LINKING@
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11 cat '${MSI_segmentation}' &&
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12 Rscript '${MSI_segmentation}'
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14 ]]>
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15 </command>
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16 <configfiles>
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17 <configfile name="MSI_segmentation"><![CDATA[
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19 ################################# load libraries and read file #################
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21 library(Cardinal)
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22 library(gridExtra)
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23 library(ggplot2)
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24 library(scales)
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5e73ae48d674 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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26 @READING_MSIDATA@
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28 msidata = as(msidata, "MSImagingExperiment")
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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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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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53 if (npeaks > 0 && NAcount==0)
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54 {
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56 ######################## II) segmentation tools #############################
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57 #############################################################################
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59 #if str( $segm_cond.segmentationtool ) == 'kmeans':
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60 number_colors = max(c($segm_cond.kmeans_k))
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62 #elif str( $segm_cond.segmentationtool ) == 'centroids':
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63 number_colors = max(c($segm_cond.centroids_k))
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65 #end if
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67 #if str($colour_conditional.colour_type) == "manual_colour"
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68 #set $color_string = ','.join(['"%s"' % $color.annotation_color for $color in $colour_conditional.colours])
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69 colourvector = c($color_string)
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71 #elif str($colour_conditional.colour_type) == "colourpalette"
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72 number_levels = (number_colors)
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73 colourvector = noquote($colour_conditional.palettes)(number_levels)
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75 #end if
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76
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78 ## set seed to make analysis reproducible
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79 set.seed($setseed)
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80
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81 #if str( $segm_cond.segmentationtool ) == 'kmeans':
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82 print('kmeans')
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83 ##k-means
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84 skm = spatialKMeans(msidata, r=c($segm_cond.kmeans_r), k=c($segm_cond.kmeans_k), method="gaussian")
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85
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86 ## remove msidata to clean up RAM space
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87 rm(msidata)
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88 gc()
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89
13
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90 k_value = c($segm_cond.kmeans_k)
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91 r_value = c($segm_cond.kmeans_r)
0
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92
13
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93 for (k in k_value) {
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94 for (r in r_value) {
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95 print(image(skm, key=TRUE, model = list(k = k, r = r),
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96 main = paste("K-means clustering (r =", r, ", k =", k, ")"),
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97 strip = FALSE, col = colourvector, layout = c(1, 1), ylim = c(maximumy+2, minimumy-2)))
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98
13
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99 print(plot(skm, model = list(k = k, r = r), key = TRUE,
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100 main = paste("K-means plot (r =", r, ", k =", k, ")"),
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101 strip = FALSE, col = colourvector, layout = c(1, 1)))
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102 }
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103 }
0
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104
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105 skm_clusters = data.frame(matrix(NA, nrow = pixelcount, ncol = 0))
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106 for (iteration in 1:length(skm@resultData)){
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107 skm_cluster = ((skm@resultData)[[iteration]]\$cluster)
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108 skm_clusters = cbind(skm_clusters, skm_cluster) }
0
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109
13
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110 skm.coordinates = coord(skm)
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111 x_coords = skm.coordinates@listData[["x"]]
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112 y_coords = skm.coordinates@listData[["y"]]
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113 pixel_names = paste0("xy_", x_coords, "_", y_coords)
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114
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115 skm_clusters2 = data.frame(pixel_names, x_coords, y_coords, skm_clusters)
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116 r_values = skm@modelData@listData[["r"]]
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117 k_values = skm@modelData@listData[["k"]]
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118 new_names = paste0("r=", r_values, ", k=", k_values)
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119 colnames(skm_clusters2) = c("pixel names", "x", "y", new_names)
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120
7
5e73ae48d674 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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121 skm_toplabels = topFeatures(skm, n=$segm_cond.kmeans_toplabels)
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122
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123 write.table(skm_toplabels, file="$mzfeatures", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
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124 write.table(skm_clusters2, file="$pixeloutput", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
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125
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126 ## optional output as .RData
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127 #if $output_rdata:
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128
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129 ## save as (.RData)
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130 save(skm, file="$segmentation_rdata")
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131
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132 #end if
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133
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134 #elif str( $segm_cond.segmentationtool ) == 'centroids':
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135 print('centroids')
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136 ##centroids
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137
13
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138 ssc = spatialShrunkenCentroids(msidata, r=c($segm_cond.centroids_r), k=c($segm_cond.centroids_k), s=c($segm_cond.centroids_s), method="gaussian")
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139
2
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140 ## remove msidata to clean up RAM space
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141 rm(msidata)
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142 gc()
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143
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144 ## new plots and summary table
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145
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146 summary_df = summary(ssc)
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147 summary_df = as.data.frame(summary_df@listData)
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148 colnames(summary_df) = c("r", "initial_k", "s", "k", "features_per_k")
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149
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150 opar <- par()
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151 par(opar)
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152 plot(0,type='n',axes=FALSE,ann=FALSE)
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153 title(main="\n Summary for the different parameters\n", adj=0.5)
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154 ## 20 rows fits in one page:
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155 if (nrow(summary_df)<=20){
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156 grid.table(summary_df, rows= NULL)
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157 }else{
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158 grid.table(summary_df[1:20,], rows= NULL)
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159 mincount = 21
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160 maxcount = 40
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161 for (count20 in 1:(ceiling(nrow(summary_df)/20)-1)){
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162 plot(0,type='n',axes=FALSE,ann=FALSE)
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163 if (maxcount <= nrow(summary_df)){
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164 grid.table(summary_df[mincount:maxcount,], rows= NULL)
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165 mincount = mincount+20
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166 maxcount = maxcount+20
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167 }else{### stop last page with last sample otherwise NA in table
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168 grid.table(summary_df[mincount:nrow(summary_df),], rows= NULL)}
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169 }
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170 }
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171
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172 ## plot
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173 summary_df\$r <- factor(summary_df\$r)
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174 summary_df\$initial_k <- factor(summary_df\$initial_k)
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175
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176 cluster_plot = ggplot(summary_df, aes(x = s, y = k, color = initial_k)) +
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177 geom_point(size = 3) + ### Add points
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178 geom_line() +
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179 theme_bw() +
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180 facet_wrap(~ paste("r =", r)) +
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181 labs(title = "Number of segments", y = "predicted number of k", x = "shrinkage parameter (s)")
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182
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183 print(cluster_plot)
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184
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185 s_value = c($segm_cond.centroids_s)
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186 k_value = c($segm_cond.centroids_k)
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187 r_value = c($segm_cond.centroids_r)
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188
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189 to_remove = subset(summary_df, features_per_k == 0)
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190 s_to_remove = unique(c(to_remove\$s))
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191 s_value = s_value[!s_value %in% s_to_remove]
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192
13
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193 for (s in s_value) {
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194 for (k in k_value) {
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195 for (r in r_value) {
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196 print(image(ssc, model = list(s = s, k = k, r = r), key = TRUE, values = "class",
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197 main = paste("Spatial shrunken centroids (s =", s, ", k =", k, ", r =", r, ")"),
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198 strip = FALSE, col = colourvector, layout = c(1, 1), ylim = c(maximumy+2, minimumy-2)))
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199
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200 print(image(ssc, model = list(s = s, k = k, r = r), key = TRUE, values = "probability",
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201 main = paste("Class Probability (s =", s, ", k =", k, ", r =", r, ")"),
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202 strip = FALSE, col = colourvector, layout = c(1, 1), ylim = c(maximumy+2, minimumy-2)))
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203
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204 print(plot(ssc, model = list(s = s, k = k, r = r), key = TRUE,
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205 main = paste("Spatial shrunken centroids features (s =", s, ", k =", k, ", r =", r, ")"),
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206 col = colourvector, strip = TRUE, layout = c(1, 1)))
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207
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208 print(plot(ssc, model = list(s = s, k = k, r = r), values = "statistic", key = TRUE,
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209 layout = c(1, 1),
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210 main = paste("t-statistics (s =", s, ", k =", k, ", r =", r, ")"),
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211 col = colourvector))
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212 }
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213 }
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214 }
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215
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216
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217 new_s_value = s_to_remove
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218
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219 for (s in new_s_value) {
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220 for (k in k_value) {
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221 for (r in r_value) {
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222 print(image(ssc, model = list(s = s, k = k, r = r), key = TRUE, values = "class",
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223 main = paste("Spatial shrunken centroids (s =", s, ", k =", k, ", r =", r, ")"),
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224 strip = FALSE, col = colourvector, layout = c(1, 1), ylim = c(maximumy+2, minimumy-2)))
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225
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226 print(image(ssc, model = list(s = s, k = k, r = r), key = TRUE, values = "probability",
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227 main = paste("Class Probability (s =", s, ", k =", k, ", r =", r, ")"),
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228 strip = FALSE, col = colourvector, layout = c(1, 1), ylim = c(maximumy+2, minimumy-2)))
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229
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230 print(plot(ssc, model = list(s = s, k = k, r = r), key = TRUE,
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231 main = paste("Spatial shrunken centroids features (s =", s, ", k =", k, ", r =", r, ")"),
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232 col = colourvector, strip = TRUE, layout = c(1, 1)))
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233
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234 plot(0, 0, type = "n", xlab = "", ylab = "", xlim = c(0, 10), ylim = c(0, 10), xaxt = "n", yaxt = "n")
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235 ## Add the text to the plot
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236 text(5, 5, "t-statistics plot can not be drawn.\nS (shrinkage parameter) is too small to result\n in meaningful segmentation.",
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237 cex = 1.5, adj = c(0.5, 0.5))
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238
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239 }
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240 }
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241 }
0
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242
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243 ssc_classes = data.frame(matrix(NA, nrow = pixelcount, ncol = 0))
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244 for (iteration in 1:length(ssc@resultData@listData)){
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245 ssc_class = ((ssc@resultData@listData)[[iteration]]\$class)
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246 ssc_classes = cbind(ssc_classes, ssc_class) }
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247
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248 ## coordinates and topFeatures of results
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249 s_values = ssc@modelData@listData[["s"]]
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250 r_values = ssc@modelData@listData[["r"]]
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251 k_values = ssc@modelData@listData[["k"]]
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252 new_names = paste0("r=", r_values, ", s=", s_values, ", k=", k_values)
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253
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254 ssc.coordinates = coord(ssc)
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255 x_coords = ssc.coordinates@listData[["x"]]
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256 y_coords = ssc.coordinates@listData[["y"]]
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257 pixel_names = paste0("xy_", x_coords, "_", y_coords)
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258
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259 ssc_classes2 = data.frame(pixel_names, x_coords, y_coords, ssc_classes)
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260 colnames(ssc_classes2) = c("pixel names", "x", "y", new_names)
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261
7
5e73ae48d674 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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262 ssc_toplabels = topFeatures(ssc, n=$segm_cond.centroids_toplabels)
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263
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264 write.table(ssc_toplabels, file="$mzfeatures", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
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265 write.table(ssc_classes2, file="$pixeloutput", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
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266
13
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267
0
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268 ## optional output as .RData
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269 #if $output_rdata:
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270
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271 ## save as (.RData)
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272 save(ssc, file="$segmentation_rdata")
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273
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274 #end if
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275
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276 #end if
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277
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278 dev.off()
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279
4
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280 ## optional svg output with original coordinates
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281 #if $svg_pixelimage:
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282 print("svg image")
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283 ## reverse y axis for svg output = correct order and nice svg image
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284
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285 svg(file="svg_pixel_output.svg", width=maximumx, height=maximumy)
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286 par(mar=c(0,0,0,0))
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287 #if str( $segm_cond.segmentationtool ) == 'pca':
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288 coord(pca_result)\$y <- max(coord(pca_result)\$y) - coord(pca_result)\$y + 1
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289 image(pca_result, strip = FALSE, colorkey=FALSE, axes=FALSE, xlab=NA, ylab=NA, col=colourvector)
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290 #elif str( $segm_cond.segmentationtool ) == 'kmeans':
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291 coord(skm)\$y <- max(coord(skm)\$y) - coord(skm)\$y + 1
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292 image(skm, key=FALSE, strip=FALSE, col= colourvector)
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293 #elif str( $segm_cond.segmentationtool ) == 'centroids':
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294 coord(ssc)\$y <- max(coord(ssc)\$y) - coord(ssc)\$y + 1
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295 image(ssc, key=FALSE, strip = FALSE, col= colourvector)
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296 #end if
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297 dev.off()
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298 #end if
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299
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300
0
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301 }else{
13
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302 plot.new()
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303 text(0.5, 0.5, "Inputfile has no intensities > 0 \n or contains NA values.", cex = 1.5)
0
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304 print("Inputfile has no intensities > 0")
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305 dev.off()
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306 }
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307
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308 ]]></configfile>
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309 </configfiles>
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310 <inputs>
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311 <expand macro="reading_msidata"/>
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312 <conditional name="segm_cond">
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313 <param name="segmentationtool" type="select" label="Select the tool for spatial clustering">
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314 <option value="kmeans">k-means</option>
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315 <option value="centroids">spatial shrunken centroids</option>
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316 </param>
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317 <when value="kmeans">
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318 <param name="kmeans_r" type="text" value="2"
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319 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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320 <expand macro="sanitizer_multiple_digits"/>
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321 </param>
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322 <param name="kmeans_k" type="text" value="3"
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323 label="The number of clusters (k)" help="Multiple values are allowed (e.g. 1,2,3 or 2:5)">
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324 <expand macro="sanitizer_multiple_digits"/>
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325 </param>
13
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326 <param name="kmeans_toplabels" type="integer" value="500"
0
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327 label="Number of toplabels (m/z) which should be written in tabular output"/>
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328 </when>
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329
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330 <when value="centroids">
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331 <param name="centroids_r" type="text" value="2"
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332 label="The spatial neighborhood radius of nearby pixels to consider (r)" help="Multiple values are allowed (e.g. 1,2,3 or 2:5)">
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333 <expand macro="sanitizer_multiple_digits"/>
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334 </param>
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335 <param name="centroids_k" type="text" value="5"
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336 label="The initial number of clusters (k)" help="Multiple values are allowed (e.g. 1,2,3 or 2:5)">
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337 <expand macro="sanitizer_multiple_digits"/>
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338 </param>
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339 <param name="centroids_s" type="text" value="2"
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340 label="The sparsity thresholding parameter by which to shrink the t-statistics (s)"
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341 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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342 <expand macro="sanitizer_multiple_digits"/>
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343 </param>
13
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344
0
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345 <param name="centroids_toplabels" type="integer" value="500"
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346 label="Number of toplabels (m/z) which should be written in tabular output"/>
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347 </when>
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348 </conditional>
4
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349 <param name="svg_pixelimage" type="boolean" label="Export first segmentation image as svg"/>
13
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350
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351 <conditional name="colour_conditional">
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352 <param name="colour_type" type="select" label="Choose a colour scheme">
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353 <option value="colourpalette" selected="True" >Colour palette</option>
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354 <option value="manual_colour">Manual selection</option>
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355 </param>
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356 <when value="manual_colour">
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357 <repeat name="colours" title="Colours for the plots" min="1" max="50">
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358 <param name="annotation_color" type="color" label="Colours" value="#ff00ff" help="Numbers of colours should be the same as number of components">
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359 <sanitizer>
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360 <valid initial="string.letters,string.digits">
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361 <add value="#" />
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362 </valid>
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363 </sanitizer>
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364 </param>
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365 </repeat>
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366 </when>
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367 <when value="colourpalette">
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368 <param name="palettes" type="select" display="radio" label="Select a colourpalette">
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369 <option value="hue_pal()" selected="True">hue</option>
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370 <option value="rainbow">rainbow</option>
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371 <option value="heat.colors">heat colors</option>
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372 <option value="terrain.colors">terrain colors</option>
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373 <option value="topo.colors">topo colors</option>
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374 <option value="cm.colors">cm colors</option>
0
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375 </param>
13
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376 </when>
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377 </conditional>
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378 <param name="output_rdata" type="boolean" label="Results as .RData output"/>
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379 <param name="setseed" type="integer" value="1" label="set seed" help="Use same value to reproduce previous results"/>
0
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380 </inputs>
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381 <outputs>
2
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382 <data format="pdf" name="segmentationimages" from_work_dir="segmentationpdf.pdf" label = "${tool.name} on ${on_string}: results"/>
0
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383 <data format="tabular" name="mzfeatures" label="${tool.name} on ${on_string}: features"/>
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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384 <data format="tabular" name="pixeloutput" label="${tool.name} on ${on_string}: pixels"/>
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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385 <data format="rdata" name="segmentation_rdata" label="${tool.name} on ${on_string}: results.RData">
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386 <filter>output_rdata</filter>
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387 </data>
4
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388 <data format="svg" name="svg_output" from_work_dir="svg_pixel_output.svg" label="${tool.name} on ${on_string}: image.svg">
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389 <filter>svg_pixelimage</filter>
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390 </data>
0
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391 </outputs>
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392 <tests>
13
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393 <test expect_num_outputs="4">
7
5e73ae48d674 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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394 <expand macro="infile_imzml"/>
0
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395 <param name="segmentationtool" value="kmeans"/>
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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396 <param name="kmeans_r" value="1:3"/>
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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397 <param name="kmeans_k" value="2,3"/>
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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398 <param name="kmeans_toplabels" value="20"/>
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399 <repeat name="colours">
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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400 <param name="feature_color" value="#ff00ff"/>
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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401 </repeat>
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402 <repeat name="colours">
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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403 <param name="feature_color" value="#0000FF"/>
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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404 </repeat>
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405 <repeat name="colours">
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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406 <param name="feature_color" value="#00C957"/>
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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407 </repeat>
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408 <param name="output_rdata" value="True"/>
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409 <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
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410 <output name="mzfeatures" file="toplabels_skm.tabular"/>
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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411 <output name="pixeloutput" file="cluster_skm.tabular"/>
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412 <output name="segmentation_rdata" file="cluster_skm.RData" compare="sim_size"/>
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413 </test>
13
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414 <test expect_num_outputs="3">
0
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415 <param name="infile" value="preprocessed.RData" ftype="rdata"/>
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416 <param name="segmentationtool" value="centroids"/>
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417 <param name="centroids_r" value="1,2"/>
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418 <param name="centroids_k" value="3"/>
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419 <param name="centroids_toplabels" value="50"/>
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420 <repeat name="colours">
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421 <param name="feature_color" value="#0000FF"/>
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422 </repeat>
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423 <repeat name="colours">
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424 <param name="feature_color" value="#00C957"/>
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425 </repeat>
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426 <repeat name="colours">
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427 <param name="feature_color" value="#B0171F"/>
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428 </repeat>
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
429 <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
430 <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
431 <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
parents:
diff changeset
432 </test>
13
199ae8af4d0d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c
galaxyp
parents: 10
diff changeset
433 <test expect_num_outputs="3">
10
46d53f24c81c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f"
galaxyp
parents: 8
diff changeset
434 <expand macro="processed_infile_imzml"/>
7
5e73ae48d674 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
435 <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
436 <param name="processed_file" value="processed"/>
10
46d53f24c81c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f"
galaxyp
parents: 8
diff changeset
437 <param name="accuracy" value="200"/>
46d53f24c81c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f"
galaxyp
parents: 8
diff changeset
438 <param name="units" value="ppm"/>
7
5e73ae48d674 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
439 </conditional>
5e73ae48d674 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
440 <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
441 <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
442 <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
443 <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
444 <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
445 <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
446 <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
447 </repeat>
5e73ae48d674 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
448 <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
449 <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
450 </repeat>
5e73ae48d674 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
451 <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
452 <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
453 </repeat>
13
199ae8af4d0d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c
galaxyp
parents: 10
diff changeset
454 <output name="segmentationimages" ftype="pdf">
199ae8af4d0d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c
galaxyp
parents: 10
diff changeset
455 <assert_contents>
199ae8af4d0d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c
galaxyp
parents: 10
diff changeset
456 <has_size value="1206464" delta="100"/>
199ae8af4d0d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c
galaxyp
parents: 10
diff changeset
457 </assert_contents>
199ae8af4d0d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c
galaxyp
parents: 10
diff changeset
458 </output>
7
5e73ae48d674 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
459 <output name="pixeloutput" file="classes_proc.tabular"/>
8
64d0651a9f76 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
galaxyp
parents: 7
diff changeset
460 <output name="mzfeatures">
64d0651a9f76 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
galaxyp
parents: 7
diff changeset
461 <assert_contents>
13
199ae8af4d0d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c
galaxyp
parents: 10
diff changeset
462 <has_text text="177.926436700994"/>
199ae8af4d0d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c
galaxyp
parents: 10
diff changeset
463 <has_text text="192.976841249583"/>
199ae8af4d0d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c
galaxyp
parents: 10
diff changeset
464 <has_text text="0.818218808031712"/>
199ae8af4d0d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c
galaxyp
parents: 10
diff changeset
465 <has_text text="0.469980133537009"/>
199ae8af4d0d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c
galaxyp
parents: 10
diff changeset
466 <has_n_columns n="7"/>
199ae8af4d0d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c
galaxyp
parents: 10
diff changeset
467 <has_n_lines n="101"/>
8
64d0651a9f76 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
galaxyp
parents: 7
diff changeset
468 </assert_contents>
64d0651a9f76 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
galaxyp
parents: 7
diff changeset
469 </output>
7
5e73ae48d674 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 4
diff changeset
470 </test>
0
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
471 </tests>
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
472 <help>
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
473 <![CDATA[
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
474
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
475 @CARDINAL_DESCRIPTION@
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
476
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
477 -----
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
478
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
479 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
480
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
481 @MSIDATA_INPUT_DESCRIPTION@
4
43049941e1ab planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
482 - NA intensities are not allowed
43049941e1ab planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
483 - duplicated coordinates will be removed
43049941e1ab planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
484
0
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
485
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
486 **Options**
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
487
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
488 - PCA: principal component analysis
4
43049941e1ab planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
489 - 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
galaxyp
parents: 3
diff changeset
490 - 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>`_)
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
491
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
492 **Output**
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
493
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
494 - 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
galaxyp
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diff changeset
495 - 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
galaxyp
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496 - Optional .RData file which contains the segmentation results and can be used for further exploration in R using the Cardinal package
4
43049941e1ab planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
497 - Optional: svg file with the first segmentation image
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
498
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
499 ]]>
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
500 </help>
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
501 <expand macro="citations"/>
be3e3cd14abc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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502 </tool>