Mercurial > repos > galaxyp > cardinal_classification

annotate classification.xml @ 1:33579f05d1f8 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
author galaxyp
date Thu, 25 Oct 2018 07:18:58 -0400
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1 <tool id="cardinal_classification" name="MSI classification" version="@VERSION@.1">
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2 <description>spatial classification of mass spectrometry imaging data</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="3.0">r-ggplot2</requirement>
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8 <requirement type="package" version="2.3">r-gridextra</requirement>
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9 <requirement type="package" version="0.20_35">r-lattice</requirement>
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10 </expand>
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11 <command detect_errors="exit_code">
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12 <![CDATA[
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14 @INPUT_LINKING@
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15 cat '${MSI_segmentation}' &&
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16 Rscript '${MSI_segmentation}'
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18 ]]>
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19 </command>
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20 <configfiles>
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21 <configfile name="MSI_segmentation"><![CDATA[
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24 ################################# load libraries and read file #########################
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26 library(Cardinal)
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27 library(gridExtra)
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28 library(lattice)
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29 library(ggplot2)
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31 @READING_MSIDATA@
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33 ## create full matrix to make processed imzML files compatible with classification
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34 iData(msidata) <- iData(msidata)[]
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36 @DATA_PROPERTIES@
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37
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38 ######################################## PDF ###################################
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39 ################################################################################
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40 ################################################################################
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42 Title = "Prediction"
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44 #if str( $type_cond.type_method) == "training":
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46 Title = "$type_cond.method_cond.class_method"
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47 #end if
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49 pdf("classificationpdf.pdf", fonts = "Times", pointsize = 12)
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50 plot(0,type='n',axes=FALSE,ann=FALSE)
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53 title(main=paste0(Title," for file: \n\n", "$infile.display_name"))
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56 ##################### I) numbers and control plots #############################
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57 ###############################################################################
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59 ## table with values
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60 grid.table(property_df, rows= NULL)
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63 if (npeaks > 0 && sum(is.na(spectra(msidata)))==0){
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65 opar <- par()
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66
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67 ######################## II) Training #############################
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68 #############################################################################
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69 #if str( $type_cond.type_method) == "training":
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70 print("training")
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73 ## load y response (will be needed in every training scenario)
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75 y_tabular = read.delim("$type_cond.annotation_file", header = $type_cond.tabular_header, stringsAsFactors = FALSE)
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76
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77 #if str($type_cond.column_fold) == "None":
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78 y_input = y_tabular[,c($type_cond.column_x, $type_cond.column_y, $type_cond.column_response)]
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79 #else
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80 y_input = y_tabular[,c($type_cond.column_x, $type_cond.column_y, $type_cond.column_response, $type_cond.column_fold)]
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81 #end if
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82
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83 colnames(y_input)[1:2] = c("x", "y")
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84 ## merge with coordinate information of msidata
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85 msidata_coordinates = cbind(coord(msidata)[,1:2], c(1:ncol(msidata)))
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86 colnames(msidata_coordinates)[3] = "pixel_index"
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87 merged_response = merge(msidata_coordinates, y_input, by=c("x", "y"), all.x=TRUE)
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88 merged_response[is.na(merged_response)] = "NA"
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89 merged_response = merged_response[order(merged_response\$pixel_index),]
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90 y_vector = as.factor(merged_response[,4])
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91
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92 ## plot of y vector
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93
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94 position_df = cbind(coord(msidata)[,1:2], y_vector)
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95 y_plot = ggplot(position_df, aes(x=x, y=y, fill=y_vector))+
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96 geom_tile() +
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97 coord_fixed()+
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98 ggtitle("Distribution of the response variable y")+
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99 theme_bw()+
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100 theme(text=element_text(family="ArialMT", face="bold", size=15))+
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101 theme(legend.position="bottom",legend.direction="vertical")+
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102 guides(fill=guide_legend(ncol=4,byrow=TRUE))
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103 coord_labels = aggregate(cbind(x,y)~y_vector, data=position_df, mean, na.rm=TRUE, na.action="na.pass")
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104 coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$y_vector)
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105 print(y_plot)
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106
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107
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108 ## plot of folds
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109
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110 #if str($type_cond.column_fold) != "None":
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111 fold_vector = as.factor(merged_response[,5])
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112
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113
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114 position_df = cbind(coord(msidata)[,1:2], fold_vector)
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115 fold_plot = ggplot(position_df, aes(x=x, y=y, fill=fold_vector))+
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116 geom_tile() +
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117 coord_fixed()+
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118 ggtitle("Distribution of the fold variable")+
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119 theme_bw()+
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120 theme(text=element_text(family="ArialMT", face="bold", size=15))+
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121 theme(legend.position="bottom",legend.direction="vertical")+
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122 guides(fill=guide_legend(ncol=4,byrow=TRUE))
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123 coord_labels = aggregate(cbind(x,y)~fold_vector, data=position_df, mean, na.rm=TRUE, na.action="na.pass")
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124 coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$fold_vector)
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125 print(fold_plot)
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126
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127 #end if
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128
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129 ######################## PLS #############################
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130 #if str( $type_cond.method_cond.class_method) == "PLS":
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131 print("PLS")
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132
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133 ######################## PLS - CV #############################
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134 #if str( $type_cond.method_cond.analysis_cond.PLS_method) == "cvapply":
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135 print("PLS cv")
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136
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137 ## set variables for components and number of response groups
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138 components = c($type_cond.method_cond.analysis_cond.plscv_comp)
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139 number_groups = length(levels(y_vector))
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140
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141 ## PLS-cvApply:
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142 msidata.cv.pls <- cvApply(msidata, .y = y_vector, .fold = fold_vector, .fun = "PLS", ncomp = components)
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143
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144 ## create table with summary
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145 count = 1
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146 summary_plscv = list()
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147 accuracy_vector = numeric()
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148 for (iteration in components){
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149 summary_iteration = summary(msidata.cv.pls)\$accuracy[[paste0("ncomp = ", iteration)]]
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150 ## change class of numbers into numeric to round and calculate mean
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151 summary_iteration2 = round(as.numeric(summary_iteration), digits=2)
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152 summary_matrix = matrix(summary_iteration2, nrow=4, ncol=number_groups)
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153 accuracy_vector[count] = mean(summary_matrix[1,]) ## vector with accuracies to find later maximum for plot
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154 summary_iteration3 = cbind(rownames(summary_iteration), summary_matrix) ## include rownames in table
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155 summary_iteration4 = t(summary_iteration3)
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156 summary_iteration5 = cbind(c(paste0("ncomp = ", iteration), colnames(summary_iteration)), summary_iteration4)
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157 summary_plscv[[count]] = summary_iteration5
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158 count = count+1} ## create list with summary table for each component
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159 summary_plscv = do.call(rbind, summary_plscv)
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160 summary_df = as.data.frame(summary_plscv)
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161 colnames(summary_df) = NULL
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162
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163 ## plots
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164 ## plot to find ncomp with highest accuracy
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165 plot(components, accuracy_vector, ylab = "mean accuracy",type="o", main="Mean accuracy of PLS classification")
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166 ncomp_max = components[which.max(accuracy_vector)] ## find ncomp with max. accuracy
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167 ## one image for each sample/fold, 4 images per page
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168 minimumy = min(coord(msidata.cv.pls)[,2])
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169 maximumy = max(coord(msidata.cv.pls)[,2])
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170 image(msidata.cv.pls, model = list(ncomp = ncomp_max),ylim= c(maximumy+0.2*maximumy,minimumy-0.2*minimumy),layout = c(2, 2))
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171
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172 ## print table with summary in pdf
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173 par(opar)
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174 plot(0,type='n',axes=FALSE,ann=FALSE)
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175 title(main="Summary for the different components\n", adj=0.5)
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176 ## 20 rows fits in one page:
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177 if (nrow(summary_df)<=20){
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178 grid.table(summary_df, rows= NULL)
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179 }else{
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180 grid.table(summary_df[1:20,], rows= NULL)
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181 mincount = 21
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182 maxcount = 40
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183 for (count20 in 1:(ceiling(nrow(summary_df)/20)-1)){
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184 plot(0,type='n',axes=FALSE,ann=FALSE)
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185 if (maxcount <= nrow(summary_df)){
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186 grid.table(summary_df[mincount:maxcount,], rows= NULL)
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187 mincount = mincount+20
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188 maxcount = maxcount+20
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189 }else{### stop last page with last sample otherwise NA in table
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190 grid.table(summary_df[mincount:nrow(summary_df),], rows= NULL)}
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191 }
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192 }
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193
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194 ## optional output as .RData
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195 #if $output_rdata:
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196 save(msidata.cv.pls, file="$classification_rdata")
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197 #end if
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198
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199
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200 ######################## PLS - analysis ###########################
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201 #elif str( $type_cond.method_cond.analysis_cond.PLS_method) == "PLS_analysis":
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202 print("PLS analysis")
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203
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204 ## set variables for components and number of response groups
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205 component = c($type_cond.method_cond.analysis_cond.pls_comp)
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206 number_groups = length(levels(y_vector))
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207
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208 ### pls analysis and coefficients plot
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209 msidata.pls <- PLS(msidata, y = y_vector, ncomp = component, scale=$type_cond.method_cond.analysis_cond.pls_scale)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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210 plot(msidata.pls, main="PLS coefficients per m/z")
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211
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212 ### summary table of PLS
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213 summary_table = summary(msidata.pls)\$accuracy[[paste0("ncomp = ",component)]]
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214 summary_table2 = round(as.numeric(summary_table), digits=2)
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215 summary_matrix = matrix(summary_table2, nrow=4, ncol=number_groups)
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216 summary_table3 = cbind(rownames(summary_table), summary_matrix) ## include rownames in table
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217 summary_table4 = t(summary_table3)
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218 summary_table5 = cbind(c(paste0("ncomp = ", component), colnames(summary_table)), summary_table4)
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219 plot(0,type='n',axes=FALSE,ann=FALSE)
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220 grid.table(summary_table5, rows= NULL)
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221
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222 ### image of the best m/z
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223 minimumy = min(coord(msidata)[,2])
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224 maximumy = max(coord(msidata)[,2])
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225 print(image(msidata, mz = topLabels(msidata.pls)[1,1], normalize.image = "linear", contrast.enhance = "histogram",ylim= c(maximumy+0.2*maximumy,minimumy-0.2*minimumy), smooth.image="gaussian", main="best m/z heatmap"))
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226
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227 ### m/z and pixel information output
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228 pls_classes = data.frame(msidata.pls\$classes[[1]])
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229 pixel_names = gsub(", y = ", "_", names(pixels(msidata)))
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230 pixel_names = gsub(" = ", "y_", pixel_names)
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231 x_coordinates = matrix(unlist(strsplit(pixel_names, "_")), ncol=3, byrow=TRUE)[,2]
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232 y_coordinates = matrix(unlist(strsplit(pixel_names, "_")), ncol=3, byrow=TRUE)[,3]
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233
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234 pls_classes2 = data.frame(pixel_names, x_coordinates, y_coordinates, pls_classes)
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235 colnames(pls_classes2) = c("pixel names", "x", "y","predicted condition")
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236 pls_toplabels = topLabels(msidata.pls, n=$type_cond.method_cond.analysis_cond.pls_toplabels)
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237 write.table(pls_toplabels, file="$mzfeatures", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
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238 write.table(pls_classes2, file="$pixeloutput", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
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239
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240 ## image with predicted classes
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241 prediction_df = cbind(coord(msidata.pls)[,1:2], pls_classes)
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242 colnames(prediction_df) = c("x", "y", "predicted_classes")
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243
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244 prediction_plot = ggplot(prediction_df, aes(x=x, y=y, fill=predicted_classes))+
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245 geom_tile() +
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246 coord_fixed()+
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247 ggtitle("Predicted condition for each pixel")+
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248 theme_bw()+
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249 theme(text=element_text(family="ArialMT", face="bold", size=15))+
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250 theme(legend.position="bottom",legend.direction="vertical")+
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251 guides(fill=guide_legend(ncol=4,byrow=TRUE))
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252 coord_labels = aggregate(cbind(x,y)~predicted_classes, data=prediction_df, mean, na.rm=TRUE, na.action="na.pass")
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253 coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$predicted_classes)
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254 print(prediction_plot)
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255
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256 ### optional output as .RData
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257 #if $output_rdata:
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258 save(msidata.pls, file="$classification_rdata")
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259 #end if
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260
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261 #end if
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262
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263 ######################## OPLS #############################
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264 #elif str( $type_cond.method_cond.class_method) == "OPLS":
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265 print("OPLS")
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266
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267 ######################## OPLS -CV #############################
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268 #if str( $type_cond.method_cond.opls_analysis_cond.opls_method) == "opls_cvapply":
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269 print("OPLS cv")
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270
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271 ## set variables for components and number of response groups
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272 components = c($type_cond.method_cond.opls_analysis_cond.opls_cvcomp)
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273 number_groups = length(levels(y_vector))
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274
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275 ## OPLS-cvApply:
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276 msidata.cv.opls <- cvApply(msidata, .y = y_vector, .fold = fold_vector, .fun = "OPLS", ncomp = components, keep.Xnew = $type_cond.method_cond.opls_analysis_cond.xnew_cv)
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277
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278 ## create table with summary
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279 count = 1
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280 summary_oplscv = list()
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281 accuracy_vector = numeric()
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282 for (iteration in components){
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283
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284 summary_iteration = summary(msidata.cv.opls)\$accuracy[[paste0("ncomp = ", iteration)]]
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285 ## change class of numbers into numeric to round and calculate mean
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286 summary_iteration2 = round(as.numeric(summary_iteration), digits=2)
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287 summary_matrix = matrix(summary_iteration2, nrow=4, ncol=number_groups)
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288 accuracy_vector[count] = mean(summary_matrix[1,]) ## vector with accuracies to find later maximum for plot
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289 summary_iteration3 = cbind(rownames(summary_iteration), summary_matrix) ## include rownames in table
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290 summary_iteration4 = t(summary_iteration3)
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291 summary_iteration5 = cbind(c(paste0("ncomp = ", iteration), colnames(summary_iteration)), summary_iteration4)
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292 summary_oplscv[[count]] = summary_iteration5
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293 count = count+1} ## create list with summary table for each component
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294 summary_oplscv = do.call(rbind, summary_oplscv)
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295 summary_df = as.data.frame(summary_oplscv)
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296 colnames(summary_df) = NULL
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297
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298 ## plots
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299 ## plot to find ncomp with highest accuracy
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300 plot(components, accuracy_vector, ylab = "mean accuracy", type="o", main="Mean accuracy of OPLS classification")
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301 ncomp_max = components[which.max(accuracy_vector)] ## find ncomp with max. accuracy
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302 ## one image for each sample/fold, 4 images per page
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303 minimumy = min(coord(msidata.cv.opls)[,2])
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304 maximumy = max(coord(msidata.cv.opls)[,2])
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305 image(msidata.cv.opls, model = list(ncomp = ncomp_max),ylim= c(maximumy+0.2*maximumy,minimumy-0.2*minimumy),layout = c(2, 2))
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306
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307 ## print table with summary in pdf
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308 par(opar)
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309 plot(0,type='n',axes=FALSE,ann=FALSE)
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310 title(main="Summary for the different components\n", adj=0.5)
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311 ## 20 rows fits in one page:
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312 if (nrow(summary_df)<=20){
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313 grid.table(summary_df, rows= NULL)
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314 }else{
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315 grid.table(summary_df[1:20,], rows= NULL)
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316 mincount = 21
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317 maxcount = 40
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318 for (count20 in 1:(ceiling(nrow(summary_df)/20)-1)){
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319 plot(0,type='n',axes=FALSE,ann=FALSE)
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320 if (maxcount <= nrow(summary_df)){
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321 grid.table(summary_df[mincount:maxcount,], rows= NULL)
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322 mincount = mincount+20
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323 maxcount = maxcount+20
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324 }else{### stop last page with last sample otherwise NA in table
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325 grid.table(summary_df[mincount:nrow(summary_df),], rows= NULL)}
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326 }
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327 }
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328
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329 ## optional output as .RData
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330 #if $output_rdata:
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331 save(msidata.cv.opls, file="$classification_rdata")
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332 #end if
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333
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334
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335 ######################## OPLS -analysis ###########################
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336 #elif str( $type_cond.method_cond.opls_analysis_cond.opls_method) == "opls_analysis":
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337 print("OPLS analysis")
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338
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339 ## set variables for components and number of response groups
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340 component = c($type_cond.method_cond.opls_analysis_cond.opls_comp)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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341 number_groups = length(levels(y_vector))
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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342
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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343
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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344 ### opls analysis and coefficients plot
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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345 msidata.opls <- PLS(msidata, y = y_vector, ncomp = component, scale=$type_cond.method_cond.opls_analysis_cond.opls_scale, keep.Xnew = $type_cond.method_cond.opls_analysis_cond.xnew)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
346 plot(msidata.opls, main="OPLS coefficients per m/z")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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347
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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348 ### summary table of OPLS
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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349 summary_table = summary(msidata.opls)\$accuracy[[paste0("ncomp = ",component)]]
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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350 summary_table2 = round(as.numeric(summary_table), digits=2)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
351 summary_matrix = matrix(summary_table2, nrow=4, ncol=number_groups)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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352 summary_table3 = cbind(rownames(summary_table), summary_matrix) ## include rownames in table
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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353 summary_table4 = t(summary_table3)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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354 summary_table5 = cbind(c(paste0("ncomp = ", component), colnames(summary_table)), summary_table4)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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355 plot(0,type='n',axes=FALSE,ann=FALSE)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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356 grid.table(summary_table5, rows= NULL)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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357
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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358 ### image of the best m/z
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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359 minimumy = min(coord(msidata)[,2])
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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360 maximumy = max(coord(msidata)[,2])
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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361 print(image(msidata, mz = topLabels(msidata.opls)[1,1], normalize.image = "linear", contrast.enhance = "histogram",smooth.image="gaussian", ylim= c(maximumy+0.2*maximumy,minimumy-0.2*minimumy), main="best m/z heatmap"))
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
362
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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363 ## m/z and pixel information output
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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364 opls_classes = data.frame(msidata.opls\$classes[[1]])
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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365 pixel_names = gsub(", y = ", "_", names(pixels(msidata)))
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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366 pixel_names = gsub(" = ", "y_", pixel_names)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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367 x_coordinates = matrix(unlist(strsplit(pixel_names, "_")), ncol=3, byrow=TRUE)[,2]
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
368 y_coordinates = matrix(unlist(strsplit(pixel_names, "_")), ncol=3, byrow=TRUE)[,3]
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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369 opls_classes2 = data.frame(pixel_names, x_coordinates, y_coordinates, opls_classes)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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370 colnames(opls_classes2) = c("pixel names", "x", "y","predicted condition")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
371
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
372 opls_toplabels = topLabels(msidata.opls, n=$type_cond.method_cond.opls_analysis_cond.opls_toplabels)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
373 write.table(opls_toplabels, file="$mzfeatures", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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374 write.table(opls_classes2, file="$pixeloutput", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
375
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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376 ## image with predicted classes
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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377 prediction_df = cbind(coord(msidata.opls)[,1:2], opls_classes)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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378 colnames(prediction_df) = c("x", "y", "predicted_classes")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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379
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
380 prediction_plot = ggplot(prediction_df, aes(x=x, y=y, fill=predicted_classes))+
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
381 geom_tile() +
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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382 coord_fixed()+
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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383 ggtitle("Predicted condition for each pixel")+
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
384 theme_bw()+
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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385 theme(text=element_text(family="ArialMT", face="bold", size=15))+
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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386 theme(legend.position="bottom",legend.direction="vertical")+
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
387 guides(fill=guide_legend(ncol=4,byrow=TRUE))
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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388 coord_labels = aggregate(cbind(x,y)~predicted_classes, data=prediction_df, mean, na.rm=TRUE, na.action="na.pass")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
389 coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$predicted_classes)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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390 print(prediction_plot)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
391
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
392 ## optional output as .RData
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
393 #if $output_rdata:
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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394 save(msidata.opls, file="$classification_rdata")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
395 #end if
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
396 #end if
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
397
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
398
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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399 ######################## SSC #############################
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
400 #elif str( $type_cond.method_cond.class_method) == "spatialShrunkenCentroids":
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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parents:
diff changeset
401 print("SSC")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
402
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
403 ######################## SSC - CV #############################
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
404 #if str( $type_cond.method_cond.ssc_analysis_cond.ssc_method) == "ssc_cvapply":
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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parents:
diff changeset
405 print("SSC cv")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
406
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
407 ## set variables for components and number of response groups
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
408 number_groups = length(levels(y_vector))
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
409
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
410 ## SSC-cvApply:
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
411 msidata.cv.ssc <- cvApply(msidata, .y = y_vector,.fold = fold_vector,.fun = "spatialShrunkenCentroids", r = c($type_cond.method_cond.ssc_r), s = c($type_cond.method_cond.ssc_s), method = "$type_cond.method_cond.ssc_kernel_method")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
412
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
413 ## create table with summary
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
414 count = 1
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
415 summary_ssccv = list()
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
416 accuracy_vector = numeric()
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
417 iteration_vector = character()
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
418 for (iteration in names(msidata.cv.ssc@resultData[[1]][,1])){
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
419
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
420 summary_iteration = summary(msidata.cv.ssc)\$accuracy[[iteration]]
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
421 ## change class of numbers into numeric to round and calculate mean
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
422 summary_iteration2 = round(as.numeric(summary_iteration), digits=2)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
423 summary_matrix = matrix(summary_iteration2, nrow=4, ncol=number_groups)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
424 accuracy_vector[count] = mean(summary_matrix[1,]) ## vector with accuracies to find later maximum for plot
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
425 summary_iteration3 = cbind(rownames(summary_iteration), summary_matrix) ## include rownames in table
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
426 summary_iteration4 = t(summary_iteration3)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
427 summary_iteration5 = cbind(c(iteration, colnames(summary_iteration)), summary_iteration4)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
428 summary_ssccv[[count]] = summary_iteration5
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
429 iteration_vector[count] = unlist(strsplit(iteration, "[,]"))[3]
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
430 count = count+1} ## create list with summary table for each component
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
431 summary_ssccv = do.call(rbind, summary_ssccv)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
432 summary_df = as.data.frame(summary_ssccv)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
433 colnames(summary_df) = NULL
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
434
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
435 ## plot to find parameters with highest accuracy
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
436 plot(c($type_cond.method_cond.ssc_s),accuracy_vector[!duplicated(iteration_vector)], type="o",ylab="Mean accuracy", xlab = "Shrinkage parameter (s)", main="Mean accuracy of SSC classification")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
437 best_params = names(msidata.cv.ssc@resultData[[1]][,1])[which.max(accuracy_vector)] ## find parameters with max. accuracy
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
438 r_value = as.numeric(substring(unlist(strsplit(best_params, ","))[1], 4))
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
439 s_value = as.numeric(substring(unlist(strsplit(best_params, ","))[3], 5)) ## remove space
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
440 minimumy = min(coord(msidata.cv.ssc)[,2])
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
441 maximumy = max(coord(msidata.cv.ssc)[,2])
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
442 image(msidata.cv.ssc, model = list( r = r_value, s = s_value ), ylim= c(maximumy+0.2*maximumy,minimumy-0.2*minimumy),layout=c(2,2))
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
443
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
444 ## print table with summary in pdf
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
445 par(opar)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
446 plot(0,type='n',axes=FALSE,ann=FALSE)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
447 title(main="Summary for the different parameters\n", adj=0.5)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
448 ## 20 rows fits in one page:
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
449 if (nrow(summary_df)<=20){
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
450 grid.table(summary_df, rows= NULL)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
451 }else{
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
452 grid.table(summary_df[1:20,], rows= NULL)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
453 mincount = 21
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
454 maxcount = 40
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
455 for (count20 in 1:(ceiling(nrow(summary_df)/20)-1)){
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
456 plot(0,type='n',axes=FALSE,ann=FALSE)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
457 if (maxcount <= nrow(summary_df)){
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
458 grid.table(summary_df[mincount:maxcount,], rows= NULL)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
459 mincount = mincount+20
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
460 maxcount = maxcount+20
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
461 }else{### stop last page with last sample otherwise NA in table
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
462 grid.table(summary_df[mincount:nrow(summary_df),], rows= NULL)}
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
463 }
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
464 }
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
465
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
466 ## optional output as .RData
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
467 #if $output_rdata:
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
468 save(msidata.cv.ssc, file="$classification_rdata")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
469 #end if
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
470
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
471 ######################## SSC -analysis ###########################
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
472 #elif str( $type_cond.method_cond.ssc_analysis_cond.ssc_method) == "ssc_analysis":
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
473 print("SSC analysis")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
474
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
475 ## set variables for components and number of response groups
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
476 number_groups = length(levels(y_vector))
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
477
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
478 ## SSC analysis and plot
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
479 msidata.ssc <- spatialShrunkenCentroids(msidata, y = y_vector, .fold = fold_vector,
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
480 r = c($type_cond.method_cond.ssc_r), s = c($type_cond.method_cond.ssc_s), method = "$type_cond.method_cond.ssc_kernel_method")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
481 plot(msidata.ssc, mode = "tstatistics", model = list("r" = c($type_cond.method_cond.ssc_r), "s" = c($type_cond.method_cond.ssc_s)))
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
482
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
483 ### summary table SSC
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
484 ##############summary_table = summary(msidata.ssc)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
485 summary_table = summary(msidata.ssc)\$accuracy[[names(msidata.ssc@resultData)]]
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
486 summary_table2 = round(as.numeric(summary_table), digits=2)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
487 summary_matrix = matrix(summary_table2, nrow=4, ncol=number_groups)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
488 summary_table3 = cbind(rownames(summary_table), summary_matrix) ## include rownames in table
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
489 summary_table4 = t(summary_table3)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
490 summary_table5 = cbind(c(names(msidata.ssc@resultData),colnames(summary_table)), summary_table4)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
491 plot(0,type='n',axes=FALSE,ann=FALSE)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
492 grid.table(summary_table5, rows= NULL)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
493
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
494 ### image of the best m/z
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
495 minimumy = min(coord(msidata)[,2])
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
496 maximumy = max(coord(msidata)[,2])
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
497 print(image(msidata, mz = topLabels(msidata.ssc)[1,1], normalize.image = "linear", contrast.enhance = "histogram",smooth.image="gaussian", ylim= c(maximumy+0.2*maximumy,minimumy-0.2*minimumy), main="best m/z heatmap"))
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
498
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
499 ## m/z and pixel information output
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
500 ssc_classes = data.frame(msidata.ssc\$classes[[1]])
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
501 pixel_names = gsub(", y = ", "_", names(pixels(msidata)))
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
502 pixel_names = gsub(" = ", "y_", pixel_names)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
503 x_coordinates = matrix(unlist(strsplit(pixel_names, "_")), ncol=3, byrow=TRUE)[,2]
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
504 y_coordinates = matrix(unlist(strsplit(pixel_names, "_")), ncol=3, byrow=TRUE)[,3]
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
505 ssc_classes2 = data.frame(pixel_names, x_coordinates, y_coordinates, ssc_classes)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
506 colnames(ssc_classes2) = c("pixel names", "x", "y","predicted condition")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
507 ssc_toplabels = topLabels(msidata.ssc, n=$type_cond.method_cond.ssc_analysis_cond.ssc_toplabels)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
508 write.table(ssc_toplabels, file="$mzfeatures", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
509 write.table(ssc_classes2, file="$pixeloutput", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
510
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
511 ## image with predicted classes
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
512 prediction_df = cbind(coord(msidata.ssc)[,1:2], ssc_classes)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
513 colnames(prediction_df) = c("x", "y", "predicted_classes")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
514
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
515 prediction_plot = ggplot(prediction_df, aes(x=x, y=y, fill=predicted_classes))+
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
516 geom_tile() +
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
517 coord_fixed()+
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
518 ggtitle("Predicted condition for each pixel")+
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
519 theme_bw()+
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
520 theme(text=element_text(family="ArialMT", face="bold", size=15))+
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
521 theme(legend.position="bottom",legend.direction="vertical")+
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
522 guides(fill=guide_legend(ncol=4,byrow=TRUE))
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
523 coord_labels = aggregate(cbind(x,y)~predicted_classes, data=prediction_df, mean, na.rm=TRUE, na.action="na.pass")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
524 coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$predicted_classes)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
525 print(prediction_plot)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
526
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
527
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
528 ## optional output as .RData
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
529 #if $output_rdata:
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
530 save(msidata.ssc, file="$classification_rdata")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
531 #end if
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
532
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
533 #end if
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
534 #end if
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
535
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
536
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
537
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
538 ######################## II) Prediction #############################
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
539 #############################################################################
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
540
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
541 #elif str($type_cond.type_method) == "prediction":
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
542 print("prediction")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
543
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
544 training_data = loadRData("$type_cond.training_result")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
545
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
546 #if str($type_cond.new_y_values_cond.new_y_values) == "new_response":
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
547 print("new response")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
548
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
549 new_y_tabular = read.delim("$type_cond.new_y_values_cond.new_response_file", header = $type_cond.new_y_values_cond.new_tabular_header, stringsAsFactors = FALSE)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
550 new_y_input = new_y_tabular[,c($type_cond.new_y_values_cond.column_new_x, $type_cond.new_y_values_cond.column_new_y, $type_cond.new_y_values_cond.column_new_response)]
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
551 colnames(new_y_input)[1:2] = c("x", "y")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
552 ## merge with coordinate information of msidata
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
553 msidata_coordinates = cbind(coord(msidata)[,1:2], c(1:ncol(msidata)))
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
554 colnames(msidata_coordinates)[3] = "pixel_index"
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
555 merged_response = merge(msidata_coordinates, new_y_input, by=c("x", "y"), all.x=TRUE)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
556 merged_response[is.na(merged_response)] = "NA"
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
557 merged_response = merged_response[order(merged_response\$pixel_index),]
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
558 new_y_vector = as.factor(merged_response[,4])
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
559 prediction = predict(training_data,msidata, newy = new_y_vector)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
560
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
561 #else
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
562 prediction = predict(training_data,msidata)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
563 #end if
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
564
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
565 ## m/z and pixel information output
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
566 predicted_classes = data.frame(prediction\$classes[[1]])
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
567 pixel_names = gsub(", y = ", "_", names(pixels(msidata)))
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
568 pixel_names = gsub(" = ", "y_", pixel_names)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
569 x_coordinates = matrix(unlist(strsplit(pixel_names, "_")), ncol=3, byrow=TRUE)[,2]
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
570 y_coordinates = matrix(unlist(strsplit(pixel_names, "_")), ncol=3, byrow=TRUE)[,3]
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
571 predicted_classes2 = data.frame(pixel_names, x_coordinates, y_coordinates, predicted_classes)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
572 colnames(predicted_classes2) = c("pixel names", "x", "y","predicted condition")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
573 predicted_toplabels = topLabels(prediction, n=$type_cond.predicted_toplabels)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
574 write.table(predicted_toplabels, file="$mzfeatures", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
575 write.table(predicted_classes2, file="$pixeloutput", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
576
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
577 ## image with predicted classes
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
578
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
579 prediction_df = cbind(coord(prediction)[,1:2], predicted_classes)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
580 colnames(prediction_df) = c("x", "y", "predicted_classes")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
581
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
582 prediction_plot = ggplot(prediction_df, aes(x=x, y=y, fill=predicted_classes))+
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
583 geom_tile() +
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
584 coord_fixed()+
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
585 ggtitle("Predicted condition for each pixel")+
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
586 theme_bw()+
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
587 theme(text=element_text(family="ArialMT", face="bold", size=15))+
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
588 theme(legend.position="bottom",legend.direction="vertical")+
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
589 guides(fill=guide_legend(ncol=4,byrow=TRUE))
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
590 coord_labels = aggregate(cbind(x,y)~predicted_classes, data=prediction_df, mean, na.rm=TRUE, na.action="na.pass")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
591 coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$predicted_classes)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
592 print(prediction_plot)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
593
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
594 ## Summary table prediction
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
595 summary_table = summary(prediction)\$accuracy[[names(prediction@resultData)]]
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
596 summary_table2 = round(as.numeric(summary_table), digits=2)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
597 summary_matrix = matrix(summary_table2, nrow=4, ncol=ncol(summary_table))
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
598 summary_table3 = cbind(rownames(summary_table), summary_matrix) ## include rownames in table
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
599 summary_table4 = t(summary_table3)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
600 summary_table5 = cbind(c(names(prediction@resultData),colnames(summary_table)), summary_table4)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
601 plot(0,type='n',axes=FALSE,ann=FALSE)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
602 grid.table(summary_table5, rows= NULL)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
603
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
604 ## optional output as .RData
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
605 #if $output_rdata:
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
606 msidata = prediction
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
607 save(msidata, file="$classification_rdata")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
608 #end if
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
609
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
610 #end if
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
611
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
612 dev.off()
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
613
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
614 }else{
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
615 print("Inputfile has no intensities > 0 or contains NA values")
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
616 dev.off()
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
617 }
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
618
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
619
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
620 ]]></configfile>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
621 </configfiles>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
622 <inputs>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
623 <expand macro="reading_msidata"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
624 <conditional name="type_cond">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
625 <param name="type_method" type="select" label="Analysis step to perform">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
626 <option value="training" selected="True">training</option>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
627 <option value="prediction">prediction</option>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
628 </param>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
629 <when value="training">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
630
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
631 <param name="annotation_file" type="data" format="tabular" label="Load tabular file with pixel coordinates and their classes"
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
632 help="Three or four columns: x values, y values, response values, optionally fold values"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
633 <param name="column_x" data_ref="annotation_file" label="Column with x values" type="data_column"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
634 <param name="column_y" data_ref="annotation_file" label="Column with y values" type="data_column"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
635 <param name="column_response" data_ref="annotation_file" label="Column with response (condition) values" type="data_column" help="This is the condition (pixel group) which will be classified"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
636 <param name="column_fold" data_ref="annotation_file" optional="True" label="Column with fold values - only neccessary for cvapply" type="data_column" help="Each fold must contain pixels of all response groups and is used for cross validation"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
637 <param name="tabular_header" type="boolean" label="Tabular files contain a header line" truevalue="TRUE" falsevalue="FALSE"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
638
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
639 <conditional name="method_cond">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
640 <param name="class_method" type="select" label="Select the method for classification">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
641 <option value="PLS" selected="True">PLS-DA</option>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
642 <option value="OPLS">OPLS-DA</option>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
643 <option value="spatialShrunkenCentroids">spatial shrunken centroids</option>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
644 </param>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
645 <when value="PLS">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
646
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
647 <conditional name="analysis_cond">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
648 <param name="PLS_method" type="select" label="Crossvalidation or analysis">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
649 <option value="cvapply" selected="True">cvApply</option>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
650 <option value="PLS_analysis">PLS-DA analysis</option>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
651 </param>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
652 <when value="cvapply">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
653 <param name="plscv_comp" type="text" value="1:2"
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
654 label="The number of PLS-DA components" help="For cvapply multiple values are allowed (e.g. 1,2,3 or 2:5)">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
655 <expand macro="sanitizer_multiple_digits"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
656 </param>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
657 </when>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
658 <when value="PLS_analysis">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
659 <param name="pls_comp" type="integer" value="5"
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
660 label="The optimal number of PLS-DA components as indicated by cross-validations" help="Run cvApply first to optain optiaml number of PLS-DA components"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
661 <param name="pls_scale" type="boolean" label="Data scaling" truevalue="TRUE" falsevalue="FALSE"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
662 <param name="pls_toplabels" type="integer" value="100"
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
663 label="Number of toplabels (m/z features) which should be written in tabular output"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
664 </when>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
665 </conditional>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
666 </when>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
667
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
668 <when value="OPLS">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
669
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
670 <conditional name="opls_analysis_cond">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
671 <param name="opls_method" type="select" label="Analysis step to perform">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
672 <option value="opls_cvapply" selected="True">cvApply</option>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
673 <option value="opls_analysis">OPLS-DA analysis</option>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
674 </param>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
675
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
676 <when value="opls_cvapply">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
677 <param name="opls_cvcomp" type="text" value="1:2"
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
678 label="The number of OPLS-DA components" help="For cvapply multiple values are allowed (e.g. 1,2,3 or 2:5)">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
679 <expand macro="sanitizer_multiple_digits"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
680 </param>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
681 <param name="xnew_cv" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Keep new matrix"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
682 </when>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
683
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
684 <when value="opls_analysis">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
685 <param name="opls_comp" type="integer" value="5"
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
686 label="The optimal number of OPLS-DA components as indicated by cross-validations" help="Run cvApply first to optain optiaml number of OPLS-DA components"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
687 <param name="xnew" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Keep new matrix"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
688 <param name="opls_scale" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Data scaling"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
689 <param name="opls_toplabels" type="integer" value="100"
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
690 label="Number of toplabels (m/z features) which should be written in tabular output"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
691 </when>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
692 </conditional>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
693 </when>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
694
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
695 <when value="spatialShrunkenCentroids">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
696 <conditional name="ssc_analysis_cond">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
697 <param name="ssc_method" type="select" label="Analysis step to perform">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
698 <option value="ssc_cvapply" selected="True">cvApply</option>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
699 <option value="ssc_analysis">spatial shrunken centroids analysis</option>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
700 </param>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
701 <when value="ssc_cvapply"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
702
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
703 <when value="ssc_analysis">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
704 <param name="ssc_toplabels" type="integer" value="100"
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
705 label="Number of toplabels (m/z features) which should be written in tabular output"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
706 </when>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
707 </conditional>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
708 <param name="ssc_r" type="text" value="2"
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
709 label="The spatial neighborhood radius of nearby pixels to consider (r)" help="For cvapply multiple values are allowed (e.g. 1,2,3 or 2:5)">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
710 <expand macro="sanitizer_multiple_digits"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
711 </param>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
712 <param name="ssc_s" type="text" value="2"
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
713 label="The sparsity thresholding parameter by which to shrink the t-statistics (s)" help="For cvapply multiple values are allowed (e.g. 1,2,3 or 2:5)">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
714 <expand macro="sanitizer_multiple_digits"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
715 </param>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
716 <param name="ssc_kernel_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">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
717 <option value="gaussian">gaussian</option>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
718 <option value="adaptive" selected="True">adaptive</option>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
719 </param>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
720
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
721 </when>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
722 </conditional>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
723 </when>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
724
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
725 <when value="prediction">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
726 <param name="training_result" type="data" format="rdata" label="Result from previous classification training"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
727 <param name="predicted_toplabels" type="integer" value="100"
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
728 label="Number of toplabels (m/z features) which should be written in tabular output"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
729 <conditional name="new_y_values_cond">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
730 <param name="new_y_values" type="select" label="Should new response values be used">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
731 <option value="no_new_response" selected="True">old response should be used</option>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
732 <option value="new_response">load new response from tabular file</option>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
733 </param>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
734 <when value="no_new_response"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
735 <when value="new_response">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
736 <param name="new_response_file" type="data" format="tabular" label="Load tabular file with pixel coordinates and the new response"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
737 <param name="column_new_x" data_ref="new_response_file" label="Column with x values" type="data_column"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
738 <param name="column_new_y" data_ref="new_response_file" label="Column with y values" type="data_column"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
739 <param name="column_new_response" data_ref="new_response_file" label="Column with new response values" type="data_column"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
740 <param name="new_tabular_header" type="boolean" label="Tabular files contain a header line" truevalue="TRUE" falsevalue="FALSE"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
741 </when>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
742 </conditional>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
743 </when>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
744 </conditional>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
745 <param name="output_rdata" type="boolean" label="Results as .RData output" help="Can be used to generate a classification prediction on new data"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
746 </inputs>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
747 <outputs>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
748 <data format="pdf" name="classification_images" from_work_dir="classificationpdf.pdf" label = "${tool.name} on ${on_string}"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
749 <data format="tabular" name="mzfeatures" label="${tool.name} on ${on_string}: features"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
750 <data format="tabular" name="pixeloutput" label="${tool.name} on ${on_string}: pixels"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
751 <data format="rdata" name="classification_rdata" label="${tool.name} on ${on_string}: results.RData">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
752 <filter>output_rdata</filter>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
753 </data>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
754 </outputs>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
755 <tests>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
756 <test expect_num_outputs="3">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
757 <param name="infile" value="testfile_squares.rdata" ftype="rdata"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
758 <conditional name="type_cond">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
759 <param name="type_method" value="training"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
760 <param name="annotation_file" value= "pixel_annotation_file1.tabular" ftype="tabular"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
761 <param name="column_x" value="1"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
762 <param name="column_y" value="2"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
763 <param name="column_response" value="4"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
764 <param name="column_fold" value="3"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
765 <param name="tabular_header" value="False"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
766 <conditional name="method_cond">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
767 <param name="class_method" value="PLS"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
768 <conditional name="analysis_cond">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
769 <param name="PLS_method" value="cvapply"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
770 <param name="plscv_comp" value="2:4"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
771 </conditional>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
772 </conditional>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
773 </conditional>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
774 <output name="mzfeatures" file="features_test1.tabular"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
775 <output name="pixeloutput" file="pixels_test1.tabular"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
776 <output name="classification_images" file="test1.pdf" compare="sim_size" delta="2000"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
777 </test>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
778
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
779 <test expect_num_outputs="4">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
780 <param name="infile" value="testfile_squares.rdata" ftype="rdata"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
781 <conditional name="type_cond">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
782 <param name="type_method" value="training"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
783 <param name="annotation_file" value= "pixel_annotation_file1.tabular" ftype="tabular"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
784 <param name="column_x" value="1"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
785 <param name="column_y" value="2"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
786 <param name="column_response" value="4"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
787 <param name="tabular_header" value="False"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
788 <conditional name="method_cond">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
789 <param name="class_method" value="PLS"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
790 <conditional name="analysis_cond">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
791 <param name="PLS_method" value="PLS_analysis"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
792 <param name="pls_comp" value="2"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
793 <param name="pls_scale" value="TRUE"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
794 <param name="pls_toplabels" value="100"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
795 </conditional>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
796 </conditional>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
797 </conditional>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
798 <param name="output_rdata" value="True"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
799 <output name="mzfeatures" file="features_test2.tabular"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
800 <output name="pixeloutput" file="pixels_test2.tabular"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
801 <output name="classification_images" file="test2.pdf" compare="sim_size"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
802 <output name="classification_rdata" file="test2.rdata" compare="sim_size"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
803 </test>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
804
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
805 <test expect_num_outputs="3">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
806 <param name="infile" value="testfile_squares.rdata" ftype="rdata"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
807 <conditional name="type_cond">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
808 <param name="type_method" value="training"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
809 <param name="annotation_file" value= "random_factors.tabular" ftype="tabular"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
810 <param name="column_x" value="1"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
811 <param name="column_y" value="2"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
812 <param name="column_response" value="4"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
813 <param name="column_fold" value="3"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
814 <param name="tabular_header" value="False"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
815 <conditional name="method_cond">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
816 <param name="class_method" value="OPLS"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
817 <conditional name="opls_analysis_cond">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
818 <param name="opls_method" value="opls_cvapply"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
819 <param name="opls_cvcomp" value="1:2"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
820 <param name="xnew_cv" value="FALSE"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
821 </conditional>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
822 </conditional>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
823 </conditional>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
824 <output name="mzfeatures" file="features_test3.tabular"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
825 <output name="pixeloutput" file="pixels_test3.tabular"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
826 <output name="classification_images" file="test3.pdf" compare="sim_size"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
827 </test>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
828
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
829 <test expect_num_outputs="4">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
830 <param name="infile" value="testfile_squares.rdata" ftype="rdata"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
831 <conditional name="type_cond">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
832 <param name="type_method" value="training"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
833 <param name="annotation_file" value= "random_factors.tabular" ftype="tabular"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
834 <param name="column_x" value="1"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
835 <param name="column_y" value="2"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
836 <param name="column_response" value="4"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
837 <param name="tabular_header" value="False"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
838 <conditional name="method_cond">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
839 <param name="class_method" value="OPLS"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
840 <conditional name="opls_analysis_cond">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
841 <param name="opls_method" value="opls_analysis"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
842 <param name="opls_comp" value="3"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
843 <param name="xnew" value="FALSE"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
844 <param name="opls_scale" value="FALSE"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
845 <param name="opls_toplabels" value="100"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
846 </conditional>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
847 </conditional>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
848 </conditional>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
849 <param name="output_rdata" value="True"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
850 <output name="mzfeatures" file="features_test4.tabular"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
851 <output name="pixeloutput" file="pixels_test4.tabular"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
852 <output name="classification_images" file="test4.pdf" compare="sim_size"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
853 <output name="classification_rdata" file="test4.rdata" compare="sim_size"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
854 </test>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
855
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
856 <test expect_num_outputs="3">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
857 <param name="infile" value="testfile_squares.rdata" ftype="rdata"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
858 <conditional name="type_cond">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
859 <param name="type_method" value="training"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
860 <param name="annotation_file" value= "pixel_annotation_file1.tabular" ftype="tabular"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
861 <param name="column_x" value="1"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
862 <param name="column_y" value="2"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
863 <param name="column_response" value="3"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
864 <param name="column_fold" value="4"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
865 <param name="tabular_header" value="False"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
866 <conditional name="method_cond">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
867 <param name="class_method" value="spatialShrunkenCentroids"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
868 <conditional name="ssc_analysis_cond">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
869 <param name="ssc_method" value="ssc_cvapply"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
870 <param name="ssc_r" value="1:2"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
871 <param name="ssc_s" value="2:3"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
872 <param name="ssc_kernel_method" value="adaptive"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
873 </conditional>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
874 </conditional>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
875 </conditional>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
876 <output name="mzfeatures" file="features_test5.tabular"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
877 <output name="pixeloutput" file="pixels_test5.tabular"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
878 <output name="classification_images" file="test5.pdf" compare="sim_size"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
879 </test>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
880
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
881 <test expect_num_outputs="4">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
882 <param name="infile" value="testfile_squares.rdata" ftype="rdata"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
883 <conditional name="type_cond">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
884 <param name="type_method" value="training"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
885 <param name="annotation_file" value= "random_factors.tabular" ftype="tabular"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
886 <param name="column_x" value="1"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
887 <param name="column_y" value="2"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
888 <param name="column_response" value="4"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
889 <conditional name="method_cond">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
890 <param name="class_method" value="spatialShrunkenCentroids"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
891 <conditional name="ssc_analysis_cond">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
892 <param name="ssc_method" value="ssc_analysis"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
893 <param name="ssc_toplabels" value="20"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
894 </conditional>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
895 <param name="ssc_r" value="2"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
896 <param name="ssc_s" value="2"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
897 <param name="ssc_kernel_method" value="adaptive"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
898 </conditional>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
899 </conditional>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
900 <param name="output_rdata" value="True"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
901 <output name="mzfeatures" file="features_test6.tabular"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
902 <output name="pixeloutput" file="pixels_test6.tabular"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
903 <output name="classification_images" file="test6.pdf" compare="sim_size"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
904 <output name="classification_rdata" file="test6.rdata" compare="sim_size" />
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
905 </test>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
906
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
907 <test expect_num_outputs="4">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
908 <param name="infile" value="testfile_squares.rdata" ftype="rdata"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
909 <conditional name="type_cond">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
910 <param name="type_method" value="prediction"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
911 <param name="training_result" value="test2.rdata" ftype="rdata"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
912 <conditional name="new_y_values_cond">
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
913 <param name="new_y_values" value="new_response"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
914 <param name="new_response_file" value="pixel_annotation_file1.tabular" ftype="tabular"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
915 <param name="column_new_x" value="1"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
916 <param name="column_new_y" value="2"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
917 <param name="column_new_response" value="4"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
918 <param name="new_tabular_header" value="False"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
919 </conditional>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
920 </conditional>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
921 <param name="output_rdata" value="True"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
922 <output name="mzfeatures" file="features_test7.tabular"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
923 <output name="pixeloutput" file="pixels_test7.tabular"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
924 <output name="classification_images" file="test7.pdf" compare="sim_size"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
925 <output name="classification_rdata" file="test7.rdata" compare="sim_size" />
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
926 </test>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
927 </tests>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
928 <help>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
929 <![CDATA[
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
930
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
931
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
932 @CARDINAL_DESCRIPTION@
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
933
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
934 -----
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
935
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
936 This tool provides three different Cardinal functions for supervised classification of mass-spectrometry imaging data.
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
937
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
938 @MSIDATA_INPUT_DESCRIPTION@
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
939 - For training: tabular file with condition and fold for each pixel: Two columns for pixel coordinates (x and y values); one column with the condition for the pixel, which will be used for classification; for the cross validation (cvapply) another column with a fold is necessary, each fold must contain pixels of all response groups and is used for cross validation. Condition and fold columns are treated as factor to perform discriminant analysis (also when numeric values are provided).
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
940
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
941 ::
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
942
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
943 x_coord y_coord condition fold
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
944 1 1 A f1
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
945 2 1 A f2
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
946 3 1 A f3
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
947 1 2 B f1
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
948 2 2 B f2
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
949 3 2 B f3
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
950 ...
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
951 ...
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
952
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
953
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
954 - For prediction: RData output from previous classification run is needed as input, optionally new response values can be loaded with a tabular file containing x values, y values and the response
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
955
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
956
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
957 **Options**
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
958
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
959 - PLS-DA: partial least square discriminant analysis
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
960 - O-PLS-DA: Orthogonal partial least squares discriminant analysis
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
961 - Spatial shrunken centroids
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
962
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
963 **Tips**
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
964
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
965 - The classification function will only run on files with valid intensity values (NA are not allowed)
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
966 - Only a single input file is accepted, several files have to be combined previously, for example with the msi_combine tool.
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
967
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
968
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
969 **Output**
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
970
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
971 - Pdf with the heatmaps and plots for the classification
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
972 - Tabular file with information on m/z features and pixels: toplabels/classes
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
973 - Optional: RData output that can be used to predict new data or to explore the results more deeply with the Cardinal package in R
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
974
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
975 ]]>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
976 </help>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
977 <expand macro="citations"/>
7d1500ecbda9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
978 </tool>