Mercurial > repos > galaxyp > cardinal_single_ion_segmentation

annotate spatial_DGMM.xml @ 1:dc07c4f727de draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
author galaxyp
date Wed, 19 Apr 2023 22:22:32 +0000
parents 75b43378fb02
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1 <tool id="cardinal_single_ion_segmentation" name="MSI single ion segmentation" version="@VERSION@.0">
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2 <description>mass spectrometry imaging spatial DGMM</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements">
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7 <requirement type="package" version="2.3">r-gridextra</requirement>
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8 </expand>
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9 <command detect_errors="exit_code">
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10 <![CDATA[
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12 @INPUT_LINKING@
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13 cat '${MSI_spatial_DGMM}' &&
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14 Rscript '${MSI_spatial_DGMM}'
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16 ]]>
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17 </command>
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18 <configfiles>
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19 <configfile name="MSI_spatial_DGMM"><![CDATA[
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21 ################################# load libraries and read file #################
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23 library(Cardinal)
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24 library(gridExtra)
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26 @READING_MSIDATA_FULLY_COMPATIBLE@
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28 #if str($sample_groups.group) == "multiple_groups":
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29 ## read and extract x,y,annotation information
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30 input_tabular <- read.delim("$sample_groups.annotation_file", header = $sample_groups.tabular_header, stringsAsFactors = FALSE)
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31 annotation_input <- input_tabular[,c($sample_groups.column_x, $sample_groups.column_y, $sample_groups.column_names)]
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32 annotation_name <- colnames(annotation_input)[3] ##extract header for annotations to later export tabular with same name
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33 colnames(annotation_input) <- c("x", "y", "annotation") ## rename annotations header to default name "annotation"
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34
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35 ## merge with coordinate information of msidata
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36 msidata_coordinates <- data.frame(coord(msidata)\$x, coord(msidata)\$y, c(1:ncol(msidata)))
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37 colnames(msidata_coordinates) <- c("x", "y", "pixel_index")
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38 merged_annotation <- merge(msidata_coordinates, annotation_input, by=c("x", "y"), all.x=TRUE)
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39 merged_annotation[is.na(merged_annotation)] <- "NA"
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40 merged_annotation <- merged_annotation[order(merged_annotation\$pixel_index),]
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41 msidata\$annotation <- as.character(merged_annotation[,4])
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42 #end if
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45 @DATA_PROPERTIES_INRAM@
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48 ## remove duplicated coordinates
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49 msidata <- msidata[,!duplicated(coord(msidata))]
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51
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52 ######################################## PDF ###################################
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53 ################################################################################
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54 ################################################################################
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57 pdf("single_ion_segmentation.pdf", fonts = "Times", pointsize = 12)
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58 plot(0,type='n',axes=FALSE,ann=FALSE)
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60 title(main=paste0("Single ion segmentation for file: \n\n", "$infile.display_name"))
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62 grid.table(property_df, rows= NULL)
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64 if (npeaks > 0)
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65 {
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67 ## set seed to make analysis reproducible
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68 set.seed($setseed)
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71 ## single ion segmentation
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72 dgmm <- spatialDGMM(msidata,
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73 r = c($r),
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74 k = c($k),
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75 #if str($sample_groups.group) == 'single_group':
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76 groups = as.factor(rep("$infile.display_name", ncol(msidata))),
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77 #else
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78 groups = msidata\$annotation,
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79 #end if
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80 method = "$method",
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81 dist = "$dist",
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82 annealing = $annealing,
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83 init = "$init",
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84 p0 = $p0,
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85 iter.max = $iter_max,
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86 tol = $tol)
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87
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88 ## Summary results table
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89 dgmm_summary <- as.data.frame(summary(dgmm))
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90 colnames(dgmm_summary) <- c('r', 'k', 'Feature', 'Classes/group')
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diff changeset
91 dgmm_summary\$'m/z' <- mz(msidata)
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galaxyp
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diff changeset
92 feature_n <- dgmm_summary\$Feature
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galaxyp
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diff changeset
93 dgmm_summary\$Feature <- NULL
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diff changeset
94 dgmm_summary\$Feature <- feature_n
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diff changeset
95 write.table(dgmm_summary, file="$dgmm_summary", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
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96
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97 ## Results images
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98 for (dgmm_repeat in 1:nrow(dgmm_summary)){
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99 print(image(dgmm, values="class", model=dgmm_repeat))}
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100 dev.off() ## closes pdf file
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101
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102 ## optional outputs
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103 pixel_names <- paste0("xy_", coord(dgmm)\$x, "_", coord(dgmm)\$y)
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104
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105 #if $output_probability:
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106 dir.create("DGMM_probability")
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diff changeset
107 for (dgmm_repeat in 1:nrow(dgmm_summary)){
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108 name_repeat <- file.path(paste0("DGMM_probability/probability_r", dgmm_summary\$r[dgmm_repeat], "_k", dgmm_summary\$k[dgmm_repeat], "_mz", dgmm_summary\$`m/z`[dgmm_repeat], ".tabular"))
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diff changeset
109 prob_df <- data.frame(coord(dgmm)\$x, coord(dgmm)\$y, pixel_names, resultData(dgmm, dgmm_repeat, "class"), resultData(dgmm, dgmm_repeat, "probability"))
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110 colnames(prob_df)[1:4] <- c("x", "y", "pixel_names", "class")
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diff changeset
111 write.table(prob_df, file=name_repeat, quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
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112 }
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113 #end if
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114
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115 #if $output_estimates:
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116 dir.create("DGMM_estimates")
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117 for (dgmm_repeat in 1:nrow(dgmm_summary)){
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diff changeset
118 name_repeat <- file.path(paste0("DGMM_estimates/estimates_r", dgmm_summary\$r[dgmm_repeat], "_k", dgmm_summary\$k[dgmm_repeat], "_mz", dgmm_summary\$`m/z`[dgmm_repeat], ".tabular"))
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diff changeset
119 est_df <- resultData(dgmm, dgmm_repeat, "estimates")
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120 write.table(est_df, file=name_repeat, quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
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diff changeset
121 }
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diff changeset
122 #end if
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123
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124 #if $output_plots:
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125 dir.create("DGMM_plots")
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126 for (dgmm_repeat in 1:nrow(dgmm_summary)){
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127 name_repeat <- file.path(paste0("DGMM_plots/plot_r", dgmm_summary\$r[dgmm_repeat], "_k", dgmm_summary\$k[dgmm_repeat], "_mz", dgmm_summary\$`m/z`[dgmm_repeat], ".png"))
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diff changeset
128 png(file=name_repeat)
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129 print(plot(dgmm, model=dgmm_repeat, lwd=2))
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130 dev.off()
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131 }
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132 #end if
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133
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134 ## optional output as .RData
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135 #if $output_rdata:
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136 ## save as (.RData)
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137 save(dgmm, file="$dgmm_rdata")
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138 #end if
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139
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diff changeset
140 }else{
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141 print("Inputfile has no intensities > 0")
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142 }
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143
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diff changeset
144 ]]></configfile>
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145 </configfiles>
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146 <inputs>
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147 <expand macro="reading_msidata"/>
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148 <conditional name="sample_groups">
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149 <param name="group" type="select" label="Dataset groups" help="Pixels from different groups will be segmented separately. For the validity of
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diff changeset
150 downstream statistical analysis, it is important that each distinct observational unit (e.g., tissue sample) is assigned to a unique group">
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151 <option value="single_group" selected="True">Dataset is a single group</option>
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152 <option value="multiple_groups">Dataset contains multiple groups</option>
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153 </param>
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diff changeset
154 <when value="single_group"/>
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155 <when value="multiple_groups">
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156 <expand macro="reading_pixel_annotations"/>
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diff changeset
157 </when>
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158 </conditional>
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159 <param name="r" type="text" value="2"
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160 label="r" help="The spatial neighborhood radius of nearby pixels to consider. Only a single value is allowed">
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161 <expand macro="sanitizer_multiple_digits"/>
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162 </param>
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163 <param name="k" type="text" value="5"
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164 label="k" help="The maximum number of segments (clusters). The final number of segments may differ. Only a single value is allowed.">
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165 <expand macro="sanitizer_multiple_digits"/>
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166 </param>
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167 <param name="method" type="select" display="radio"
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168 label="weights method" help="The method to use to calculate the spatial smoothing weights. The 'gaussian' method refers to spatially-aware (SA) weights, and 'adaptive' refers to spatially-aware structurally-adaptive (SASA) weights">
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169 <option value="gaussian" selected="True">gaussian</option>
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170 <option value="adaptive">adaptive</option>
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171 </param>
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172 <param name="dist" type="select" display="radio"
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173 label="distance metric" help="The type of distance metric to use when calculating neighboring pixels based on r. The options are ‘radial’, ‘manhattan’, ‘minkowski’, and ‘chebyshev’ (the
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174 default).">
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175 <option value="chebyshev" selected="True">chebyshev</option>
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176 <option value="manhattan">manhattan</option>
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177 <option value="radial">radial</option>
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178 <option value="minkowski">minkowski</option>
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179 </param>
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180 <param name="annealing" type="boolean" label="annealing" help="Should simulated annealing be used during the optimization process to improve parameter estimates?" truevalue="TRUE" falsevalue="FALSE" />
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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181 <param name="init" type="select" display="radio"
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182 label="init" help="Should the parameter estimates be initialized using k-means (’kmeans’) or Gaussian mixture model (’gmm’)?">
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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183 <option value="kmeans" selected="True">kmeans</option>
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184 <option value="gmm">gmm</option>
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185 </param>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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186 <param name="p0" type="float" value="0.05" label="p0" help="A regularization parameter applied to estimated posterior class probabilities to avoid singularities. Must be positive for successful gradient descent optimization.Changing this value (within reason) should have only minimal impact on values of parameter estimates, but may greatly affect the algorithm’s speed and stability." />
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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187 <param name="iter_max" type="integer" value="100" label="iter.max" help="The maximum number of EM-algorithm iterations." />
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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188 <param name="tol" type="float" value="0.05" label="tolerance" help="The tolerance convergence criterion for the EM-algorithm. Corresponds to the
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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189 change in log-likelihood."/>
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190 <param name="setseed" type="integer" value="1" label="set seed" help="Use same value to reproduce previous results"/>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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191 <param name="output_estimates" type="boolean" label="Generate estimates results"/>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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diff changeset
192 <param name="output_probability" type="boolean" label="Generate probability and class results"/>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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193 <param name="output_plots" type="boolean" label="Generate plots results"/>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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194 <param name="output_rdata" type="boolean" label="Results as .RData output"/>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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diff changeset
195 </inputs>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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196 <outputs>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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197 <data format="tabular" name="dgmm_summary" label="${tool.name} on ${on_string}: summary"/>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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diff changeset
198 <data format="pdf" name="file_info" from_work_dir="single_ion_segmentation.pdf" label = "${tool.name} on ${on_string}: file_info"/>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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diff changeset
199 <data format="rdata" name="dgmm_rdata" label="${tool.name} on ${on_string}: dgmm.RData">
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
200 <filter>output_rdata</filter>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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diff changeset
201 </data>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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diff changeset
202 <collection name="estimates_output" type="list" label="${tool.name} logs: ${on_string}: estimates">
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
203 <filter>output_estimates</filter>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
204 <discover_datasets pattern="__designation_and_ext__" directory="DGMM_estimates" format="tabular"/>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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diff changeset
205 </collection>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
206 <collection name="probability_output" type="list" label="${tool.name} logs: ${on_string}: probability">
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
207 <filter>output_probability</filter>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
208 <discover_datasets pattern="__designation_and_ext__" directory="DGMM_probability" format="tabular"/>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
209 </collection>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
210 <collection name="plots_output" type="list" label="${tool.name} logs: ${on_string}: plots">
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
211 <filter>output_plots</filter>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
parents:
diff changeset
212 <discover_datasets pattern="__designation_and_ext__" directory="DGMM_plots" format="tabular"/>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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diff changeset
213 </collection>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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diff changeset
214 </outputs>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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diff changeset
215 <tests>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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diff changeset
216 <test>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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217 <param name="infile" value="" ftype="imzml">
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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diff changeset
218 <composite_data value="spatial_DGMM_input.imzML"/>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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diff changeset
219 <composite_data value="spatial_DGMM_input.ibd"/>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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diff changeset
220 </param>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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diff changeset
221 <param name="r" value="1"/>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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diff changeset
222 <param name="k" value="6"/>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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diff changeset
223 <param name="method" value="adaptive"/>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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diff changeset
224 <param name="dist" value="radial"/>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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225 <param name="annealing" value="TRUE"/>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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diff changeset
226 <param name="output_estimates" value="True"/>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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diff changeset
227 <param name="output_probability" value="True"/>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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228 <output name="file_info" file="dgmm_test1.pdf" compare="sim_size"/>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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229 <output name="dgmm_summary" file="dgmm_summary1.tabular"/>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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230 <output_collection name="estimates_output" type="list" count="10">
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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231 <element name="estimates_r1_k6_mz1135.93347167969" file="estimates_r1_k6_mz1135.93347167969.tabular"/>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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diff changeset
232 </output_collection>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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diff changeset
233 <output_collection name="probability_output" type="list" count="10">
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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234 <element name="probability_r1_k6_mz1023.70806884766" file="probability_r1_k6_mz1023.70806884766.tabular"/>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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235 </output_collection>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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236 </test>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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diff changeset
237 <test>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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238 <param name="infile" value="" ftype="imzml">
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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diff changeset
239 <composite_data value="spatial_DGMM_input.imzML"/>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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diff changeset
240 <composite_data value="spatial_DGMM_input.ibd"/>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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241 </param>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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242 <conditional name="sample_groups">
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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243 <param name="group" value="multiple_groups"/>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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244 <param name="annotation_file" value="DGMM_annotations.tabular"/>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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245 <param name="column_x" value="1"/>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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246 <param name="column_y" value="2"/>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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247 <param name="column_names" value="3"/>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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248 <param name="tabular_header" value="True"/>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
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249 </conditional>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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250 <param name="r" value="2"/>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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251 <param name="k" value="10"/>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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252 <param name="annealing" value="TRUE"/>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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253 <param name="output_estimates" value="True"/>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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diff changeset
254 <param name="output_probability" value="True"/>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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255 <param name="output_plots" value="True"/>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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256 <param name="output_rdata" value="True"/>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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257 <output name="file_info" file="dgmm_test2.pdf" compare="sim_size"/>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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258 <output name="dgmm_summary" file="dgmm_summary2.tabular"/>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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259 <output name="dgmm_rdata" file="dgmm_test2.RData" compare="sim_size"/>
75b43378fb02 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
galaxyp
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260 <output_collection name="estimates_output" type="list" count="10">
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261 <element name="estimates_r2_k10_mz1200.46533203125" file="estimates_r2_k10_mz1200.46533203125.tabular"/>
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262 </output_collection>
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263 <output_collection name="probability_output" type="list" count="10">
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264 <element name="probability_r2_k10_mz1135.93347167969" file="probability_r2_k10_mz1135.93347167969.tabular"/>
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265 </output_collection>
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266 </test>
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267 </tests>
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268 <help>
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269 <![CDATA[
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270
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271 @CARDINAL_DESCRIPTION@
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272
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273 -----
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274
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275 This tool fits spatially-aware Dirichlet Gaussian mixture models (DGMM) to each feature and each run in an mass spectrometry imaging
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276 experiment. Each image is segmented and the means and variances of all Gaussian components are estimated. A linear filter with a spatial kernel is applied to the component probabilities to achieve
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277 spatial smoothing. Simulated annealing is used in the EM-algorithm to avoid local optima and achieve more accurate parameter estimates.
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278
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279 @MSIDATA_INPUT_DESCRIPTION@
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280 - NA intensities are not allowed
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281 - duplicated coordinates will be removed
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282 - It is highly recommended to use a dataset that is reduced for the number of m/z features e.g. pre-processed, binned, filtered for m/z of interest in order to keep computational times reasonable. In addition, it is beneficial to run the tool first without generating all possible results data and upon inspection of the summary of the results decide on the best tool parameters and m/z features (which can be filtered in the MSI filtering tool).
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283
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284 @SPECTRA_TABULAR_INPUT_DESCRIPTION@
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285
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286 **Tips**
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287
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288 - The input dataset should contain as few m/z features as possible to keep computational times reasonable. In addition, it is beneficial to run the tool first without generating all possible results data and upon inspection of the summary of the results decide on the best tool parameters and m/z features (which can be filtered in the MSI filtering tool).
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289 - Pixels from distinct ovbservational units (e.g. sample, patient) should be assigned to a unique group via the annotation file and segmented separately for the validity of downstream statistical analysis.
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290
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291 **Output**
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292
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293 - Pdf with file info and an image of the clusters for each m/z feature
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294 - Tabular file summarizing spatial DGMM performance for each feature
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295 - (optional) Tabular files for each spatial DGMM run and feature with
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296
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297 - probabilities (The probability of class membership for each Gaussian component) and classes (The predicted Gaussian component)
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298 - estimates (A list giving the parameter estimates for the means and variances for each Gaussian component)
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299 - (optional) Visualization of features density plots
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300 - (optional) .RData file which contains the segmentation results and can be used for further exploration in R using the Cardinal package
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301
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302 ]]>
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303 </help>
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304 <citations>
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305 <citation type="doi">10.1093/bioinformatics/btv146</citation>
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306 <citation type="doi">10.1093/bioinformatics/btz345</citation>
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307 </citations>
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308
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309 </tool>