Mercurial > repos > galaxyp > cardinal_data_exporter

annotate data_exporter.xml @ 17:56da27be956a draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c
author galaxyp
date Thu, 04 Jul 2024 13:34:08 +0000
parents b6a4dd06cde0
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1 <tool id="cardinal_data_exporter" name="MSI data exporter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
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2 <description>
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3 exports imzML and Analyze7.5 to tabular files
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4 </description>
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="requirements"/>
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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 '${cardinal_imzml_exporter}' &&
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14 Rscript '${cardinal_imzml_exporter}'
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16 ]]>
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17 </command>
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18 <configfiles>
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19 <configfile name="cardinal_imzml_exporter"><![CDATA[
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21 ################################# load libraries and read file #################
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23 library(Cardinal)
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25 @READING_MSIDATA@
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27 ## in case RData input is MSImageSet:
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28 if (class(msidata) == "MSImageSet"){
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29 msidata = as(msidata, "MSImagingExperiment")
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30 run(msidata) = "infile"
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31 }
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33 ## extract spectra matrix once:
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34 msidata_matrix = as.matrix(iData(msidata))
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35 ###################### Intensity matrix output ################################
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37 #if "int_matrix" in str($output_options).split(","):
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38 print("intensity matrix output")
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40 mz_names = paste0("mz_", mz(msidata))
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41 pixel_names = paste0("xy_", coord(msidata)\$x, "_", coord(msidata)\$y)
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43 write.table(
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44 rbind(c("mz_name", pixel_names), cbind(mz_names,msidata_matrix)), ##create matrix
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45 file="$intensity_matrix", quote = FALSE, row.names = FALSE, col.names=FALSE, sep = "\t")
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46 ## free up RAM space in case furhter steps will be run:
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47 rm(newmatrix)
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48 gc()
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50 #end if
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53 ############################## m/z feature output ##########################
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54 #if "mz_tabular" in str($output_options).split(","):
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55 print("mz feature output")
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57 full_sample_mean = apply(msidata_matrix,1,mean, na.rm=TRUE)
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58 full_sample_sd = apply(msidata_matrix,1,sd, na.rm=TRUE)
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60 mz_df = data.frame(paste0("mz_", mz(msidata)), ##mz names
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61 mz(msidata), ##mz values
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62 full_sample_mean, ##mean
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63 apply(msidata_matrix,1,median, na.rm=TRUE), ##median
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64 full_sample_sd, ##sd
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65 full_sample_sd/full_sample_mean*100, ##SEM
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66 rowSums(msidata_matrix, na.rm=TRUE), ## calculate intensity sum for each m/z
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67 rowSums(msidata_matrix > 0, na.rm=TRUE)) ## calculate number of intensities > 0 for each m/z (max = number of spectra)
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69 colnames(mz_df) = c("mz_names", "mz", "sample_mean", "sample_median", "sample_sd", "sample_sem", "intensity_sum", "number_peaks")
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70 write.table(mz_df, file="$feature_output", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
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71 ## free up RAM space in case furhter steps will be run:
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72 rm(mz_df)
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73 gc()
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74 #end if
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76 ###################### summarized m/z feature output #######################
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78 #if str($tabular_annotation.load_annotation) == 'yes_annotation':
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79 print("summarized annotation output")
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81 ## read and extract x,y,annotation information
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82 input_tabular = read.delim("$tabular_annotation.annotation_file", header = $tabular_annotation.tabular_header, stringsAsFactors = FALSE)
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83 annotation_input = input_tabular[,c($tabular_annotation.column_x, $tabular_annotation.column_y, $tabular_annotation.column_names)]
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84 colnames(annotation_input) = c("x", "y", "annotation")
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85
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86 ## merge with coordinate information of msidata
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87 msidata_coordinates = data.frame(coord(msidata)\$x, coord(msidata)\$y, c(1:ncol(msidata)))
350a84ea795c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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88 colnames(msidata_coordinates) = c("x", "y", "pixel_index")
0
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89 merged_annotation = merge(msidata_coordinates, annotation_input, by=c("x", "y"), all.x=TRUE)
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90 merged_annotation[is.na(merged_annotation)] = "NA"
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91 merged_annotation = merged_annotation[order(merged_annotation\$pixel_index),]
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92 msidata\$annotation = as.factor(merged_annotation[,4])
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93
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94 ## create m/z feature name
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95 mz_names = paste0("mz_", mz(msidata))
0
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96
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97 #if "mean" in str($tabular_annotation.summary_type).split(","):
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98 print("summarized mean")
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99
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100 ## calculate mean per annotation group
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101 sample_matrix = matrix(,ncol=0, nrow=nrow(msidata))
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102 count = 1
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103 for (subsample in levels(msidata\$annotation)){
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104 subsample_pixels = msidata[,msidata\$annotation == subsample]
17
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105 subsample_calc = rowMeans(as.matrix(spectra(subsample_pixels)), na.rm=TRUE)
0
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106 sample_matrix = cbind(sample_matrix, subsample_calc)
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107 count = count+1}
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108 sample_matrix_mean = cbind(mz_names,sample_matrix)
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109 sample_matrix_mean = rbind(c("mz_name", levels(msidata\$annotation)), sample_matrix_mean)
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110 write.table(sample_matrix_mean, file="$summarized_mean", quote = FALSE, row.names = FALSE, col.names=FALSE, sep = "\t")
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111 #end if
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112
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113 #if "median" in str($tabular_annotation.summary_type).split(","):
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114 print("summarized median")
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115
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116 sample_matrix = matrix(,ncol=0, nrow=nrow(msidata))
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117 count = 1
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118 for (subsample in levels(msidata\$annotation)){
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119 subsample_pixels = msidata[,msidata\$annotation == subsample]
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120 subsample_calc = apply(as.matrix(spectra(subsample_pixels)),1,median, na.rm=TRUE)
0
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121 sample_matrix = cbind(sample_matrix, subsample_calc)
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122 count = count+1}
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123 sample_matrix_median = cbind(mz_names,sample_matrix)
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124 sample_matrix_median = rbind(c("mz name", levels(msidata\$annotation)), sample_matrix_median)
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125 write.table(sample_matrix_median, file="$summarized_median", quote = FALSE, row.names = FALSE, col.names=FALSE, sep = "\t")
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126 #end if
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127
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128 #if "sd" in str($tabular_annotation.summary_type).split(","):
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129 print("summarized sd")
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130
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131 sample_matrix = matrix(,ncol=0, nrow=nrow(msidata))
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132 count = 1
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133 for (subsample in levels(msidata\$annotation)){
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134 subsample_pixels = msidata[,msidata\$annotation == subsample]
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135 subsample_calc = apply(as.matrix(spectra(subsample_pixels)),1,sd, na.rm=TRUE)
0
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136 sample_matrix = cbind(sample_matrix, subsample_calc)
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137 count = count+1}
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138 sample_matrix_sd = cbind(mz_names,sample_matrix)
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139 sample_matrix_sd = rbind(c("mz name", levels(msidata\$annotation)), sample_matrix_sd)
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140 write.table(sample_matrix_sd, file="$summarized_sd", quote = FALSE, row.names = FALSE, col.names=FALSE, sep = "\t")
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141 #end if
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142
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143 #end if
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144
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145
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146 ############################ spectra (pixel) output ############################
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147 #if "pixel_tabular" in str($output_options).split(","):
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148 print("pixel output")
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149
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150 ## coordinates
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151 xycoordinates = data.frame(coord(msidata)\$x, coord(msidata)\$y)
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152 colnames(xycoordinates) = c("x", "y")
0
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153
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154 ## pixel name
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155 pixel_names = paste0("xy_", coord(msidata)\$x, "_", coord(msidata)\$y)
0
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156
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157 ## Combine into dataframe; order is the same for all vectors
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158 spectra_df = data.frame(pixel_names,
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159 xycoordinates,
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160 1:length(pixels(msidata)), ##pixel order
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161 colSums(msidata_matrix>0, na.rm=TRUE), ##peaks per pixel
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162 round(apply(msidata_matrix, 2, median, na.rm=TRUE), digits = 2), ## median intensity
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163 round(colSums(msidata_matrix, na.rm=TRUE), digits = 2), ##TICs
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164 round(apply(msidata_matrix, 2, max, na.rm=TRUE), digits = 2), ##max intensity
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165 mz(msidata)[apply(msidata_matrix,2,which.max) ]) ##highest mz
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166
2
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167 colnames(spectra_df) = c("spectra_names", "x_values", "y_values","pixel_order", "peaks_per_spectrum", "median_intensity", "spectrum_TIC", "maximum_intensity", "most_abundant_mz")
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168
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169 #if str($counting_calibrants.pixel_with_calibrants) == "yes_calibrants":
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170
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171 calibrant_list = read.delim("$counting_calibrants.mz_tabular", header = $counting_calibrants.feature_header, na.strings=c("","NA"), stringsAsFactors = FALSE)
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172 calibrant_list = calibrant_list[,$counting_calibrants.feature_column, drop=FALSE]
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173
0
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174 ### calculate how many input calibrant m/z are valid:
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175 inputcalibrants = calibrant_list[calibrant_list[,1]>min(mz(msidata)) & calibrant_list[,1]<max(mz(msidata)),,drop = FALSE]
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176
0
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177 inputcalibrantmasses = inputcalibrants[,1]
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178
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179 ##QC plot number 2) Number of calibrants per spectrum
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180
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181 ## matrix with calibrants in columns and in rows if there is peak intensity in range or not
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182 pixelmatrix = matrix(ncol=ncol(msidata), nrow = 0)
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183
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184 if (length(inputcalibrantmasses) != 0){
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185
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186 ## calculate plusminus values in m/z for each calibrant
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187 plusminusvalues = rep($counting_calibrants.plusminus_ppm/1000000, length(inputcalibrantmasses))*inputcalibrantmasses
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188
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189 ## filter for m/z window of each calibrant and calculate if sum of peak intensities > 0
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190
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191 for (mass in 1:length(inputcalibrantmasses)){
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192 filtered_data = msidata[mz(msidata) >= inputcalibrantmasses[mass]-plusminusvalues[mass] & mz(msidata) <= inputcalibrantmasses[mass]+plusminusvalues[mass],]
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193 if (nrow(filtered_data) > 1 & sum(as.matrix(spectra(filtered_data)), na.rm=TRUE) > 0){
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194 ## intensity of all m/z > 0
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195 intensity_sum = colSums(as.matrix(spectra(filtered_data)), na.rm=TRUE) > 0
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196
17
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197 }else if(nrow(filtered_data) == 1 & sum(as.matrix(spectra(filtered_data)), na.rm=TRUE) > 0){
0
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198 ## intensity of only m/z > 0
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199 intensity_sum = as.matrix(spectra(filtered_data)) > 0
0
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200 }else{
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201 intensity_sum = rep(FALSE, ncol(filtered_data))}
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202 ## for each pixel add sum of intensities > 0 in the given m/z range
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203 pixelmatrix = rbind(pixelmatrix, intensity_sum)
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204 }
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205 ## for each pixel count TRUE (each calibrant m/z range with intensity > 0 is TRUE)
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206 countvector= as.factor(apply(pixelmatrix, 2,sum,na.rm=TRUE))
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207
0
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208 }else{countvector = rep(0,ncol(msidata))}
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209 countdf= cbind(coord(msidata)[,1:2], countvector) ## add pixel coordinates to counts
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210 colnames(countdf) = c("x_values", "y_values", "mz_count")
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211 spectra_df = merge(spectra_df, countdf, by=c("x_values", "y_values"))
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212
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213 ## sort columns to have spectra_names as rowname in first column
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214 spectra_df = spectra_df[c("spectra_names", "x_values", "y_values","pixel_order", "peaks_per_spectrum", "median_intensity", "spectrum_TIC", "maximum_intensity", "most_abundant_mz", "mz_count")]
0
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215
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216 #end if
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217 #if str($tabular_annotation.load_annotation) == 'yes_annotation':
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218
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219 colnames(annotation_input) = c("x_values", "y_values", "annotation")
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220 spectra_df = merge(spectra_df,annotation_input, by=c("x_values", "y_values"), all.x=TRUE)
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221
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222 ## sort columns to have spectra_names as rowname in first column
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223 #if str($counting_calibrants.pixel_with_calibrants) == "yes_calibrants":
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224 spectra_df = spectra_df[c("spectra_names", "x_values", "y_values","pixel_order", "peaks_per_spectrum", "median_intensity", "spectrum_TIC", "maximum_intensity", "most_abundant_mz", "mz_count", "annotation")]
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225 #else
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226 spectra_df = spectra_df[c("spectra_names", "x_values", "y_values","pixel_order", "peaks_per_spectrum", "median_intensity", "spectrum_TIC", "maximum_intensity", "most_abundant_mz", "annotation")]
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227 #end if
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228
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229 #end if
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230 ## sort rows according to original pixel order
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231 spectra_df = spectra_df[match(pixel_names, spectra_df\$spectra_names),]
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232
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233 ## Create list and output tabular
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234 write.table(spectra_df, file="$pixel_output", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
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235 #end if
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236
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237
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238 ]]></configfile>
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239 </configfiles>
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240 <inputs>
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241 <expand macro="reading_msidata"/>
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242 <param name="output_options" type="select" optional="False" multiple="true" label="Multiple output files can be selected">
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243 <option value="int_matrix" selected="True" >intensity matrix</option>
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244 <option value="mz_tabular">mz feature output</option>
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245 <option value="pixel_tabular">pixel output</option>
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246 </param>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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247 <conditional name="counting_calibrants">
2
e30d8b72415f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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parents: 0
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248 <param name="pixel_with_calibrants" type="select" label="Use file with m/z of interest to calculate their occurrence in each spectrum">
0
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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249 <option value="no_calibrants" selected="True">no</option>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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250 <option value="yes_calibrants">yes</option>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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251 </param>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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252 <when value="no_calibrants"/>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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253 <when value="yes_calibrants">
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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254 <expand macro="reading_1_column_mz_tabular" label="For each spectrum the occurrence of the provided m/z values is counted"/>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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255 <param name="plusminus_ppm" value="200" type="float" label="ppm range will be added in both directions to input m/z" help="The m/z window is used to search for peaks, if intensity > 0 found in the window the m/z is considered present, if all intensities are 0 the m/z is considered not present"/>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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256 </when>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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257 </conditional>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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258 <conditional name="tabular_annotation">
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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259 <param name="load_annotation" type="select" label="Pixel annotation can be used to summarize intensities per annotation group">
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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260 <option value="no_annotation" selected="True">no</option>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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261 <option value="yes_annotation">yes</option>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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262 </param>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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263 <when value="no_annotation"/>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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264 <when value="yes_annotation">
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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265 <expand macro="reading_pixel_annotations"/>
15
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266 <param name="summary_type" type="select" optional="False" multiple="true" label="Calculation for each m/z and all pixels of a annotation group" help="This step will only work if pixel annotations are provided">
0
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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267 <option value="mean">mean</option>
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268 <option value="median">median</option>
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269 <option value="sd">standard deviation</option>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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270 </param>
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271 </when>
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272 </conditional>
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273 </inputs>
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274 <outputs>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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275 <data format="tabular" name="intensity_matrix" label="${tool.name} on ${on_string}: intensity_matrix">
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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276 <filter>"int_matrix" in output_options</filter>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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277 </data>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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278 <data format="tabular" name="pixel_output" label="${tool.name} on ${on_string}: spectra">
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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279 <filter>"pixel_tabular" in output_options</filter>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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280 </data>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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281 <data format="tabular" name="feature_output" label="${tool.name} on ${on_string}: features">
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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282 <filter>"mz_tabular" in output_options</filter>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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283 </data>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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284 <data format="tabular" name="summarized_mean" label="${tool.name} on ${on_string}: group_mean">
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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285 <filter>tabular_annotation['load_annotation'] == 'yes_annotation' and 'mean' in tabular_annotation['summary_type']</filter>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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286 </data>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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287 <data format="tabular" name="summarized_median" label="${tool.name} on ${on_string}: group_median">
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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288 <filter>tabular_annotation['load_annotation'] == 'yes_annotation' and 'median' in tabular_annotation['summary_type']</filter>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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289 </data>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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290 <data format="tabular" name="summarized_sd" label="${tool.name} on ${on_string}: group_sd">
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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291 <filter>tabular_annotation['load_annotation'] == 'yes_annotation' and 'sd' in tabular_annotation['summary_type']</filter>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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292 </data>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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293 </outputs>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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294 <tests>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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295 <test expect_num_outputs="2">
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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296 <expand macro="infile_imzml"/>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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297 <param name="output_options" value="int_matrix,mz_tabular"/>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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298 <output name="intensity_matrix" file="int_matrix1.tabular"/>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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299 <output name="feature_output" file="features_out1.tabular"/>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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300 </test>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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301 <test expect_num_outputs="3">
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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302 <expand macro="infile_analyze75"/>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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303 <param name="output_options" value="pixel_tabular"/>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
304 <conditional name="tabular_annotation">
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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305 <param name="load_annotation" value="yes_annotation"/>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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306 <param name="annotation_file" value="annotations.tabular"/>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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307 <param name="column_x" value="1"/>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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308 <param name="column_y" value="2"/>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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309 <param name="column_names" value="4"/>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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310 <param name="tabular_header" value="True"/>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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311 <param name="summary_type" value="mean,sd"/>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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312 </conditional>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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313 <output name="pixel_output" file="pixel_out2.tabular"/>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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314 <output name="summarized_mean" file="mean_out2.tabular"/>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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315 <output name="summarized_sd" file="sd_out2.tabular"/>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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316 </test>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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317 <test expect_num_outputs="3">
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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318 <expand macro="infile_imzml"/>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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319 <param name="output_options" value="int_matrix,pixel_tabular,mz_tabular"/>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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320 <conditional name="counting_calibrants">
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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321 <param name="pixel_with_calibrants" value="yes_calibrants"/>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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322 <param name="mz_tabular" value="inputcalibrantfile2.txt"/>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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323 <param name="feature_column" value="1"/>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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324 <param name="feature_header" value="False"/>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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325 <param name="plusminus_ppm" value="200"/>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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326 </conditional>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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327 <output name="intensity_matrix" file="int_matrix3.tabular"/>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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328 <output name="feature_output" file="features_out3.tabular"/>
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329 <output name="pixel_output" file="pixel_out3.tabular"/>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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330 </test>
7
350a84ea795c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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331 <test expect_num_outputs="2">
350a84ea795c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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332 <expand macro="processed_infile_imzml"/>
350a84ea795c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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333 <conditional name="processed_cond">
350a84ea795c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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334 <param name="processed_file" value="processed"/>
9
a5d09f2daf71 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
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335 <param name="accuracy" value="200"/>
7
350a84ea795c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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336 <param name="units" value="ppm"/>
350a84ea795c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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337 </conditional>
350a84ea795c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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338 <param name="output_options" value="pixel_tabular,mz_tabular"/>
350a84ea795c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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339 <conditional name="counting_calibrants">
350a84ea795c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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340 <param name="pixel_with_calibrants" value="yes_calibrants"/>
350a84ea795c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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341 <param name="mz_tabular" ftype="tabular" value = "featuresofinterest5.tabular"/>
350a84ea795c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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342 <param name="feature_column" value="1"/>
350a84ea795c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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343 <param name="feature_header" value="False"/>
350a84ea795c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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344 <param name="plusminus_ppm" value="200"/>
350a84ea795c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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345 </conditional>
17
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346 <output name="feature_output">
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347 <assert_contents>
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348 <has_text text="100.120072029209"/>
56da27be956a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c
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349 </assert_contents>
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350 </output>
7
350a84ea795c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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351 <output name="pixel_output" file="pixel_out4.tabular"/>
350a84ea795c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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352 </test>
0
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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353 </tests>
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354 <help>
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355 <![CDATA[
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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356
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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357 @CARDINAL_DESCRIPTION@
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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358
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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359 -----
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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360
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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361 This tool provides multiple tabular output options for mass spectrometry imaging data files.
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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362
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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363 @MSIDATA_INPUT_DESCRIPTION@
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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364
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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365 @SPECTRA_TABULAR_INPUT_DESCRIPTION@
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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366
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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367 @MZ_TABULAR_INPUT_DESCRIPTION@
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368
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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369 **Output options**
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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370
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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371 - intensity matrix: m/z in rows, spectra in columns, filled with intensity values
2
e30d8b72415f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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372 - spectra output: spectra in rows - for each spectrum: name, x and y coordinates,order, number of peaks (intensities > 0), total ion chromatogram (TIC), median intensity, maximum intensity, highest m/z feature per spectrum, optional count of m/z per spectrum, optional spectrum annotation
0
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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373 - mz feature output: m/z in rows - for each m/z: name, m/z, mean, median, standard deviation (sd), standard error of the mean (sem), sum of all intensities per m/z, number of peaks (intensity > 0) per m/z
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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374 - summarized intensities: pixel annotations will be used to group spectra into annotation groups and calculate mean, median and sd of the intensities per group
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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375
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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376 ]]>
28ba52c9548c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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377 </help>
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378 <expand macro="citations"/>
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379 </tool>