Mercurial > repos > galaxyp > maldi_quant_peak_detection

annotate maldi_quant_peakdetection.xml @ 2:17c54820f3be draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
author galaxyp
date Thu, 25 Oct 2018 07:32:17 -0400
parents eaaa73b043e6
children 36d38d2cf88c
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1 <tool id="maldi_quant_peak_detection" name="MALDIquant peak detection" version="@VERSION@.2">
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2 <description>
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3 Peak detection, binning and filtering for mass-spectrometry imaging data
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4 </description>
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5 <macros>
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6 <import>maldi_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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11 #if $infile.ext == 'imzml'
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12 cp '${infile.extra_files_path}/imzml' infile.imzML &&
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13 cp '${infile.extra_files_path}/ibd' infile.ibd &&
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14 #elif $infile.ext == 'analyze75'
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15 cp '${infile.extra_files_path}/hdr' infile.hdr &&
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16 cp '${infile.extra_files_path}/img' infile.img &&
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17 cp '${infile.extra_files_path}/t2m' infile.t2m &&
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18 #else
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19 ln -s $infile infile.RData &&
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20 #end if
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21 Rscript '${maldi_quant_peak_detection}'&&
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22 mkdir $outfile_imzml.files_path &&
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23 mv ./out.imzMl "${os.path.join($outfile_imzml.files_path, 'imzml')}" | true &&
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24 mv ./out.ibd "${os.path.join($outfile_imzml.files_path, 'ibd')}" | true &&
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25 echo "imzML file:" > $outfile_imzml &&
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26 ls -l "$outfile_imzml.files_path" >> $outfile_imzml
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27 ]]>
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28 </command>
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29 <configfiles>
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30 <configfile name="maldi_quant_peak_detection"><![CDATA[
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32 @R_IMPORTS@
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34 #if $restriction_conditional.restriction == 'restrict':
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36 print('Reading mask region')
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37
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38 ## Import imzML file
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39 coordinate_matrix = as.matrix(read.delim("$restriction_conditional.coordinates_file", header = $restriction_conditional.coordinates_header, stringsAsFactors = FALSE))[,1:2]
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41 maldi_data <- importImzMl('infile.imzML',
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42 coordinates = coordinate_matrix, centroided = $centroids)
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43 pixelnames = paste("xy", coordinates(maldi_data)[,1],coordinates(maldi_data)[,2], sep="_")
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44
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46 #else:
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47
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48 print('Reading entire file')
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49 ## Import imzML file
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51 #if $infile.ext == 'imzml'
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52 print('imzML file')
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53 #if str($centroids) == "TRUE"
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54 peaks <- importImzMl('infile.imzML', centroided = $centroids)
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55 pixelnames = paste("xy", coordinates(peaks)[,1],coordinates(peaks)[,2], sep="_")
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56 coordinates_info = cbind(coordinates(peaks)[,1:2], c(1:length(peaks)))
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57 #else
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58 maldi_data <- importImzMl('infile.imzML', centroided = $centroids)
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59 pixelnames = paste("xy", coordinates(maldi_data)[,1],coordinates(maldi_data)[,2], sep="_")
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60 coordinates_info = cbind(coordinates(maldi_data)[,1:2], c(1:length(maldi_data)))
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61 #end if
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62
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63
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64 #elif $infile.ext == 'tabular'
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65 print('tabular file')
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66 #set $centroids = "TRUE" ## will be used in some if conditions
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67 peak_tabular = read.delim("$infile", header = TRUE, stringsAsFactors = FALSE)
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68 peak_list = split(peak_tabular, f = peak_tabular\$spectrum) ## will be ordered according to spectrum
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69 pixelnames = unique(peak_tabular\$spectrum)
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70
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71 peaks = list()
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72 for (spectra in 1:length(peak_list))
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73 {
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74 single_peaks = createMassPeaks(peak_list[[spectra]]\$mass, peak_list[[spectra]]\$intensity, snr=peak_list[[spectra]]\$snr)
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75 peaks[[spectra]] = single_peaks
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76 }
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77
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78 #else
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79 print('rdata file')
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80 loadRData <- function(fileName){
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81 #loads an RData file, and returns it
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82 load(fileName)
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83 get(ls()[ls() != "fileName"])
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84 }
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85 msidata = loadRData('infile.RData')
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86 centroided(msidata) = $centroids
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87 ## change to correct pixelnames
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88
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89 x_coords = unlist(lapply(strsplit(names(Cardinal::pixels(msidata)), ","), `[[`, 1))
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90 y_coords = unlist(lapply(strsplit(names(Cardinal::pixels(msidata)), ","), `[[`, 2))
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91 x_coordinates = gsub("x = ","",x_coords)
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92 y_coordinates = gsub(" y = ","",y_coords)
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93 pixelnames = paste0("xy_", x_coordinates, "_", y_coordinates)
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94
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95 cardinal_coordinates = as.matrix(Cardinal::coord(msidata)[,1:2])
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96
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97 if (centroided(msidata) == FALSE){
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98 ## create mass spectrum object
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99 cardinal_mzs = Cardinal::mz(msidata)
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100 maldi_data = list()
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101 for(number_spectra in 1:ncol(msidata)){
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102 maldi_data[[number_spectra]] = createMassSpectrum(mass = cardinal_mzs, intensity = iData(msidata)[,number_spectra])
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103 coordinates_info = cbind(cardinal_coordinates, c(1:length(maldi_data)))}
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104 }else{
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105 peaks = list()
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106 for (spectra in 1:ncol(msidata))
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107 {
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108 single_peaks = createMassPeaks(Cardinal::mz(msidata), Cardinal::spectra(msidata)[,spectra], snr=as.numeric(rep("NA", nrow(msidata))))
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109 peaks[[spectra]] = single_peaks
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110 }}
0
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111 #end if
1
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112 #end if
0
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113
1
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114 ## default summarized = FALSE
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115 summarized_spectra = FALSE
0
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116
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117 ## Quality control plots during peak detection
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118 pdf("peaks_qc_plot.pdf", fonts = "Times", pointsize = 12)
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119 plot(0,type='n',axes=FALSE,ann=FALSE)
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120
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121 ## if no filename is given, name of file in Galaxy history is used
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122 #set $filename = $infile.display_name
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123
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124 title(main=paste("$filename"))
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125
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126 ## plot input file spectrum:
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127 #if $centroids:
1
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128 plot(peaks[[1]], main="First spectrum of input file")
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129 #else
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130 avgSpectra <- averageMassSpectra(maldi_data,method="mean")
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131 plot(avgSpectra, main="Average spectrum of input file")
0
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132 #end if
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133
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134
1
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135 ## QC numbers for input file
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136 #if str($centroids) == "TRUE"
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137 pixel_number = length(peaks)
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138 minmz = round(min(unlist(lapply(peaks,mass))), digits=4)
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139 maxmz = round(max(unlist(lapply(peaks,mass))), digits=4)
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140 mean_features = round(length(unlist(lapply(peaks,mass)))/length(peaks), digits=2)
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141 medint = round(median(unlist(lapply(peaks,intensity))), digits=2)
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142 number_features = length(unique(unlist(lapply(peaks,mass))))
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143 inputdata = c(minmz, maxmz,number_features,mean_features, medint)
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144 QC_numbers= data.frame(inputdata = c(minmz, maxmz,number_features, mean_features, medint))
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145 vectorofactions = "inputdata"
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146 #else
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147 pixel_number = length(maldi_data)
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148 minmz = round(min(unlist(lapply(maldi_data,mass))), digits=4)
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149 maxmz = round(max(unlist(lapply(maldi_data,mass))), digits=4)
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150 mean_features = round(length(unlist(lapply(maldi_data,mass)))/length(maldi_data), digits=2)
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151 medint = round(median(unlist(lapply(maldi_data,intensity))), digits=2)
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152 number_features = length(unique(unlist(lapply(maldi_data,mass))))
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153 inputdata = c(minmz, maxmz,number_features,mean_features, medint)
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154 QC_numbers= data.frame(inputdata = c(minmz, maxmz,number_features, mean_features, medint))
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155 vectorofactions = "inputdata"
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156 #end if
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157
0
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158 #if str($tabular_annotation.load_annotation) == 'yes_annotation':
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159
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160 ## read and extract x,y,annotation information
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161 input_tabular = read.delim("$tabular_annotation.annotation_file", header = $tabular_annotation.tabular_header, stringsAsFactors = FALSE)
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162 annotation_input = input_tabular[,c($tabular_annotation.column_x, $tabular_annotation.column_y, $tabular_annotation.column_names)]
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163 colnames(annotation_input) = c("x", "y", "annotation") ## rename annotations header to default name "annotation"
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164
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165 ## merge with coordinate information of MSI data
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166 colnames(coordinates_info)[3] = "pixel_index"
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167 merged_annotation = merge(coordinates_info, annotation_input, by=c("x", "y"), all.x=TRUE)
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168 merged_annotation[is.na(merged_annotation)] = "NA"
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169 merged_annotation = merged_annotation[order(merged_annotation\$pixel_index),]
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170 samples = as.factor(merged_annotation\$annotation)
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171
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172 ## print annotation overview into PDF output
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173
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174 combine_plot = ggplot(merged_annotation, aes(x=x, y=y, fill=annotation))+
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175 geom_tile() +
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176 coord_fixed()+
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177 ggtitle("Spatial orientation of annotated data")+
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178 theme_bw()+
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179 theme(plot.title = element_text(hjust = 0.5))+
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180 theme(text=element_text(family="ArialMT", face="bold", size=12))+
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181 theme(legend.position="bottom",legend.direction="vertical")+
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182 theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = 8))+
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183 theme(legend.position="bottom",legend.direction="vertical")+
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184 guides(fill=guide_legend(ncol=4,byrow=TRUE))
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185
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186 print(combine_plot)
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187
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188 #end if
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189
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190 #################### Preprocessing methods #####################################
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191
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192 #for $method in $methods:
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193
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194 #if str( $method.methods_conditional.method ) == 'Peak_detection':
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195 print('peak detection')
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196 ##peak detection
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197
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198 #if $method.methods_conditional.use_annotations:
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199 maldi_data <- averageMassSpectra(maldi_data, labels=samples,method="mean") ## use average spectra for peak picking
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200 pixelnames = levels(samples)
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201 summarized_spectra = TRUE
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202
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203 #end if
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204
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205 peaks <- detectPeaks(maldi_data, method="$method.methods_conditional.peak_method",
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206 halfWindowSize=$method.methods_conditional.halfWindowSize,SNR=$method.methods_conditional.snr)
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207
1
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208 ## QC plot and numbers
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209 ## plot old spectrum with baseline in blue and picked peaks in green
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210 noise = estimateNoise(maldi_data[[1]], method= "$method.methods_conditional.peak_method")
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211 plot(maldi_data[[1]], main="First spectrum with noise line (blue) and picked peaks (green)")
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212 lines(noise[,1], noise[,2]*$method.methods_conditional.snr, col="blue")
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213 points(peaks[[1]], col="green", pch=20)
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214 ## plot new spectrum
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215 plot(peaks[[1]], main="First spectrum after peak detection")
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216 pixel_number = length(peaks)
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217 minmz = round(min(unlist(lapply(peaks,mass))), digits=4)
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218 maxmz = round(max(unlist(lapply(peaks,mass))), digits=4)
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219 mean_features = round(length(unlist(lapply(peaks,mass)))/length(peaks), digits=2)
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220 medint = round(median(unlist(lapply(peaks,intensity))), digits=2)
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221 number_features = length(unique(unlist(lapply(peaks,mass))))
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222 peaks_picked = c(minmz, maxmz,number_features,mean_features, medint)
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223 QC_numbers= cbind(QC_numbers, peaks_picked)
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224 vectorofactions = append(vectorofactions, "peaks_picked")
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225
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226 if (length(peaks[!sapply(peaks, isEmpty)])>0){
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227 featureMatrix <- intensityMatrix(peaks)
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228 #if $infile.ext == 'imzml'
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229 #if str($centroids) == "FALSE"
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230 featureMatrix <- intensityMatrix(peaks, maldi_data)
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231 #end if
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232 #end if
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233 featureMatrix2 =cbind(pixelnames, featureMatrix)
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234 colnames(featureMatrix2)[1] = c("mz")
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235 featureMatrix2 = t(featureMatrix2)
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236 write.table(featureMatrix2, file="$intensity_matrix", quote = FALSE, row.names = TRUE, col.names=FALSE, sep = "\t")
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237 }else{print("There are no spectra with peaks left")}
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238
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239
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240 #elif str( $method.methods_conditional.method ) == 'monoisotopic_peaks':
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241
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242 print('monoisotopic peaks')
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243 ##monoisotopic peaks
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244
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245 peaks = monoisotopicPeaks(peaks, minCor=$method.methods_conditional.minCor, tolerance=$method.methods_conditional.tolerance, distance=$method.methods_conditional.distance, size=$method.methods_conditional.size)
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246
1
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247 ## QC plot and numbers
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248 ## plot old spectrum with picked isotopes as green dots
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249 plot(peaks[[1]], main="First spectrum with picked monoisotopic peaks (green)")
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250 points(peaks[[1]], col="green", pch=20)
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251 ## plot new spectrum
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252 plot(peaks[[1]], main="First spectrum after monoisotopic peaks detection")
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253 minmz = round(min(unlist(lapply(peaks,mass))), digits=4)
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254 maxmz = round(max(unlist(lapply(peaks,mass))), digits=4)
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255 mean_features = round(length(unlist(lapply(peaks,mass)))/length(peaks), digits=2)
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256 medint = round(median(unlist(lapply(peaks,intensity))), digits=2)
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257 number_features = length(unique(unlist(lapply(peaks,mass))))
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258 monoisotopes = c(minmz, maxmz,number_features,mean_features, medint)
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259 QC_numbers= cbind(QC_numbers, monoisotopes)
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260 vectorofactions = append(vectorofactions, "monoisotopes")
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261
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262 if (length(peaks[!sapply(peaks, isEmpty)])>0){
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263 featureMatrix <- intensityMatrix(peaks)
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264 ## only for profile imzML file: featurematrix is overwritten:
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265 #if $infile.ext == 'imzml'
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266 #if str($centroids) == "FALSE"
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267 featureMatrix <- intensityMatrix(peaks, maldi_data)
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268 #end if
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269 #end if
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270 featureMatrix2 =cbind(pixelnames, featureMatrix)
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271 colnames(featureMatrix2)[1] = c("mz")
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272 featureMatrix2 = t(featureMatrix2)
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273 write.table(featureMatrix2, file="$intensity_matrix", quote = FALSE, row.names = TRUE, col.names=FALSE, sep = "\t")
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274 }else{print("There are no spectra with peaks left")}
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275
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276 #elif str( $method.methods_conditional.method ) == 'Binning':
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277
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278 print('binning')
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279 ##m/z binning
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280
2
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281 peaks <- binPeaks(peaks, tolerance=$method.methods_conditional.bin_tolerance, method="$method.methods_conditional.bin_method")
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282
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283 ## QC plot and numbers
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284 plot(peaks[[1]], main="First spectrum after binning")
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285 minmz = round(min(unlist(lapply(peaks,mass))), digits=4)
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286 maxmz = round(max(unlist(lapply(peaks,mass))), digits=4)
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287 mean_features = round(length(unlist(lapply(peaks,mass)))/length(peaks), digits=2)
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288 medint =round( median(unlist(lapply(peaks,intensity))), digits=2)
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289 number_features = length(unique(unlist(lapply(peaks,mass))))
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290 binned = c(minmz, maxmz,number_features,mean_features, medint)
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291 QC_numbers= cbind(QC_numbers, binned)
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292 vectorofactions = append(vectorofactions, "binned")
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293
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294 if (length(peaks[!sapply(peaks, isEmpty)])>0){
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295 featureMatrix <- intensityMatrix(peaks)
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296 #if $infile.ext == 'imzml'
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297 #if str($centroids) == "FALSE"
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298 featureMatrix <- intensityMatrix(peaks, maldi_data)
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299 #elif str($centroids) == "TRUE"
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300 featureMatrix <- intensityMatrix(peaks)
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301 #end if
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302 #end if
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303 featureMatrix2 =cbind(pixelnames, featureMatrix)
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304 colnames(featureMatrix2)[1] = c("mz")
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305 featureMatrix2 = t(featureMatrix2)
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306 write.table(featureMatrix2, file="$intensity_matrix", quote = FALSE, row.names = TRUE, col.names=FALSE, sep = "\t")
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307 }else{print("There are no spectra with peaks left")}
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308
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309
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310 #elif str( $method.methods_conditional.method ) == 'Filtering':
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311
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312 print('filtering')
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313 ##m/z filtering
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314
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315 ## filtering on all pixels or on pixel groups:
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316 #if str($method.methods_conditional.filter_annot_groups ) == 'FALSE':
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317
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318 peaks <- filterPeaks(peaks,
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319 minFrequency=$method.methods_conditional.minFrequency,
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320 minNumber=$method.methods_conditional.minNumber,
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321 mergeWhitelists=$method.methods_conditional.mergeWhitelists)
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322
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323 #elif str( $method.methods_conditional.filter_annot_groups ) == 'TRUE':
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324
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325 peaks <- filterPeaks(peaks,
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326 minFrequency=$method.methods_conditional.minFrequency,
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327 minNumber=$method.methods_conditional.minNumber,
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328 mergeWhitelists=$method.methods_conditional.mergeWhitelists, label = samples)
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329 #end if
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330
1
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331 ##QC plot and numbers
0
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332 plot(peaks[[1]], main="First spectrum after m/z filtering")
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333 minmz = round(min(unlist(lapply(peaks,mass))), digits=4)
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334 maxmz = round(max(unlist(lapply(peaks,mass))), digits=4)
2
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335 mean_features = round(length(unlist(lapply(peaks,mass)))/length(peaks), digits=2)
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336 medint = round(median(unlist(lapply(peaks,intensity))), digits=2)
2
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337 number_features = length(unique(unlist(lapply(peaks,mass))))
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338 filtered = c(minmz, maxmz,number_features,mean_features, medint)
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339 QC_numbers= cbind(QC_numbers, filtered)
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340 vectorofactions = append(vectorofactions, "filtered")
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341
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342 if (length(peaks[!sapply(peaks, isEmpty)])>0){
2
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343 featureMatrix <- intensityMatrix(peaks)
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344 #if $infile.ext == 'imzml'
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345 #if str($centroids) == "FALSE"
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346 featureMatrix <- intensityMatrix(peaks, maldi_data)
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347 #end if
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348 #end if
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349 featureMatrix2 =cbind(pixelnames, featureMatrix)
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350 colnames(featureMatrix2)[1] = c("mz")
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351 featureMatrix2 = t(featureMatrix2)
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352 }else{print("There are no spectra with peaks left")
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353 featureMatrix2 = matrix(0, ncol=1, nrow=1)}
0
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354 write.table(featureMatrix2, file="$intensity_matrix", quote = FALSE, row.names = TRUE, col.names=FALSE, sep = "\t")
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355 #end if
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356 #end for
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357
1
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358 if (length(peaks[!sapply(peaks, isEmpty)])>0){
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359 ## mass peaks output
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360 mass_peaks = data.frame(matrix(,ncol=3, nrow=0))
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361 for (spectrum in 1:length(peaks)){
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362 spectrum_df = data.frame(peaks[[spectrum]]@snr, peaks[[spectrum]]@mass, peaks[[spectrum]]@intensity)
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363 spectrum_df\$spectrum_id = rep(pixelnames[[spectrum]], length(peaks[[spectrum]]@mass))
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364 mass_peaks = rbind(mass_peaks,spectrum_df)
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365 }
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366 colnames(mass_peaks) = c("snr", "mass", "intensity", "spectrum")
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367 write.table(mass_peaks, file="$masspeaks", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
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368 }else{print("There are no spectra with peaks left")}
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369
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370 ## print table with QC values
2
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371 rownames(QC_numbers) = c("min m/z", "max mz", "# features", "median \n# features", "median\nintensity")
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372 plot(0,type='n',axes=FALSE,ann=FALSE)
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373 grid.table(t(QC_numbers))
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374
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375 dev.off()
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376
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377 if (summarized_spectra == FALSE){
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378 #if $infile.ext == 'imzml'
1
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379 MALDIquantForeign::exportImzMl(peaks, file="out.imzMl", processed=$export_processed)
0
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380 #elif $infile.ext == 'tabular'
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381 masspeaks_coordinates = matrix(unlist(strsplit(as.character(pixelnames), "\\_")), ncol=3, byrow=TRUE)
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382 ## extract x and y values and create the coordinate matrix in case tabular was input
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383 peaklist_coordinates = unique(cbind(as.numeric(masspeaks_coordinates[,2]), as.numeric(masspeaks_coordinates[,3])))
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384 exportImzMl(peaks, file="out.imzMl", processed=$export_processed, coordinates=peaklist_coordinates)
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385 #elif $infile.ext == 'rdata'
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386 MALDIquantForeign::exportImzMl(peaks, file="out.imzMl", processed=$export_processed, coordinates=cardinal_coordinates)
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387 #end if
1
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388
0
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389 }
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390
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391 ]]>
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392 </configfile>
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393 </configfiles>
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394 <inputs>
2
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395 <param name="infile" type="data" format="imzml,tabular,rdata" label="Inputfile as imzML, peaklist or Cardinal MSImageSet saved as RData" help="imzML or tabular format (peak list) or Cardinal MSImageSet saved as RData"/>
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396 <param name="centroids" type="boolean" label="Input data is centroided (picked)" help="Choose Yes if peak detection has already been done. Peak detection cannot be run again on centroided data" truevalue="TRUE" falsevalue="FALSE"/>
0
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397 <conditional name="restriction_conditional">
1
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398 <param name="restriction" type="select" label="Read in only spectra of interest" help="This option only works for imzML files">
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399 <option value="no_restriction" selected="True">Calculate on entire file</option>
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400 <option value="restrict">Restrict to coordinates of interest</option>
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401 </param>
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402 <when value="restrict">
1
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403 <param name="coordinates_file" type="data" format="tabular" label="Tabular file with coordinates" help="x-values in first column, y-values in second column"/>
2
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404 <param name="coordinates_header" type="boolean" label="File contains a header line" truevalue="TRUE" falsevalue="FALSE"/>
0
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405 </when>
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406 <when value="no_restriction"/>
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407 </conditional>
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408
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409 <conditional name="tabular_annotation">
2
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410 <param name="load_annotation" type="select" label="Pixels have annotations" help="Annotations can be used during peak detection or filteringfsplit">
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411 <option value="no_annotation" selected="True">pixels have no annotations</option>
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412 <option value="yes_annotation">pixel annotation from file</option>
0
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diff changeset
413 </param>
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414 <when value="yes_annotation">
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415 <param name="annotation_file" type="data" format="tabular" label="Use annotations from tabular file"
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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416 help="Tabular file with three columns: x values, y values and pixel annotations"/>
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417 <param name="column_x" data_ref="annotation_file" label="Column with x values" type="data_column"/>
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diff changeset
418 <param name="column_y" data_ref="annotation_file" label="Column with y values" type="data_column"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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419 <param name="column_names" data_ref="annotation_file" label="Column with pixel annotations" type="data_column"/>
2
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420 <param name="tabular_header" type="boolean" label="File contains a header line" truevalue="TRUE" falsevalue="FALSE"/>
0
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diff changeset
421 </when>
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diff changeset
422 <when value="no_annotation"/>
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diff changeset
423 </conditional>
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diff changeset
424 <repeat name="methods" title="Method" min="1">
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diff changeset
425 <conditional name="methods_conditional">
1
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426 <param name="method" type="select" label="Select a method">
0
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427 <option value="Peak_detection">Peak detection</option>
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428 <option value="monoisotopic_peaks">Keep only monoisotopic peaks</option>
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429 <option value="Binning">Binning</option>
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430 <option value="Filtering">Filtering</option>
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diff changeset
431 </param>
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diff changeset
432 <when value="Peak_detection">
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433 <param name="peak_method" type="select" label="Noise estimation function">
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434 <option value="MAD" selected="True">MAD</option>
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435 <option value="SuperSmoother">SuperSmoother</option>
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diff changeset
436 </param>
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437 <param name="halfWindowSize" type="integer" value="20"
2
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438 label="Half window size (number of data points)"
0
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diff changeset
439 help="The resulting window reaches from
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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diff changeset
440 mass[currentIndex-halfWindowSize] to mass[currentIndex+halfWindowSize]
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diff changeset
441 (window size is 2*halfWindowSize+1).
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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diff changeset
442 The best size differs depending on the selected smoothing method."/>
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diff changeset
443 <param name="snr" type="integer" value="2" label="Signal-to-noise-ratio" help=""/>
2
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444 <param name="use_annotations" type="boolean" label="Detect peaks on average mass spectra" help="Spectra with same annotation are averaged before peak detection, no imzML output" truevalue="TRUE" falsevalue="FALSE"/>
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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445 </when>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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446 <when value="monoisotopic_peaks">
2
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447 <param name="minCor" type="float" value="0.95" label="Minimal correlation"
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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448 help="Minimal correlation between the peak pattern generated by the model and the experimental peaks in the MassPeaks object to be recognized as isotopic pattern"/>
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449 <param name="tolerance" type="float" label="Tolerance" value="0.00005"
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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450 help="Maximal relative deviation of a peak position (m/z) to be considered as identical: abs(((mass[i]+distance)-mass[i+1])/mass[i]) smaller than 'tolerance'. For 50ppm use 0.00005 or 50e-6" />
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451 <param name="distance" type="float" label="Distance" value="1.00235" help="Distance between two consecutive peaks in an isotopic pattern. 1.00235 is average distance for polypeptides."/>
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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452 <param name="size" type="integer" label="Size" value="3" help="Size (length) of isotopic pattern, longer patterns are prefered over shorter ones, min size is 2."/>
0
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453 </when>
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454 <when value="Binning">
2
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455 <param name="bin_tolerance" type="float" value="0.002" label="Binning tolerance"
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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456 help="After the alignment the peak positions (mass) are very similar but not identical. The binning is needed to make similar peak mass values identical."/>
2
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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457 <param name="bin_method" display="radio" type="select" label="Bin creation rule" help="strict - creates bins never containing two or more peaks of the sampe sample. relaxed - allows multiple peaks of the same sample in one bin.">
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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458 <option value="strict" selected="True" >strict</option>
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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459 <option value="relaxed" >relaxed</option>
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diff changeset
460 </param>
0
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461 </when>
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diff changeset
462 <when value="Filtering">
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463 <param name="minFrequency" type="float" value="0.25"
2
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464 label="Removal of all peaks which occur in less than minFrequency spectra" help="Relative threshold. The higher value from relative and absolute threshold is taken. Set one value to zero to be sure it will not be used."/>
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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465 <param name="minNumber" type="float" value="1.0"
2
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466 label="Removal of all peaks which occur in less than minNumber spectra" help="Absolute threshold. The higher value from relative and absolute threshold is taken. Set one value to zero to be sure it will not be used."/>
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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467 <param name="filter_annot_groups" type="boolean" label="Group wise filtering with pixel annotations." help="If not specified a single group is assumed or when filtering has been done group wise it will automatically be group wise when selecting filtering on all pixel" truevalue="TRUE" falsevalue="FALSE"/>
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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468 <param name="mergeWhitelists" type="boolean" truevalue="TRUE" falsevalue="FALSE"
2
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469 label="mergeWhitelists" help="Yes means that peaks that survive the filtering in one annotation group are also kept in other groups regardless if the filtering criteria are met in these groups"/>
0
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470 </when>
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471 </conditional>
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472 </repeat>
2
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473 <param name="export_processed" type="boolean" label="Export file as processed imzML" help="otherwise continuous imzML will be exported" checked="True" truevalue="TRUE" falsevalue="FALSE"/>
0
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474 </inputs>
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475 <outputs>
2
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476 <data format="imzml" name="outfile_imzml" label="${tool.name} on ${on_string}">
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477 <!--filter>methods_conditional['method'] == 'Peak_detection'</filter-->
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diff changeset
478 </data>
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479 <data format="pdf" name="plots" from_work_dir="peaks_qc_plot.pdf" label = "${tool.name} on ${on_string}: QC"/>
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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480 <data format="tabular" name="masspeaks" label="${tool.name} on ${on_string}: peaklist"/>
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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481 <data format="tabular" name="intensity_matrix" label="${tool.name} on ${on_string}: intensity_matrix"/>
0
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482 </outputs>
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diff changeset
483 <tests>
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484 <test>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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485 <param name="infile" value="" ftype="imzml">
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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486 <composite_data value="Example_Continuous.imzML"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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diff changeset
487 <composite_data value="Example_Continuous.ibd"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
488 </param>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
489 <conditional name="tabular_annotation">
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
490 <param name="load_annotation" value="yes_annotation"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
491 <param name="annotation_file" value="pixel_annotations.tabular"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
492 <param name="column_x" value="1"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
493 <param name="column_y" value="2"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
494 <param name="column_names" value="3"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
495 <param name="tabular_header" value="TRUE"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
496 </conditional>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
497 <repeat name="methods">
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
498 <conditional name="methods_conditional">
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
499 <param name="method" value="Peak_detection"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
500 <param name="peak_method" value="SuperSmoother"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
501 <param name="halfWindowSize" value="1"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
502 <param name="snr" value="5"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
503 <param name="use_annotations" value="TRUE"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
504 </conditional>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
505 </repeat>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
506 <output name="plots" file="peakdetection1_QC.pdf" compare="sim_size"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
507 <output name="masspeaks" file="masspeaks1.tabular"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
508 <output name="intensity_matrix" file="int1.tabular"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
509 </test>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
510 <test>
1
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
511 <param name="infile" value="masspeaks3_forinput.tabular"/>
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
512 <param name="centroids" value="TRUE"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
513 <repeat name="methods">
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
514 <conditional name="methods_conditional">
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
515 <param name="method" value="monoisotopic_peaks"/>
2
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
516 <param name="tolerance" value="0.0004"/>
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
517 </conditional>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
518 </repeat>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
519 <output name="plots" file="peakdetection2_QC.pdf" compare="sim_size"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
520 <output name="masspeaks" file="masspeaks2.tabular"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
521 <output name="intensity_matrix" file="int2.tabular"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
522 </test>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
523 <test>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
524 <param name="infile" value="" ftype="imzml">
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
525 <composite_data value="Example_Continuous.imzML"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
526 <composite_data value="Example_Continuous.ibd"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
527 </param>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
528 <conditional name="tabular_annotation">
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
529 <param name="load_annotation" value="yes_annotation"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
530 <param name="annotation_file" value="pixel_annotations.tabular"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
531 <param name="column_x" value="1"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
532 <param name="column_y" value="2"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
533 <param name="column_names" value="3"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
534 <param name="tabular_header" value="TRUE"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
535 </conditional>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
536 <repeat name="methods">
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
537 <conditional name="methods_conditional">
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
538 <param name="method" value="Peak_detection"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
539 <param name="peak_method" value="MAD"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
540 <param name="halfWindowSize" value="1"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
541 <param name="snr" value="2"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
542 </conditional>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
543 </repeat>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
544 <repeat name="methods">
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
545 <conditional name="methods_conditional">
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
546 <param name="method" value="Binning"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
547 <param name="bin_tolerance" value="0.01"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
548 </conditional>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
549 </repeat>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
550 <repeat name="methods">
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
551 <conditional name="methods_conditional">
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
552 <param name="method" value="Filtering"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
553 <param name="minFrequency" value="0.5"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
554 <param name="minNumber" value="3"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
555 <param name="filter_annot_groups" value="TRUE"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
556 <param name="mergeWhitelists" value="FALSE"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
557 </conditional>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
558 </repeat>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
559 <output name="plots" file="peakdetection3_QC.pdf" compare="sim_size"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
560 <output name="intensity_matrix" file="intensity_matrix3.tabular"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
561 <output name="masspeaks" file="masspeaks3.tabular"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
562 </test>
2
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
563 <test>
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
564 <param name="infile" value="testfile_squares.rdata" ftype="rdata"/>
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
565 <param name="method" value="Peak_detection"/>
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
566 <param name="peak_method" value="MAD"/>
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
567 <param name="halfWindowSize" value="20"/>
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
568 <param name="snr" value="2"/>
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
569 <output name="plots" file="peakdetection4_QC.pdf" compare="sim_size"/>
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
570 <output name="intensity_matrix" file="intensity_matrix4.tabular"/>
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
571 <output name="masspeaks" file="masspeaks4.tabular"/>
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
572 </test>
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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573 </tests>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
574 <help>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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575 <![CDATA[
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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576
1
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
577 @MADLI_QUANT_DESCRIPTION@
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
578
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
579 -----
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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580
1
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
581 **Input data**
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
582
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
583 - MSI data: 3 types of input data can be used:
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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diff changeset
584
1
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
585 - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/wp/imzml/>`_
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
586 - Cardinal "MSImageSet" data saved as .RData
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
587 - MSI data as peak list (tabular file) with the columns named "snr", "mass", "intensity" and "spectrum". The spectrum has to be in the following format: xy_1_1 (for pixel coordinates x1y1). The header must have exactly the four column names.
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
588
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
589 ::
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
590
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
591 snr mass intensity spectrum
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
592 5.34 304.16 0.10 xy_1_1
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
593 12.09 305 0.2 xy_1_1
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
594 6.80 306.25 0.133 xy_1_1
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
595 ...
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
596 ...
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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diff changeset
597
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
598
1
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
599 - Optional: Tabular file with pixel coordinates to restrict reading of imzML files to coordinates of interest. The file has to contain x values in the first column and y values in the second columns. Further columns are allowed. Tabular files with any header name or no header at all are supported.
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
600
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
601 ::
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
602
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
603 x_coord y_coord
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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604 1 1
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
605 2 1
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
606 3 1
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
607 ...
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
608 ...
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
609
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
610
2
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
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diff changeset
611 - Optional: Tabular file(s) containing pixel coordinates and annotation. X and y values in separate columns and the corresponding annotation in a third column. Tabular files with any header name or no header at all are supported. The annotations can be used to either detect peak on the average mass spectrum of each annotation group ('Detect peaks on average mass spectra') or to filter for peaks within pixel groups ('Group wise filtering'). This option is not compatible with tabular peak list inputs.
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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diff changeset
612
1
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
613 ::
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
614
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
615 x_coord y_coord annotation
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
616 1 1 healthy
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
617 2 1 healthy
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
618 3 1 disease
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
619 ...
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
620 ...
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
621
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
622 **Options**
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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623
2
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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diff changeset
624 - Peak detection: detection of peaks, only possible with profile mode input. A peak is a local maximum above a user defined noise threshold.
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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diff changeset
625
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
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diff changeset
626 - Two functions exist to estimate the noise: MAD and supersmoother.
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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diff changeset
627 - SNR is an abbreviation for signal-to-noise-ratio. A local maximum has to be higher than SNR*noise to be recognize as peak.
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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628 - 'halfWindowSize': The resulting window reaches from mass[currentIndex-halfWindowSize] to mass[currentIndex+halfWindowSize]. A local maximum has to be the highest one in the given window to be recognized as peak.
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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629 - Detect peaks on average mass spectra: Spectra with the same annotation (taken from the annotation tabular input) are averaged and peak picking is performed on the average spectrum of each annotation group. The exported imzML is empty and cannot be used for further analysis steps. The peaklist and intensity matrix outputs contain the annotation group names with their averaged intensity values. Filtering steps have to be done in the same run as the peak picking.
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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diff changeset
630
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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diff changeset
631
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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632 - Monoisotopic peaks: detection of monoisotopic peaks
2
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633
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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diff changeset
634
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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diff changeset
635
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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diff changeset
636
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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diff changeset
637 - Peak binning: After the alignment the peak positions (m/z) are very similar but not identical. The binning is needed to make similar peak m/z values identical. The algorithm is based on the following workflow:
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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diff changeset
638
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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diff changeset
639 1. Put all mass in a sorted vector.
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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diff changeset
640 2. Calculate differences between each neighbor.
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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641 3. Divide the mass vector at the largest gap (largest difference) and form a left and a right bin.
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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642 4. Rerun step 3 for the left and/or the right bin if they don't fulfill the following criteria:
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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643
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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644 - All peaks in a bin are near to the mean (abs(mass-meanMass)/meanMass < tolerance).
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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645 - method == "strict": The bin doesn't contain two or more peaks of the same sample.
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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diff changeset
646
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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diff changeset
647
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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diff changeset
648 - Peak filtering: Removal of less frequent m/z features:
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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diff changeset
649
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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diff changeset
650 - minFrequency : between 0 and 1: m/z has to occur in 0 - 100% of all spectra; minNumber: m/z has to occur in at least this amount of spectra --> out of those two criteria the stricter value will be used
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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diff changeset
651 - Group wise filtering with pixel annotations: 'Yes' means that the filtering criteria are applied for each annotation group separately.
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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diff changeset
652 - mergeWhitelists: 'Yes' means that peaks that survive the filtering in one annotation group are also kept in other groups regardless if the filtering criteria are met in these groups
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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653 - To filter data that was averaged before peak detection: Filtering has to be done in the same tool run as the peak detection. The filtering criteria are automatically applied per annotation group (Group wise filtering can be 'No') and not per pixel. Example: to keep only m/z that were detected in at least half of all annotation groups set minFrequency to 0.5.
0
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654
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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655
1
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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656 **Output**
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01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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657
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17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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658 - centroided imzML file (processed or continuous), imzML file is empty when 'Detect peaks on average mass spectra' is chosen.
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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659 - pdf with mass spectra plots after each preprocessing step and a table with key values after each preprocessing step
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01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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660 - peak list (tabular file) with the columns "snr", "mass", "intensity" and "spectrum"
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17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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661 - tabular file with intensity matrix (m/z in rows and spectra in columns). If the input file was imzML in profile mode the intensities before peak picking are also stored in the matrix . For all other inputs not picked values are set to NA. For peak picking on the average of multiple spectra, each spectra group is a column with mean intensities for each m/z.
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01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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662
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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663 .. _MALDIquant: http://strimmerlab.org/software/maldiquant/
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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664
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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665 ]]>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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666 </help>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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667 <expand macro="citation"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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668 </tool>