Mercurial > repos > galaxyp > maldi_quant_preprocessing

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
author galaxyp
date Sat, 04 Mar 2023 19:13:31 +0000
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82b1de5c142b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
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1 <tool id="maldi_quant_preprocessing" name="MALDIquant preprocessing" version="@VERSION@.0">
3
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2 <description>
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3 Preprocessing of 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 cat '${maldi_quant_preprocessing}' &&
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12 #if $infile.ext == 'imzml'
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13 cp '${infile.extra_files_path}/imzml' infile.imzML &&
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14 cp '${infile.extra_files_path}/ibd' infile.ibd &&
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15 #elif $infile.ext == 'analyze75'
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16 cp '${infile.extra_files_path}/hdr' infile.hdr &&
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17 cp '${infile.extra_files_path}/img' infile.img &&
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18 cp '${infile.extra_files_path}/t2m' infile.t2m &&
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19 du infile.hdr &&
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20 du infile.img &&
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21 du -s -B1 infile.hdr &&
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22 #end if
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23 Rscript "${maldi_quant_preprocessing}" &&
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24
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25 mkdir $outfile_imzml.files_path &&
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26 mv ./out.imzMl "${os.path.join($outfile_imzml.files_path, 'imzml')}" | true &&
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27 mv ./out.ibd "${os.path.join($outfile_imzml.files_path, 'ibd')}" | true &&
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28 echo "imzML file:" > $outfile_imzml &&
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29 ls -l "$outfile_imzml.files_path" >> $outfile_imzml
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30 ]]>
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31 </command>
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32 <configfiles>
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33 <configfile name="maldi_quant_preprocessing"><![CDATA[
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34
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35 @R_IMPORTS@
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36
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37 #if $restriction_conditional.restriction == 'restrict':
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38
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39 print('Reading mask region')
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40 ## Import imzML file
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41
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42 coordinate_matrix = as.matrix(read.delim("$restriction_conditional.coordinates_file", header = $restriction_conditional.coordinates_header, stringsAsFactors = FALSE))[,1:2]
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43 coordinate_matrix = coordinate_matrix[,c($restriction_conditional.column_x, $restriction_conditional.column_y)]
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44
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45 maldi_data = importImzMl('infile.imzML',
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46 coordinates = coordinate_matrix)
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47 pixelnames = paste0("x = ", coordinates(maldi_data)[,1],", y = ", coordinates(maldi_data)[,2])
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48
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49 #else:
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50
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51 print('Reading entire file')
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52 #if $infile.ext == 'imzml'
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53 ## Import imzML file
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54 maldi_data = import( 'infile.imzML', type="imzML" )
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55 coordinates_info = cbind(coordinates(maldi_data)[,1:2], c(1:length(maldi_data)))
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56 #elif $infile.ext == 'analyze75'
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57 ## Import analyze7.5 file
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58 maldi_data = importAnalyze( 'infile.hdr' )
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59 coordinates_info = cbind(coordinates(maldi_data)[,1:2], c(1:length(maldi_data)))
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60 #end if
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61
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62 #end if
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63
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64 ## Quality control plots during preprocessing
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65
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66 pdf("prepro_qc_plot.pdf", fonts = "Times", pointsize = 12)
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67 plot(0,type='n',axes=FALSE,ann=FALSE)
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68
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69 ## if no filename is given, name of file in Galaxy history is used
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70 #set $filename = $infile.display_name
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71 title(main=paste("$filename"))
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72
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73
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74 #################### Preprocessing methods #####################################
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75
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76 ## QC plot on input file
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77 avgSpectra = averageMassSpectra(maldi_data,method="mean")
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78 plot(avgSpectra, main="Average spectrum for input file")
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79
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80 pixel_number = length(maldi_data)
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81 minmz = round(min(unlist(lapply(maldi_data,mass))), digits=4)
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82 maxmz = round(max(unlist(lapply(maldi_data,mass))), digits=4)
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83 mean_features = round(length(unlist(lapply(maldi_data,mass)))/length(maldi_data), digits=2)
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84 number_features = length(unique(unlist(lapply(maldi_data,mass))))
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85 medint = round(median(unlist(lapply(maldi_data,intensity))), digits=2)
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86 inputdata = c(minmz, maxmz,number_features,mean_features,medint, pixel_number)
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87 QC_numbers= data.frame(inputdata = c(minmz, maxmz,number_features, mean_features, medint, pixel_number))
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88 vectorofactions = "inputdata"
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89
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90
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91 #for $method in $methods:
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92
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93 #if str( $method.methods_conditional.method ) == 'Transformation':
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94
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95 print('transforming')
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96 ##transformation
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97 maldi_data = transformIntensity(maldi_data, method="$method.methods_conditional.transform_method")
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98 ## QC plot and numbers
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99 avgSpectra = averageMassSpectra(maldi_data,method="mean")
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100 plot(avgSpectra, main="Average spectrum after transformation")
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101 pixel_number = length(maldi_data)
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102 minmz = round(min(unlist(lapply(maldi_data,mass))), digits=4)
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103 maxmz = round(max(unlist(lapply(maldi_data,mass))), digits=4)
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104 mean_features = round(length(unlist(lapply(maldi_data,mass)))/length(maldi_data), digits=2)
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105 medint = round(median(unlist(lapply(maldi_data,intensity))), digits=2)
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106 number_features = length(unique(unlist(lapply(maldi_data,mass))))
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107 transformed = c(minmz, maxmz,number_features,mean_features,medint,pixel_number)
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108 QC_numbers= cbind(QC_numbers, transformed)
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109 vectorofactions = append(vectorofactions, "transformed")
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110
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111
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112 #elif str( $method.methods_conditional.method ) == 'Smoothing':
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113
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114 print('smoothing')
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115 ##smoothing
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116
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117 #if str($method.methods_conditional.methods_for_smoothing.smooth_method ) == 'SavitzkyGolay':
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118 print('SavitzkyGolay')
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119
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120 maldi_data = smoothIntensity(maldi_data,
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121 method="SavitzkyGolay", polynomialOrder=$method.methods_conditional.methods_for_smoothing.polynomial,
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122 halfWindowSize=$method.methods_conditional.halfWindowSize)
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123
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124 #elif str($method.methods_conditional.methods_for_smoothing.smooth_method ) == 'MovingAverage':
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125 print('MovingAverage')
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126
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127 maldi_data = smoothIntensity(maldi_data,
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128 method="MovingAverage", weighted=$method.methods_conditional.methods_for_smoothing.weighted,
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129 halfWindowSize=$method.methods_conditional.halfWindowSize)
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130
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131 #end if
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132
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133 ## QC plot and numbers
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134 avgSpectra = averageMassSpectra(maldi_data,method="mean")
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135 plot(avgSpectra, main="Average spectrum after smoothing", sub="")
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136 pixel_number = length(maldi_data)
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137 minmz = round(min(unlist(lapply(maldi_data,mass))), digits=4)
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138 maxmz = round(max(unlist(lapply(maldi_data,mass))), digits=4)
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139 mean_features = round(length(unlist(lapply(maldi_data,mass)))/length(maldi_data), digits=2)
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140 medint = round(median(unlist(lapply(maldi_data,intensity))), digits=2)
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141 number_features = length(unique(unlist(lapply(maldi_data,mass))))
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142 smoothed = c(minmz, maxmz,number_features,mean_features,medint,pixel_number)
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143 QC_numbers= cbind(QC_numbers, smoothed)
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144 vectorofactions = append(vectorofactions, "smoothed")
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145
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146
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147 #elif str( $method.methods_conditional.method ) == 'Baseline':
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148
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149 print('baseline removing')
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150 ## Remove baseline
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151
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152 ## Choose random spectra for QC plots
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153 random_spectra = sample(1:length(maldi_data), 4, replace=FALSE)
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154
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155 #if str($method.methods_conditional.methods_for_baseline.baseline_method ) == 'SNIP':
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156 print('SNIP')
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157
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158 par(mfrow = c(2,2))
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159 for (random_sample in random_spectra){
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160 maldi_data_baseline = estimateBaseline(maldi_data[[random_sample]],
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161 method="SNIP", iterations=$method.methods_conditional.methods_for_baseline.iterations)
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162 plot(maldi_data[[random_sample]], sub="", main=paste0("Estimated baseline for spectrum ", random_sample))
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163 lines(maldi_data_baseline, col="blue", lwd=2)}
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164
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165 maldi_data = removeBaseline(maldi_data,
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166 method="SNIP",
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167 iterations=$method.methods_conditional.methods_for_baseline.iterations)
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168
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169
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170 #elif str($method.methods_conditional.methods_for_baseline.baseline_method ) == 'TopHat':
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171 print('TopHat')
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172
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173 par(mfrow = c(2,2))
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174 for (random_sample in random_spectra){
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175 maldi_data_baseline = estimateBaseline(maldi_data[[random_sample]],
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176 method="TopHat", halfWindowSize=$method.methods_conditional.methods_for_baseline.tophat_halfWindowSize)
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177 plot(maldi_data[[random_sample]], sub="", main=paste0("Estimated baseline for spectrum ", random_sample))
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178 lines(maldi_data_baseline, col="blue", lwd=2)}
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179
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180 maldi_data = removeBaseline(maldi_data,
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181 method="TopHat",
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182 halfWindowSize=$method.methods_conditional.methods_for_baseline.tophat_halfWindowSize)
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183
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184
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185 #elif str($method.methods_conditional.methods_for_baseline.baseline_method ) == 'ConvexHull':
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186 print('ConvexHull')
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187
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188 par(mfrow = c(2,2))
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189 for (random_sample in random_spectra){
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190 maldi_data_baseline = estimateBaseline(maldi_data[[random_sample]],
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191 method="ConvexHull")
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192 plot(maldi_data[[random_sample]], sub="", main=paste0("Estimated baseline for spectrum ", random_sample))
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193 lines(maldi_data_baseline, col="blue", lwd=2)}
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194
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195 maldi_data = removeBaseline(maldi_data,
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196 method="ConvexHull")
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197
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198
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199 #elif str($method.methods_conditional.methods_for_baseline.baseline_method ) == 'median':
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200 print('median')
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201
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202 par(mfrow = c(2,2))
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203 for (random_sample in random_spectra){
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204 maldi_data_baseline = estimateBaseline(maldi_data[[random_sample]],
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205 method="median", halfWindowSize=$method.methods_conditional.methods_for_baseline.median_halfWindowSize)
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206 plot(maldi_data[[random_sample]], sub="", main=paste0("Estimated baseline for spectrum ", random_sample))
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207 lines(maldi_data_baseline, col="blue", lwd=2)}
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208
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209 maldi_data = removeBaseline(maldi_data,
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210 method="median",
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211 halfWindowSize=$method.methods_conditional.methods_for_baseline.median_halfWindowSize)
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212
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213 #end if
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214
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215 ## QC plot and numbers
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216 par(mfrow = c(1,1))
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217 avgSpectra = averageMassSpectra(maldi_data,method="mean")
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218 plot(avgSpectra, main="Average spectrum after baseline removal")
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219 pixel_number = length(maldi_data)
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220 minmz = round(min(unlist(lapply(maldi_data,mass))), digits=4)
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221 maxmz = round(max(unlist(lapply(maldi_data,mass))), digits=4)
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222 mean_features = round(length(unlist(lapply(maldi_data,mass)))/length(maldi_data), digits=2)
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223 medint = round(median(unlist(lapply(maldi_data,intensity))), digits=2)
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224 number_features = length(unique(unlist(lapply(maldi_data,mass))))
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225 baseline_removed = c(minmz, maxmz,number_features,mean_features,medint,pixel_number)
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226 QC_numbers= cbind(QC_numbers, baseline_removed)
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227 vectorofactions = append(vectorofactions, "bl_removed")
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228
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229
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230 #elif str( $method.methods_conditional.method ) == 'Calibrate':
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231
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232 print('calibrate')
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233 ##calibrate
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234
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235 #if str($method.methods_conditional.cond_calibration_range) == "yes":
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236 ## calibrate only given m/z range
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237 maldi_data = calibrateIntensity(maldi_data,
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238 method="$method.methods_conditional.calibrate_method",
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239 range=c($method.methods_conditional.cond_calibration_range.mass_start, $method.methods_conditional.cond_calibration_range.mass_end))
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240 #else:
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241 maldi_data = calibrateIntensity(maldi_data,
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242 method="$method.methods_conditional.calibrate_method")
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243 #end if
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244 ## QC plot and numbers
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245 avgSpectra = averageMassSpectra(maldi_data,method="mean")
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246 plot(avgSpectra, main="Average spectrum after normalization")
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247 pixel_number = length(maldi_data)
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248 minmz = round(min(unlist(lapply(maldi_data,mass))), digits=4)
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249 maxmz = round(max(unlist(lapply(maldi_data,mass))), digits=4)
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250 mean_features = round(length(unlist(lapply(maldi_data,mass)))/length(maldi_data), digits=2)
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251 medint = round(median(unlist(lapply(maldi_data,intensity))), digits=2)
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252 number_features = length(unique(unlist(lapply(maldi_data,mass))))
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253 intensity_calibrated = c(minmz, maxmz,number_features,mean_features,medint,pixel_number)
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254 QC_numbers= cbind(QC_numbers, intensity_calibrated)
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255 vectorofactions = append(vectorofactions, "calibrated")
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256
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257
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258 #elif str( $method.methods_conditional.method ) == 'Align':
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259
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260 print('align')
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261 ##align spectra with 3 separate functions
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262
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263 ## create reference if needed
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264
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265 ## 1) detect peaks:
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266 peaks <- detectPeaks(maldi_data, halfWindowSize=$method.methods_conditional.halfWindowSize,
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267 method="$method.methods_conditional.peak_method", SNR=$method.methods_conditional.snr)
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268
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269
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270 #if str($method.methods_conditional.reference_for_alignment.align_ref) == 'no_reference':
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271
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272 ## 2) calculate warping:
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273 warping_function <- determineWarpingFunctions(peaks,
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274 tolerance=$method.methods_conditional.tolerance, method="$method.methods_conditional.warping_method",
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275 allowNoMatches=$method.methods_conditional.allow_nomatch, minFrequency = $method.methods_conditional.reference_for_alignment.min_frequency)
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276
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277 ## 3) warp spectra:
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278 maldi_data = warpMassSpectra(maldi_data, warping_function, emptyNoMatches=$method.methods_conditional.empty_nomatch)
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279
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280
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281 #elif str($method.methods_conditional.reference_for_alignment.align_ref) == 'yes_reference':
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282
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283 ## create reference mass_vector from tabular file
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284 mass_vector = read.delim("$method.methods_conditional.reference_for_alignment.reference_file", header = $method.methods_conditional.reference_for_alignment.reference_header, stringsAsFactors = FALSE)[,$method.methods_conditional.reference_for_alignment.mz_column]
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285 int_vector = rep(1,length(mass_vector))
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286 mass_list = createMassPeaks(mass_vector, int_vector)
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287
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288 #if str($method.methods_conditional.reference_for_alignment.separate_alignment) == "FALSE"
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289 print('default alignment')
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290
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291 ## 2) calculate warping:
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292 warping_function <- determineWarpingFunctions(peaks,
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293 tolerance=$method.methods_conditional.tolerance, method="$method.methods_conditional.warping_method",
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294 allowNoMatches=$method.methods_conditional.allow_nomatch, reference = mass_list)
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295
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296 ## 3) warp spectra:
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297 maldi_data = warpMassSpectra(maldi_data, warping_function, emptyNoMatches=$method.methods_conditional.empty_nomatch)
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298
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299 #elif str($method.methods_conditional.reference_for_alignment.separate_alignment) == "TRUE"
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300 print('spectra wise alignment')
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301
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302 maldi_data_new_list =list()
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303
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304 for (pixelnb in 1:length(peaks))
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305 {
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306 ## 2) calculate warping:
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307 warping_function <- determineWarpingFunctions(peaks[[pixelnb]],
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308 tolerance=$method.methods_conditional.tolerance, method="$method.methods_conditional.warping_method",
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309 allowNoMatches=$method.methods_conditional.allow_nomatch, reference = mass_list)
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310
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311 ## 3) warp spectra:
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312 maldi_data_new = warpMassSpectra(list(maldi_data[[pixelnb]]), warping_function, emptyNoMatches=$method.methods_conditional.empty_nomatch)
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313 maldi_data_new_list = c(maldi_data_new_list, maldi_data_new)
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314
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315 }
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316 maldi_data = maldi_data_new_list
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317 #end if
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318 #end if
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319
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320
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321 #if $method.methods_conditional.remove_empty:
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322 print(paste(length(findEmptyMassObjects(maldi_data)), " empty spectra were removed", sep=" "))
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323
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324 ## only if there are empty spectra to remove
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325
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326 if (length(findEmptyMassObjects(maldi_data))>0)
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327
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328 {
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329 maldi_data = removeEmptyMassObjects(maldi_data)
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330 }
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331 #end if
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332
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333 ## QC plot
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334
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335 if (length(maldi_data)>0){
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336 avgSpectra = averageMassSpectra(maldi_data,method="mean")
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337 plot(avgSpectra, main="Average spectrum after alignment")
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338 medint = round(median(unlist(lapply(maldi_data,intensity))), digits=2)
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339 }else{print("All spectra are empty")}
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340
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341 pixel_number = length(maldi_data)
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342 minmz = round(min(unlist(lapply(maldi_data,mass))), digits=4)
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343 maxmz = round(max(unlist(lapply(maldi_data,mass))), digits=4)
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344 mean_features = round(length(unlist(lapply(maldi_data,mass)))/length(maldi_data), digits=2)
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345
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346 number_features = length(unique(unlist(lapply(maldi_data,mass))))
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347 spectra_aligned = c(minmz, maxmz,number_features,mean_features, medint,pixel_number)
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348 QC_numbers= cbind(QC_numbers, spectra_aligned)
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349 vectorofactions = append(vectorofactions, "aligned")
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350
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351 #elif str( $method.methods_conditional.method ) == 'skip_preprocessing':
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352 ##for now as option to filter large files
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353
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354 #end if
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355
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356 #end for
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357
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358 rownames(QC_numbers) = c("min m/z", "max mz", "# features", "median \n# peaks (int.>0)", "median\nintensity", "pixel\nnumber")
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359 colnames(QC_numbers) = vectorofactions
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360 plot(0,type='n',axes=FALSE,ann=FALSE)
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361 grid.table(t(QC_numbers))
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362
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363 dev.off()
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364
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365 ## export imzML file
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366 if (length(maldi_data)>0){
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367 MALDIquantForeign::exportImzMl(maldi_data, file="out.imzMl", processed=$export_processed)
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368
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369 }else{"All spectra are empty, outputfiles will be empty,too."}
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370
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371 ]]>
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372 </configfile>
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373 </configfiles>
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374 <inputs>
4
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375 <param name="infile" type="data" format="imzml,analyze75" label="MSI data" help="Input file as imzML (composite upload). The file must be in profile mode, not centroided."/>
3
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376 <conditional name="restriction_conditional">
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377 <param name="restriction" type="select" label="Use only spectra of interest" help="This option only works for imzML files">
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378 <option value="no_restriction" selected="True">No, calculate on entire file</option>
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379 <option value="restrict">Yes, restrict to spectra of interest</option>
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380 </param>
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381 <when value="restrict">
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382 <param name="coordinates_file" type="data" format="tabular" label="Tabular file with coordinates"/>
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383 <param name="column_x" data_ref="coordinates_file" label="Column with x values" type="data_column"/>
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384 <param name="column_y" data_ref="coordinates_file" label="Column with y values" type="data_column"/>
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385 <param name="coordinates_header" type="boolean" label="File contains a header line" truevalue="TRUE" falsevalue="FALSE"/>
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386 </when>
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387 <when value="no_restriction"/>
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388 </conditional>
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389 <repeat name="methods" title="Method" min="1">
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390 <conditional name="methods_conditional">
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391 <param name="method" type="select" label="Select a method">
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392 <option value="Transformation" selected="True">Transformation</option>
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393 <option value="Smoothing">Smoothing</option>
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394 <option value="Baseline">Baseline removal</option>
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395 <option value="Calibrate">Intensity calibration (normalization)</option>
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396 <option value="Align">Align spectra (warping/phase correction)</option>
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397 <option value="skip_preprocessing">Skip preprocessing</option>
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398 <validator type="empty_field" />
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399 </param>
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400 <when value="Transformation">
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401 <param name="transform_method" type="select" label="Transformation method">
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402 <option value="sqrt" selected="True">sqrt</option>
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403 <option value="log">log</option>
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404 <option value="log2">log2</option>
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405 <option value="log10">log10</option>
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406 <validator type="empty_field" />
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407 </param>
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408 </when>
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409 <when value="Smoothing">
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410 <conditional name="methods_for_smoothing">
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411 <param name="smooth_method" type="select" label="Smoothing method" help="This method smoothes the intensity values of a MassSpectrum object.">
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412 <option value="SavitzkyGolay" selected="True">SavitzkyGolay</option>
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413 <option value="MovingAverage">MovingAverage</option>
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414 </param>
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415 <when value="SavitzkyGolay">
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416 <param name="polynomial" value="3" type="text" label="Polynomial order"
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417 help="Controls the order of the filter, should be smaller than the resulting window."/>
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418 </when>
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419 <when value="MovingAverage">
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420 <param name="weighted" type="boolean" label="Weighted average" help = "Indicates if the average should be equal weight or if it should have weights depending on the distance from the center as calculated as 1/2^abs(-halfWindowSize:halfWindowSize) with the sum of all weigths normalized to 1" truevalue="TRUE" falsevalue="FALSE"/>
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421 </when>
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422 </conditional>
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423 <param name="halfWindowSize" type="integer" value="10"
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424 label="Half window size"
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425 help="Number of data points, the resulting window reaches from
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426 mass[currentIndex-halfWindowSize] to mass[currentIndex+halfWindowSize]
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427 (window size is 2*halfWindowSize+1)."/>
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428 </when>
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429 <when value="Baseline">
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430 <conditional name="methods_for_baseline">
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431 <param name="baseline_method" type="select" label="Baseline removal method">
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432 <option value="SNIP" selected="True">SNIP</option>
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433 <option value="TopHat">TopHat</option>
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434 <option value="ConvexHull">ConvexHull</option>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
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435 <option value="median">median</option>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
436 <validator type="empty_field" />
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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diff changeset
437 </param>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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diff changeset
438 <when value="SNIP">
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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439 <param name="iterations" type="integer" value="100"
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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diff changeset
440 label="Number of iterations" help="Corresponds to half window size: The resulting window reaches from mass[cur_index-iterations] to mass[cur_index+iterations]"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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441 </when>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
442 <when value="TopHat">
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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443 <param name="tophat_halfWindowSize" type="integer" value="10"
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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parents: 2
diff changeset
444 label="Half window size"
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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parents: 2
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445 help="Number of data points, the resulting window reaches from
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
446 mass[currentIndex-halfWindowSize] to mass[currentIndex+halfWindowSize]"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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447 </when>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
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448 <when value="ConvexHull"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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449 <when value="median">
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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450 <param name="median_halfWindowSize" type="integer" value="10"
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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451 label="Half window size"
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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452 help="Number of data points, the resulting window reaches from
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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parents: 2
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453 mass[currentIndex-halfWindowSize] to mass[currentIndex+halfWindowSize]"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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454 </when>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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455 </conditional>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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456 </when>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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457 <when value="Calibrate">
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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458 <param name="calibrate_method" type="select" label="Intensity calibration method" help="Intensity normalization">
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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459 <option value="TIC" selected="True">TIC</option>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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460 <option value="PQN">PQN</option>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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461 <option value="median">median</option>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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parents: 2
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462 <validator type="empty_field" />
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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diff changeset
463 </param>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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464 <conditional name="cond_calibration_range">
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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465 <param name="calibration_range" type="select" label="m/z range" help="Instead of the whole m/z range, a specified m/z range can be used to calculate the scaling factor.">
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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466 <option value="no" selected="True">complete m/z range</option>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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467 <option value="yes">specify a m/z range</option>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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468 </param>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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469 <when value="no"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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470 <when value="yes">
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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471 <param name="mass_start" type="integer" value="800"
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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472 label="Start of m/z range, has to be inside m/z range"
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473 help="Scaling factor is calculated on the mass range and applied to the whole spectrum."/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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474 <param name="mass_end" type="integer" value="3000"
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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475 label="End of m/z range, has to be inside m/z range"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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476 </when>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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477 </conditional>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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478 </when>
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diff changeset
479 <when value="Align">
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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480 <param name="warping_method" type="select" label="Alignment method">
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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481 <option value="lowess" selected="True">Lowess</option>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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482 <option value="linear">Linear</option>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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483 <option value="quadratic">Quadratic</option>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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484 <option value="cubic">Cubic</option>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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485 </param>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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486
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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487 <param name="tolerance" type="float" value="0.00005"
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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488 label="Tolerance"
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489 help="abs(mz1 - mz2)/mz2, maximal relative deviation of a peak position (m/z) to be considered as identical. For 50ppm use 0.00005 or 5e-5" />
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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490
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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491 <param name="halfWindowSize" type="integer" value="20"
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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492 label="Half window size"
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493 help="Number of data points, the resulting window reaches from
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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diff changeset
494 mass[currentIndex-halfWindowSize] to mass[currentIndex+halfWindowSize]
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495 (window size is 2*halfWindowSize+1).
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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496 The best size differs depending on the selected smoothing method."/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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diff changeset
497
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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diff changeset
498 <param name="peak_method" type="select" label="Noise estimation function">
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499 <option value="MAD" selected="True">MAD</option>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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500 <option value="SuperSmoother">SuperSmoother</option>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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501 </param>
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diff changeset
502
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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503 <param name="snr" type="integer" value="2" label="Signal-to-noise-ratio"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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504 <param name="allow_nomatch" type="boolean" label="Allow no matches" help="Don't throw an error when less than 2 reference m/z were found in a spectrum" truevalue="TRUE" falsevalue="FALSE"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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505 <param name="empty_nomatch" type="boolean" label="Empty no matches" help="If TRUE the intensity values of MassSpectrum or MassPeaks objects with missing (NA) warping functions are set to zero" truevalue="TRUE" falsevalue="FALSE"/>
4
82b1de5c142b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
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506 <param name="remove_empty" type="boolean" label="Remove empty spectra" truevalue="TRUE" falsevalue="FALSE"/>
3
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diff changeset
507
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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diff changeset
508 <conditional name="reference_for_alignment">
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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509 <param name="align_ref" type="select" label="Reference" help="If given, samples will be aligned to reference, use internal calibrants to perform m/z calibration">
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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510 <option value="no_reference" selected="True">no reference</option>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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511 <option value="yes_reference">reference from tabular file</option>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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diff changeset
512 </param>
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diff changeset
513 <when value="no_reference">
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514 <param name="min_frequency" type="float" value="0.9" label = "minFrequency" help="Removal of all peaks which occur in less than minFrequency spectra to generate the reference m/z"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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515 </when>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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516 <when value="yes_reference">
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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517 <param name="reference_file" type="data" format="tabular"
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518 label="Reference m/z values"
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diff changeset
519 help="Tabular file"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
520 <param name="mz_column" data_ref="reference_file" label="Column with m/z values" type="data_column"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
521 <param name="reference_header" type="boolean" label="File contains a header line" truevalue="TRUE" falsevalue="FALSE"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
522 <param name="separate_alignment" type="boolean" label="Spectrum wise alignment" help="Internal binning is omitted to avoid interaction between spectra" truevalue="TRUE" falsevalue="FALSE"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
523 </when>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
524 </conditional>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
525 </when>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
526 <when value="skip_preprocessing"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
527 </conditional>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
528 </repeat>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
529 <param name="export_processed" type="boolean" label="Export processed imzML" help="otherwise continuous imzML will be exported" truevalue="TRUE" falsevalue="FALSE"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
530 </inputs>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
531 <outputs>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
532 <data format="imzml" name="outfile_imzml" label="${tool.name} on ${on_string}" />
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
533 <data format="pdf" name="plots" from_work_dir="prepro_qc_plot.pdf" label="${tool.name} on ${on_string}: QC"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
534 </outputs>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
535 <tests>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
536 <test>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
537 <param name="infile" value="" ftype="imzml">
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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538 <composite_data value="Example_Continuous.imzML"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
539 <composite_data value="Example_Continuous.ibd"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
540 </param>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
541 <conditional name="restriction_conditional">
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
542 <param name="restriction" value="restrict"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
543 <param name="coordinates_file" value="restricted_pixels.tabular"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
544 <param name="column_x" value="1"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
545 <param name="column_y" value="2"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
546 </conditional>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
547 <conditional name="methods_conditional">
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
548 <param name="method" value="Transformation"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
549 <param name="transform_method" value="log2"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
550 <param name="method" value="Smoothing"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
551 <param name="smooth_method" value="SavitzkyGolay"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
552 <param name="method" value="Basline"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
553 <param name="baseline_method" value ="TopHat"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
554 </conditional>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
555 <output name="outfile_imzml" ftype="imzml" file="preprocessing1.imzml.txt" lines_diff="4">
4
82b1de5c142b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 3
diff changeset
556 <extra_files type="file" file="outfile1.imzml" name="imzml" lines_diff="8"/>
3
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
557 <extra_files type="file" file="outfile1.ibd" name="ibd" compare="sim_size"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
558 </output>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
559 <output name="plots" file="Preprocessing1_QC.pdf" compare="sim_size"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
560 </test>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
561 <test>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
562 <param name="infile" value="" ftype="imzml">
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
563 <composite_data value="Example_Continuous.imzML"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
564 <composite_data value="Example_Continuous.ibd"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
565 </param>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
566 <conditional name="methods_conditional">
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
567 <param name="method" value="Calibrate"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
568 <param name="calibrate_method" value="median"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
569 </conditional>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
570 <output name="outfile_imzml" ftype="imzml" file="preprocessing3.imzml.txt" lines_diff="4">
4
82b1de5c142b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 3
diff changeset
571 <extra_files type="file" file="outfile3.imzml" name="imzml" lines_diff="8"/>
3
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
572 <extra_files type="file" file="outfile3.ibd" name="ibd" compare="sim_size"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
573 </output>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
574 <output name="plots" file="Preprocessing3_QC.pdf" compare="sim_size"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
575 </test>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
576 </tests>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
577 <help><![CDATA[
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
578
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
579 @MADLI_QUANT_DESCRIPTION@
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
580
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
581 -----
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
582
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
583 **Input data**
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
584
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
585 - MSI data: 2 types of input data can be used:
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
586
4
82b1de5c142b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
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diff changeset
587 - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/imzml/>`_
3
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
588
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
589 - Optional: Tabular file with pixel coordinates to restrict reading of imzML files to coordinates of interest. Tabular files with any header name or no header at all are supported.
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
590
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
591 ::
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
592
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
593 x_coord y_coord
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
594 1 1
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
595 2 1
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
596 3 1
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
597 ...
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
598 ...
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
599
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
600 - Optional: Tabular file with reference m/z for the spectra align function. At least 2 m/z values of the input list must be present in every spectrum to peform the alignment. First column must contain m/z values, without empty fields or letters. Tabular files with any header name or no header at all are supported.
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
601
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
602 ::
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
603
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
604
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
605 m/z
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
606 100.0
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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607 100.01
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608 100.02
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609 ...
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610 ...
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aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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613
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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614 **Options**
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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615
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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616 - Transformation: Variance stabilization through intensity transformation:'log', 'log2', 'log10' and 'squareroot' (sqrt) are available
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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617 - Smoothing: Smoothing of the peaks reduces noise and improves peak detection. Available smoothing methods are 'SavitzkyGolay' and 'Moving Average'
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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618
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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619 - For all smoothing methods: The larger the 'Half window size', the stronger the smoothing. The resulting window should be smaller than the FWHM (full width at half maximum) of the typical peaks. Moving average needs smaller window size than SavitzkyGolay.
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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620 - Moving average: Recommended for broader peaks/high m/z range spectra. Weighted moving average: Points in the center get larger weight factors than points away from the center.
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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621 - SavitzkyGolay: Recommended for sharp peaks/low m/z range, preserves the shape of the local maxima. The PolynomialOrder should be smaller than the resulting window. Negative values will be replaced with 0.
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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622
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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623 - Baseline reduction: Baseline reduction removes background intensity generated by chemical noise (common in MALDI datasets).
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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624
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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625 - Available methods are SNIP, TopHat,ConvexHull and median:
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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626 - SNIP is the default baseline reduction method in MALDIquant.
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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627 - ConvexHull is not appropriate for MALDI-TOF baseline removal.
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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628 - The moving median may generate negative intensities.
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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629 - Except for the ConvexHull all methods have a parameter for the 'Half window size' (in SNIP it is called 'iterations'). The smaller the window the more baseline will be removed but also parts of the peaks. Wider windows preserve the peak height better and produce a smoother baseline, but some local background variation will remain.
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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630
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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631 - Intensity calibration (normalization): Normalization of intensities to Total Ion Current (TIC), median spectrum, Probabilistic Quotient Normalization (PQN)
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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632
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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633 - TIC and median are local calibration methods: each spectrum is normalized on its own (each peak is divided by the TIC or median of the spectrum)
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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634 - PQN is a global calibration method: In PQN all spectra are calibrated using the TIC calibration first. Subsequently, a median reference spectrum is created and the intensities in all spectra are standardized using the reference spectrum and a spectrum-specific median is calculated for each spectrum. Finally, each spectrum is rescaled by the median of the ratios of its intensity values and that of the reference spectrum
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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635
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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636 - Spectra alignment (warping): alignment for (re)calibration of m/z values.
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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637
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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638 - peak detection is performed, the reference peaks will be matched to those detected peaks
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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639 - without external reference m/z: internal reference is obtained by filtering and binning the picked peaks to find landmark peaks and their average m/z
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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640 - with external reference m/z: the given m/z are used as a reference, at least 10 reference values are recommended
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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641 - non linear warping (parametric time warping plus binning) to match the reference peaks (internal or external) to the present (picked) peaks with the given tolerance. At least two m/z per spectrum are needed for the alignment. To prevent an error when this criterium is not fullfilled, "Don't throw an error when less than 2 reference m/z were found in a spectrum" should be set to yes. If the not aligned spectra should be set to zero select yes in "If TRUE the intensity values of MassSpectrum or MassPeaks objects with missing (NA) warping functions are set to zero". In order to remove such empty spectra set "Should empty spectra be removed" to yes.
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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642
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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643
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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644 **Output**
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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645
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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646 - imzML file (imzML format can be continuous or processed)
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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647 - PDF with average mass spectra after each preprocessing step
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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648
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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649 .. _MALDIquant: http://strimmerlab.org/software/maldiquant/
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650
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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651 ]]>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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652 </help>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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653 <expand macro="citation"/>
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654 </tool>
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655