Mercurial > repos > galaxyp > maldi_quant_preprocessing

annotate maldi_quant_preprocessing.xml @ 3:aa81463e21ea draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
author galaxyp
date Fri, 15 Feb 2019 10:13:30 -0500
parents 3f3812d36027
children 82b1de5c142b
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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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1 <tool id="maldi_quant_preprocessing" name="MALDIquant preprocessing" version="@VERSION@.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 #else
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23 ln -s $infile infile.RData &&
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24 #end if
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25 Rscript "${maldi_quant_preprocessing}" &&
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26
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27 mkdir $outfile_imzml.files_path &&
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28 mv ./out.imzMl "${os.path.join($outfile_imzml.files_path, 'imzml')}" | true &&
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29 mv ./out.ibd "${os.path.join($outfile_imzml.files_path, 'ibd')}" | true &&
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30 echo "imzML file:" > $outfile_imzml &&
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31 ls -l "$outfile_imzml.files_path" >> $outfile_imzml
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32 ]]>
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33 </command>
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34 <configfiles>
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35 <configfile name="maldi_quant_preprocessing"><![CDATA[
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36
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37 @R_IMPORTS@
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38
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39 #if $restriction_conditional.restriction == 'restrict':
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40
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41 print('Reading mask region')
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42 ## Import imzML file
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43
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44 coordinate_matrix = as.matrix(read.delim("$restriction_conditional.coordinates_file", header = $restriction_conditional.coordinates_header, stringsAsFactors = FALSE))[,1:2]
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45 coordinate_matrix = coordinate_matrix[,c($restriction_conditional.column_x, $restriction_conditional.column_y)]
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46
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47 maldi_data = importImzMl('infile.imzML',
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48 coordinates = coordinate_matrix)
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49 pixelnames = paste0("x = ", coordinates(maldi_data)[,1],", y = ", coordinates(maldi_data)[,2])
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50
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51 #else:
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52
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53 print('Reading entire file')
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54 #if $infile.ext == 'imzml'
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55 ## Import imzML file
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56 maldi_data = import( 'infile.imzML', type="imzML" )
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57 coordinates_info = cbind(coordinates(maldi_data)[,1:2], c(1:length(maldi_data)))
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58 #elif $infile.ext == 'analyze75'
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59 ## Import analyze7.5 file
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60 maldi_data = importAnalyze( 'infile.hdr' )
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61 coordinates_info = cbind(coordinates(maldi_data)[,1:2], c(1:length(maldi_data)))
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62 #else
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63 loadRData <- function(fileName){
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64 ##loads an RData file, and returns it
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65 load(fileName)
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66 get(ls()[ls() != "fileName"])
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67 }
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68 msidata = loadRData('infile.RData')
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69 ## save coordinates
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70 cardinal_coordinates = as.matrix(Cardinal::coord(msidata)[,1:2])
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71 ## save mz values
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72 cardinal_mzs = Cardinal::mz(msidata)
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73 ## create MALDIquant MassSpectrum object, order of pixels in iData is same as in coord(msidata):
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74 maldi_data = list()
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75 for(number_spectra in 1:ncol(msidata)){
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76 maldi_data[[number_spectra]] = MALDIquant::createMassSpectrum(mass = cardinal_mzs, intensity = iData(msidata)[,number_spectra])
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77 }
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78 #end if
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79
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80 #end if
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81
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82 ## Quality control plots during preprocessing
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83
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84 pdf("prepro_qc_plot.pdf", fonts = "Times", pointsize = 12)
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85 plot(0,type='n',axes=FALSE,ann=FALSE)
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86
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87 ## if no filename is given, name of file in Galaxy history is used
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88 #set $filename = $infile.display_name
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89 title(main=paste("$filename"))
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90
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91
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92 #################### Preprocessing methods #####################################
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93
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94 ## QC plot on input file
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95 avgSpectra = averageMassSpectra(maldi_data,method="mean")
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96 plot(avgSpectra, main="Average spectrum for input file")
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97
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98 pixel_number = length(maldi_data)
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99 minmz = round(min(unlist(lapply(maldi_data,mass))), digits=4)
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100 maxmz = round(max(unlist(lapply(maldi_data,mass))), digits=4)
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101 mean_features = round(length(unlist(lapply(maldi_data,mass)))/length(maldi_data), digits=2)
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102 number_features = length(unique(unlist(lapply(maldi_data,mass))))
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103 medint = round(median(unlist(lapply(maldi_data,intensity))), digits=2)
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104 inputdata = c(minmz, maxmz,number_features,mean_features,medint, pixel_number)
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105 QC_numbers= data.frame(inputdata = c(minmz, maxmz,number_features, mean_features, medint, pixel_number))
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106 vectorofactions = "inputdata"
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107
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108
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109 #for $method in $methods:
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110
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111 #if str( $method.methods_conditional.method ) == 'Transformation':
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112
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113 print('transforming')
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114 ##transformation
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115 maldi_data = transformIntensity(maldi_data, method="$method.methods_conditional.transform_method")
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116 ## QC plot and numbers
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117 avgSpectra = averageMassSpectra(maldi_data,method="mean")
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118 plot(avgSpectra, main="Average spectrum after transformation")
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119 pixel_number = length(maldi_data)
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120 minmz = round(min(unlist(lapply(maldi_data,mass))), digits=4)
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121 maxmz = round(max(unlist(lapply(maldi_data,mass))), digits=4)
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122 mean_features = round(length(unlist(lapply(maldi_data,mass)))/length(maldi_data), digits=2)
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123 medint = round(median(unlist(lapply(maldi_data,intensity))), digits=2)
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124 number_features = length(unique(unlist(lapply(maldi_data,mass))))
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125 transformed = c(minmz, maxmz,number_features,mean_features,medint,pixel_number)
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126 QC_numbers= cbind(QC_numbers, transformed)
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127 vectorofactions = append(vectorofactions, "transformed")
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128
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129
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130 #elif str( $method.methods_conditional.method ) == 'Smoothing':
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131
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132 print('smoothing')
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133 ##smoothing
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134
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135 #if str($method.methods_conditional.methods_for_smoothing.smooth_method ) == 'SavitzkyGolay':
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136 print('SavitzkyGolay')
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137
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138 maldi_data = smoothIntensity(maldi_data,
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139 method="SavitzkyGolay", polynomialOrder=$method.methods_conditional.methods_for_smoothing.polynomial,
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140 halfWindowSize=$method.methods_conditional.halfWindowSize)
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141
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142 #elif str($method.methods_conditional.methods_for_smoothing.smooth_method ) == 'MovingAverage':
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143 print('MovingAverage')
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144
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145 maldi_data = smoothIntensity(maldi_data,
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146 method="MovingAverage", weighted=$method.methods_conditional.methods_for_smoothing.weighted,
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147 halfWindowSize=$method.methods_conditional.halfWindowSize)
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148
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149 #end if
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150
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151 ## QC plot and numbers
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152 avgSpectra = averageMassSpectra(maldi_data,method="mean")
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153 plot(avgSpectra, main="Average spectrum after smoothing", sub="")
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154 pixel_number = length(maldi_data)
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155 minmz = round(min(unlist(lapply(maldi_data,mass))), digits=4)
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156 maxmz = round(max(unlist(lapply(maldi_data,mass))), digits=4)
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157 mean_features = round(length(unlist(lapply(maldi_data,mass)))/length(maldi_data), digits=2)
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158 medint = round(median(unlist(lapply(maldi_data,intensity))), digits=2)
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159 number_features = length(unique(unlist(lapply(maldi_data,mass))))
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160 smoothed = c(minmz, maxmz,number_features,mean_features,medint,pixel_number)
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161 QC_numbers= cbind(QC_numbers, smoothed)
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162 vectorofactions = append(vectorofactions, "smoothed")
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163
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164
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165 #elif str( $method.methods_conditional.method ) == 'Baseline':
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166
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167 print('baseline removing')
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168 ## Remove baseline
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169
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170 ## Choose random spectra for QC plots
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171 random_spectra = sample(1:length(maldi_data), 4, replace=FALSE)
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172
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173 #if str($method.methods_conditional.methods_for_baseline.baseline_method ) == 'SNIP':
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174 print('SNIP')
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175
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176 par(mfrow = c(2,2))
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177 for (random_sample in random_spectra){
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178 maldi_data_baseline = estimateBaseline(maldi_data[[random_sample]],
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179 method="SNIP", iterations=$method.methods_conditional.methods_for_baseline.iterations)
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180 plot(maldi_data[[random_sample]], sub="", main=paste0("Estimated baseline for spectrum ", random_sample))
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181 lines(maldi_data_baseline, col="blue", lwd=2)}
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182
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183 maldi_data = removeBaseline(maldi_data,
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184 method="SNIP",
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185 iterations=$method.methods_conditional.methods_for_baseline.iterations)
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186
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187
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188 #elif str($method.methods_conditional.methods_for_baseline.baseline_method ) == 'TopHat':
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189 print('TopHat')
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190
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191 par(mfrow = c(2,2))
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192 for (random_sample in random_spectra){
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193 maldi_data_baseline = estimateBaseline(maldi_data[[random_sample]],
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194 method="TopHat", halfWindowSize=$method.methods_conditional.methods_for_baseline.tophat_halfWindowSize)
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195 plot(maldi_data[[random_sample]], sub="", main=paste0("Estimated baseline for spectrum ", random_sample))
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196 lines(maldi_data_baseline, col="blue", lwd=2)}
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197
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198 maldi_data = removeBaseline(maldi_data,
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199 method="TopHat",
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200 halfWindowSize=$method.methods_conditional.methods_for_baseline.tophat_halfWindowSize)
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201
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202
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203 #elif str($method.methods_conditional.methods_for_baseline.baseline_method ) == 'ConvexHull':
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204 print('ConvexHull')
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205
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206 par(mfrow = c(2,2))
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207 for (random_sample in random_spectra){
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208 maldi_data_baseline = estimateBaseline(maldi_data[[random_sample]],
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209 method="ConvexHull")
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210 plot(maldi_data[[random_sample]], sub="", main=paste0("Estimated baseline for spectrum ", random_sample))
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211 lines(maldi_data_baseline, col="blue", lwd=2)}
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212
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213 maldi_data = removeBaseline(maldi_data,
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214 method="ConvexHull")
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215
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216
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217 #elif str($method.methods_conditional.methods_for_baseline.baseline_method ) == 'median':
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218 print('median')
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219
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220 par(mfrow = c(2,2))
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221 for (random_sample in random_spectra){
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222 maldi_data_baseline = estimateBaseline(maldi_data[[random_sample]],
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223 method="median", halfWindowSize=$method.methods_conditional.methods_for_baseline.median_halfWindowSize)
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224 plot(maldi_data[[random_sample]], sub="", main=paste0("Estimated baseline for spectrum ", random_sample))
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225 lines(maldi_data_baseline, col="blue", lwd=2)}
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226
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227 maldi_data = removeBaseline(maldi_data,
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228 method="median",
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229 halfWindowSize=$method.methods_conditional.methods_for_baseline.median_halfWindowSize)
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230
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231 #end if
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232
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233 ## QC plot and numbers
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234 par(mfrow = c(1,1))
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235 avgSpectra = averageMassSpectra(maldi_data,method="mean")
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236 plot(avgSpectra, main="Average spectrum after baseline removal")
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237 pixel_number = length(maldi_data)
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238 minmz = round(min(unlist(lapply(maldi_data,mass))), digits=4)
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239 maxmz = round(max(unlist(lapply(maldi_data,mass))), digits=4)
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240 mean_features = round(length(unlist(lapply(maldi_data,mass)))/length(maldi_data), digits=2)
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241 medint = round(median(unlist(lapply(maldi_data,intensity))), digits=2)
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242 number_features = length(unique(unlist(lapply(maldi_data,mass))))
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243 baseline_removed = c(minmz, maxmz,number_features,mean_features,medint,pixel_number)
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244 QC_numbers= cbind(QC_numbers, baseline_removed)
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245 vectorofactions = append(vectorofactions, "bl_removed")
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246
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247
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248 #elif str( $method.methods_conditional.method ) == 'Calibrate':
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249
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250 print('calibrate')
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251 ##calibrate
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252
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253 #if str($method.methods_conditional.cond_calibration_range) == "yes":
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254 ## calibrate only given m/z range
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255 maldi_data = calibrateIntensity(maldi_data,
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256 method="$method.methods_conditional.calibrate_method",
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257 range=c($method.methods_conditional.cond_calibration_range.mass_start, $method.methods_conditional.cond_calibration_range.mass_end))
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258 #else:
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259 maldi_data = calibrateIntensity(maldi_data,
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260 method="$method.methods_conditional.calibrate_method")
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261 #end if
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262 ## QC plot and numbers
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263 avgSpectra = averageMassSpectra(maldi_data,method="mean")
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264 plot(avgSpectra, main="Average spectrum after normalization")
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265 pixel_number = length(maldi_data)
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266 minmz = round(min(unlist(lapply(maldi_data,mass))), digits=4)
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267 maxmz = round(max(unlist(lapply(maldi_data,mass))), digits=4)
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268 mean_features = round(length(unlist(lapply(maldi_data,mass)))/length(maldi_data), digits=2)
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269 medint = round(median(unlist(lapply(maldi_data,intensity))), digits=2)
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270 number_features = length(unique(unlist(lapply(maldi_data,mass))))
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271 intensity_calibrated = c(minmz, maxmz,number_features,mean_features,medint,pixel_number)
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272 QC_numbers= cbind(QC_numbers, intensity_calibrated)
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273 vectorofactions = append(vectorofactions, "calibrated")
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274
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275
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276 #elif str( $method.methods_conditional.method ) == 'Align':
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277
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278 print('align')
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279 ##align spectra with 3 separate functions
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280
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281 ## create reference if needed
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282
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283 ## 1) detect peaks:
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284 peaks <- detectPeaks(maldi_data, halfWindowSize=$method.methods_conditional.halfWindowSize,
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285 method="$method.methods_conditional.peak_method", SNR=$method.methods_conditional.snr)
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286
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287
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288 #if str($method.methods_conditional.reference_for_alignment.align_ref) == 'no_reference':
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289
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290 ## 2) calculate warping:
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291 warping_function <- determineWarpingFunctions(peaks,
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292 tolerance=$method.methods_conditional.tolerance, method="$method.methods_conditional.warping_method",
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293 allowNoMatches=$method.methods_conditional.allow_nomatch, minFrequency = $method.methods_conditional.reference_for_alignment.min_frequency)
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294
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295 ## 3) warp spectra:
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296 maldi_data = warpMassSpectra(maldi_data, warping_function, emptyNoMatches=$method.methods_conditional.empty_nomatch)
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297
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298
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299 #elif str($method.methods_conditional.reference_for_alignment.align_ref) == 'yes_reference':
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300
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301 ## create reference mass_vector from tabular file
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302 mass_vector = read.delim("$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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303 int_vector = rep(1,length(mass_vector))
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304 mass_list = createMassPeaks(mass_vector, int_vector)
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305
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306 #if str($method.methods_conditional.reference_for_alignment.separate_alignment) == "FALSE"
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307 print('default alignment')
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308
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309 ## 2) calculate warping:
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310 warping_function <- determineWarpingFunctions(peaks,
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311 tolerance=$method.methods_conditional.tolerance, method="$method.methods_conditional.warping_method",
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312 allowNoMatches=$method.methods_conditional.allow_nomatch, reference = mass_list)
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313
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314 ## 3) warp spectra:
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315 maldi_data = warpMassSpectra(maldi_data, warping_function, emptyNoMatches=$method.methods_conditional.empty_nomatch)
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316
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317 #elif str($method.methods_conditional.reference_for_alignment.separate_alignment) == "TRUE"
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318 print('spectra wise alignment')
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319
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320 maldi_data_new_list =list()
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321
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322 for (pixelnb in 1:length(peaks))
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323 {
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324 ## 2) calculate warping:
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325 warping_function <- determineWarpingFunctions(peaks[[pixelnb]],
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326 tolerance=$method.methods_conditional.tolerance, method="$method.methods_conditional.warping_method",
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327 allowNoMatches=$method.methods_conditional.allow_nomatch, reference = mass_list)
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328
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329 ## 3) warp spectra:
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330 maldi_data_new = warpMassSpectra(list(maldi_data[[pixelnb]]), warping_function, emptyNoMatches=$method.methods_conditional.empty_nomatch)
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331 maldi_data_new_list = c(maldi_data_new_list, maldi_data_new)
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332
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333 }
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334 maldi_data = maldi_data_new_list
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335 #end if
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336 #end if
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337
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338
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339 #if $method.methods_conditional.remove_empty:
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340 print(paste(length(findEmptyMassObjects(maldi_data)), " empty spectra were removed", sep=" "))
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341
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342 ## only if there are empty spectra to remove
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343
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344 if (length(findEmptyMassObjects(maldi_data))>0)
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345
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346 {
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347 #if $infile.ext == 'rdata'
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348 cardinal_coordinates = cardinal_coordinates[-findEmptyMassObjects(maldi_data),,drop=FALSE] ## remove coordinates of empty spectra for Cardinal RData input
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349 #end if
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350
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351 maldi_data = removeEmptyMassObjects(maldi_data)
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352 }
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353 #end if
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354
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355 ## QC plot
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356
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357 if (length(maldi_data)>0){
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358 avgSpectra = averageMassSpectra(maldi_data,method="mean")
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359 plot(avgSpectra, main="Average spectrum after alignment")
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360 medint = round(median(unlist(lapply(maldi_data,intensity))), digits=2)
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361 }else{print("All spectra are empty")}
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362
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363 pixel_number = length(maldi_data)
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364 minmz = round(min(unlist(lapply(maldi_data,mass))), digits=4)
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365 maxmz = round(max(unlist(lapply(maldi_data,mass))), digits=4)
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366 mean_features = round(length(unlist(lapply(maldi_data,mass)))/length(maldi_data), digits=2)
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367
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368 number_features = length(unique(unlist(lapply(maldi_data,mass))))
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369 spectra_aligned = c(minmz, maxmz,number_features,mean_features, medint,pixel_number)
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370 QC_numbers= cbind(QC_numbers, spectra_aligned)
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371 vectorofactions = append(vectorofactions, "aligned")
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372
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373 #elif str( $method.methods_conditional.method ) == 'skip_preprocessing':
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374 ##for now as option to filter large files
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375
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376 #end if
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377
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378 #end for
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379
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380 rownames(QC_numbers) = c("min m/z", "max mz", "# features", "median \n# peaks (int.>0)", "median\nintensity", "pixel\nnumber")
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381 colnames(QC_numbers) = vectorofactions
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382 plot(0,type='n',axes=FALSE,ann=FALSE)
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383 grid.table(t(QC_numbers))
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384
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385 dev.off()
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386
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387 ## export imzML file
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388 if (length(maldi_data)>0){
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389 #if $infile.ext == 'rdata'
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390 MALDIquantForeign::exportImzMl(maldi_data, file="out.imzMl", processed=$export_processed, coordinates=cardinal_coordinates)
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391 #else
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392 MALDIquantForeign::exportImzMl(maldi_data, file="out.imzMl", processed=$export_processed)
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393 #end if
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394
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395 }else{"All spectra are empty, outputfiles will be empty,too."}
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396
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397 ]]>
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398 </configfile>
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399 </configfiles>
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400 <inputs>
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401 <param name="infile" type="data" format="imzml,rdata,analyze75" label="MSI data" help="Input file as imzML (composite upload), or Cardinal MSImageSet saved as RData (regular upload). The file must be in profile mode, not centroided."/>
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402 <conditional name="restriction_conditional">
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403 <param name="restriction" type="select" label="Use only spectra of interest" help="This option only works for imzML files">
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404 <option value="no_restriction" selected="True">No, calculate on entire file</option>
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405 <option value="restrict">Yes, restrict to spectra of interest</option>
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406 </param>
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407 <when value="restrict">
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408 <param name="coordinates_file" type="data" format="tabular" label="Tabular file with coordinates"/>
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409 <param name="column_x" data_ref="coordinates_file" label="Column with x values" type="data_column"/>
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410 <param name="column_y" data_ref="coordinates_file" label="Column with y values" type="data_column"/>
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411 <param name="coordinates_header" type="boolean" label="File contains a header line" truevalue="TRUE" falsevalue="FALSE"/>
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412 </when>
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413 <when value="no_restriction"/>
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414 </conditional>
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415 <repeat name="methods" title="Method" min="1">
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416 <conditional name="methods_conditional">
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417 <param name="method" type="select" label="Select a method">
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418 <option value="Transformation" selected="True">Transformation</option>
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419 <option value="Smoothing">Smoothing</option>
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420 <option value="Baseline">Baseline removal</option>
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421 <option value="Calibrate">Intensity calibration (normalization)</option>
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422 <option value="Align">Align spectra (warping/phase correction)</option>
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423 <option value="skip_preprocessing">Skip preprocessing</option>
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424 <validator type="empty_field" />
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425 </param>
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426 <when value="Transformation">
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427 <param name="transform_method" type="select" label="Transformation method">
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428 <option value="sqrt" selected="True">sqrt</option>
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429 <option value="log">log</option>
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430 <option value="log2">log2</option>
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431 <option value="log10">log10</option>
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432 <validator type="empty_field" />
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433 </param>
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434 </when>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
435 <when value="Smoothing">
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
436 <conditional name="methods_for_smoothing">
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
437 <param name="smooth_method" type="select" label="Smoothing method" help="This method smoothes the intensity values of a MassSpectrum object.">
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
438 <option value="SavitzkyGolay" selected="True">SavitzkyGolay</option>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
439 <option value="MovingAverage">MovingAverage</option>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
440 </param>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
441 <when value="SavitzkyGolay">
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
442 <param name="polynomial" value="3" type="text" label="Polynomial order"
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
443 help="Controls the order of the filter, should be smaller than the resulting window."/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
444 </when>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
445 <when value="MovingAverage">
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 <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"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
447 </when>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
448 </conditional>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
449 <param name="halfWindowSize" type="integer" value="10"
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
450 label="Half window size"
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
451 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
452 mass[currentIndex-halfWindowSize] to mass[currentIndex+halfWindowSize]
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
453 (window size is 2*halfWindowSize+1)."/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
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454 </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
455 <when value="Baseline">
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
456 <conditional name="methods_for_baseline">
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
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457 <param name="baseline_method" type="select" label="Baseline removal method">
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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458 <option value="SNIP" selected="True">SNIP</option>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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459 <option value="TopHat">TopHat</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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460 <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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461 <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
462 <validator type="empty_field" />
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
463 </param>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
464 <when value="SNIP">
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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465 <param name="iterations" type="integer" value="100"
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
466 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
galaxyp
parents: 2
diff changeset
467 </when>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
468 <when value="TopHat">
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
469 <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
galaxyp
parents: 2
diff changeset
470 label="Half window size"
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
471 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
parents: 2
diff changeset
472 mass[currentIndex-halfWindowSize] to mass[currentIndex+halfWindowSize]"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
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473 </when>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
474 <when value="ConvexHull"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
475 <when value="median">
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
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476 <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
galaxyp
parents: 2
diff changeset
477 label="Half window size"
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
478 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
parents: 2
diff changeset
479 mass[currentIndex-halfWindowSize] to mass[currentIndex+halfWindowSize]"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
480 </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
481 </conditional>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
482 </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
483 <when value="Calibrate">
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
484 <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
galaxyp
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485 <option value="TIC" selected="True">TIC</option>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
486 <option value="PQN">PQN</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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487 <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
488 <validator type="empty_field" />
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
489 </param>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
490 <conditional name="cond_calibration_range">
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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491 <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
galaxyp
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492 <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
galaxyp
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493 <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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diff changeset
494 </param>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
495 <when value="no"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
496 <when value="yes">
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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497 <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
galaxyp
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498 label="Start 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
galaxyp
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diff changeset
499 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
galaxyp
parents: 2
diff changeset
500 <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
galaxyp
parents: 2
diff changeset
501 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
galaxyp
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diff changeset
502 </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
503 </conditional>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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504 </when>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
505 <when value="Align">
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
506 <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
galaxyp
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diff changeset
507 <option value="lowess" selected="True">Lowess</option>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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508 <option value="linear">Linear</option>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
509 <option value="quadratic">Quadratic</option>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
510 <option value="cubic">Cubic</option>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
511 </param>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
512
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
513 <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
galaxyp
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diff changeset
514 label="Tolerance"
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
515 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
galaxyp
parents: 2
diff changeset
516
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
517 <param name="halfWindowSize" type="integer" value="20"
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
518 label="Half window size"
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
519 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
parents: 2
diff changeset
520 mass[currentIndex-halfWindowSize] to mass[currentIndex+halfWindowSize]
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
521 (window size is 2*halfWindowSize+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
522 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
galaxyp
parents: 2
diff changeset
523
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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diff changeset
524 <param name="peak_method" type="select" label="Noise estimation function">
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
525 <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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diff changeset
526 <option value="SuperSmoother">SuperSmoother</option>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
527 </param>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
528
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="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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diff changeset
530 <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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531 <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"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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diff changeset
532 <param name="remove_empty" type="boolean" label="Remove empty spectra" truevalue="TRUE" falsevalue="FALSE" help="For Cardinal RData files this step can only be performed if pixel annotations were provided"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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diff changeset
533
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 <conditional name="reference_for_alignment">
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
535 <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
galaxyp
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diff changeset
536 <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
galaxyp
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diff changeset
537 <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
galaxyp
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diff changeset
538 </param>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
539 <when value="no_reference">
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 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
galaxyp
parents: 2
diff changeset
541 </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
542 <when value="yes_reference">
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
543 <param name="reference_file" type="data" format="tabular"
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
544 label="Reference m/z values"
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
545 help="Tabular file"/>
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 <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
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diff changeset
547 <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
548 <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
549 </when>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
550 </conditional>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
551 </when>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
552 <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
553 </conditional>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
554 </repeat>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
555 <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
parents: 2
diff changeset
556 </inputs>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
557 <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
558 <data format="imzml" name="outfile_imzml" label="${tool.name} on ${on_string}" />
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
559 <data format="pdf" name="plots" from_work_dir="prepro_qc_plot.pdf" label="${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
560 </outputs>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
561 <tests>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
562 <test>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
563 <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
564 <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
565 <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
566 </param>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
567 <conditional name="restriction_conditional">
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="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
569 <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
570 <param name="column_x" value="1"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
571 <param name="column_y" value="2"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
572 </conditional>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
573 <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
574 <param name="method" value="Transformation"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
575 <param name="transform_method" value="log2"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
576 <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
577 <param name="smooth_method" value="SavitzkyGolay"/>
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 <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
579 <param name="baseline_method" value ="TopHat"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
580 </conditional>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
581 <output name="outfile_imzml" ftype="imzml" file="preprocessing1.imzml.txt" lines_diff="4">
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
582 <extra_files type="file" file="outfile1.imzml" name="imzml" lines_diff="6"/>
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 <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
584 </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
585 <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
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diff changeset
586 </test>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
587 <test>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
588 <param name="infile" value="msidata_1.RData" ftype="rdata"/>
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 <conditional name="methods_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
590 <param name="method" value="Align"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
591 <param name="warping_method" value="lowess"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
592 <param name="halfWindowSize" value="5"/>
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 <param name="tolerance" value="0.001"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
594 <param name="allow_nomatch" value="TRUE"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
595 <param name="remove_empty" value="TRUE"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
596 <param name="empty_nomatch" value="TRUE"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
597 <conditional name="reference_for_alignment">
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
598 <param name="align_ref" value="yes_reference"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
599 <param name="reference_file" value="inputpeptides.tabular" ftype="tabular"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
600 </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
601 </conditional>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
602 <output name="outfile_imzml" ftype="imzml" file="preprocessing2.imzml.txt" lines_diff="4">
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
603 <extra_files type="file" file="outfile2.imzml" name="imzml" lines_diff="6"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
604 <extra_files type="file" file="outfile2.ibd" name="ibd" compare="sim_size"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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diff changeset
605 </output>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
606 <output name="plots" file="Preprocessing2_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
607 </test>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
608 <test>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
609 <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
610 <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
611 <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
612 </param>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
613 <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
614 <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
615 <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
616 </conditional>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
617 <output name="outfile_imzml" ftype="imzml" file="preprocessing3.imzml.txt" lines_diff="4">
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
618 <extra_files type="file" file="outfile3.imzml" name="imzml" lines_diff="6"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
619 <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
620 </output>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
621 <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
622 </test>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
623 </tests>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
624 <help><![CDATA[
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
625
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
626 @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
627
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
628 -----
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
629
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
630 **Input data**
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
631
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
632 - 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
633
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
634 - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/wp/imzml/>`_
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
635 - Cardinal "MSImageSet" data saved as .RData
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
636
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
637 - 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
638
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
639 ::
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
640
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
641 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
642 1 1
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
643 2 1
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
644 3 1
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
645 ...
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
646 ...
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
647
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
648 - 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
649
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
650 ::
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
651
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
652
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
653 m/z
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
654 100.0
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
655 100.01
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
656 100.02
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
657 ...
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
658 ...
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
659
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
660
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
661
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
662 **Options**
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
663
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
664 - 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
galaxyp
parents: 2
diff changeset
665 - 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
galaxyp
parents: 2
diff changeset
666
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
667 - 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
galaxyp
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diff changeset
668 - 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
galaxyp
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diff changeset
669 - 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
galaxyp
parents: 2
diff changeset
670
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
671 - 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
galaxyp
parents: 2
diff changeset
672
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
673 - 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
galaxyp
parents: 2
diff changeset
674 - 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
galaxyp
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diff changeset
675 - 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
galaxyp
parents: 2
diff changeset
676 - The moving median may generate negative intensities.
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
677 - 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
galaxyp
parents: 2
diff changeset
678
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
679 - 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
galaxyp
parents: 2
diff changeset
680
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
681 - 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
galaxyp
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diff changeset
682 - 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
galaxyp
parents: 2
diff changeset
683
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
684 - 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
galaxyp
parents: 2
diff changeset
685
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
686 - 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
galaxyp
parents: 2
diff changeset
687 - 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
galaxyp
parents: 2
diff changeset
688 - 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
galaxyp
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diff changeset
689 - 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
galaxyp
parents: 2
diff changeset
690
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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691
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692 **Output**
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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693
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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694 - 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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695 - 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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696
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697 .. _MALDIquant: http://strimmerlab.org/software/maldiquant/
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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698
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699 ]]>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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700 </help>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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701 <expand macro="citation"/>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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702 </tool>
aa81463e21ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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703