Mercurial > repos > galaxyp > maldi_quant_peak_detection

annotate maldi_quant_peakdetection.xml @ 4:c6b47c89a2f5 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
author galaxyp
date Fri, 22 Mar 2019 08:30:45 -0400
parents c42549f04fdd
children af766257766e
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1 <tool id="maldi_quant_peak_detection" name="MALDIquant peak detection" version="@VERSION@.4">
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2 <description>
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3 Peak detection, binning and filtering for mass-spectrometry imaging data
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4 </description>
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5 <macros>
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6 <import>maldi_macros.xml</import>
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7 </macros>
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8 <expand macro="requirements"/>
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9 <command detect_errors="exit_code">
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10 <![CDATA[
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11 #if $infile.ext == 'imzml'
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12 cp '${infile.extra_files_path}/imzml' infile.imzML &&
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13 cp '${infile.extra_files_path}/ibd' infile.ibd &&
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14 #elif $infile.ext == 'analyze75'
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15 cp '${infile.extra_files_path}/hdr' infile.hdr &&
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16 cp '${infile.extra_files_path}/img' infile.img &&
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17 cp '${infile.extra_files_path}/t2m' infile.t2m &&
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18 #else
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19 ln -s $infile infile.RData &&
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20 #end if
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21 Rscript '${maldi_quant_peak_detection}'&&
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22 mkdir $outfile_imzml.files_path &&
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23 mv ./out.imzMl "${os.path.join($outfile_imzml.files_path, 'imzml')}" | true &&
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24 mv ./out.ibd "${os.path.join($outfile_imzml.files_path, 'ibd')}" | true &&
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25 echo "imzML file:" > $outfile_imzml &&
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26 ls -l "$outfile_imzml.files_path" >> $outfile_imzml
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27 ]]>
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28 </command>
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29 <configfiles>
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30 <configfile name="maldi_quant_peak_detection"><![CDATA[
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32 @R_IMPORTS@
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34 #if $restriction_conditional.restriction == 'restrict':
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35
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36 print('Reading mask region')
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37
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38 ## Import imzML file
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39 coordinate_matrix = as.matrix(read.delim("$restriction_conditional.coordinates_file", header = $restriction_conditional.coordinates_header, stringsAsFactors = FALSE))[,1:2]
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40 coordinate_matrix = coordinate_matrix[,c($restriction_conditional.column_x, $restriction_conditional.column_y)]
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42 maldi_data <- importImzMl('infile.imzML',
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43 coordinates = coordinate_matrix, centroided = $centroids)
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44 pixelnames = paste("xy", coordinates(maldi_data)[,1],coordinates(maldi_data)[,2], sep="_")
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45
0
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47 #else:
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49 print('Reading entire file')
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50 ## Import imzML file
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52 #if $infile.ext == 'imzml'
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53 print('imzML file')
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54 #if str($centroids) == "TRUE"
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55 peaks <- importImzMl('infile.imzML', centroided = $centroids)
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56 pixelnames = paste("xy", coordinates(peaks)[,1],coordinates(peaks)[,2], sep="_")
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57 coordinates_info = cbind(coordinates(peaks)[,1:2], c(1:length(peaks)))
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58 #else
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59 maldi_data <- importImzMl('infile.imzML', centroided = $centroids)
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60 pixelnames = paste("xy", coordinates(maldi_data)[,1],coordinates(maldi_data)[,2], sep="_")
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61 coordinates_info = cbind(coordinates(maldi_data)[,1:2], c(1:length(maldi_data)))
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62 #end if
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63
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64
0
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65 #elif $infile.ext == 'tabular'
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66 print('tabular file')
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67 #set $centroids = "TRUE" ## will be used in some if conditions
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68 peak_tabular = read.delim("$infile", header = TRUE, stringsAsFactors = FALSE)
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69 peak_list = split(peak_tabular, f = peak_tabular\$spectrum) ## will be ordered according to spectrum
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70 pixelnames = unique(peak_tabular\$spectrum)
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71
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72 peaks = list()
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73 for (spectra in 1:length(peak_list))
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74 {
1
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75 single_peaks = createMassPeaks(peak_list[[spectra]]\$mass, peak_list[[spectra]]\$intensity, snr=peak_list[[spectra]]\$snr)
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76 peaks[[spectra]] = single_peaks
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77 }
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78
1
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79 #else
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80 print('rdata file')
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81 loadRData <- function(fileName){
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82 #loads an RData file, and returns it
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83 load(fileName)
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84 get(ls()[ls() != "fileName"])
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85 }
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86 msidata = loadRData('infile.RData')
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87 centroided(msidata) = $centroids
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88 ## change to correct pixelnames
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89
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90 x_coords = unlist(lapply(strsplit(names(Cardinal::pixels(msidata)), ","), `[[`, 1))
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91 y_coords = unlist(lapply(strsplit(names(Cardinal::pixels(msidata)), ","), `[[`, 2))
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92 x_coordinates = gsub("x = ","",x_coords)
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93 y_coordinates = gsub(" y = ","",y_coords)
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94 pixelnames = paste0("xy_", x_coordinates, "_", y_coordinates)
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95
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96 cardinal_coordinates = as.matrix(Cardinal::coord(msidata)[,1:2])
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97
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98 if (centroided(msidata) == FALSE){
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99 ## create mass spectrum object
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100 cardinal_mzs = Cardinal::mz(msidata)
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101 maldi_data = list()
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102 for(number_spectra in 1:ncol(msidata)){
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103 maldi_data[[number_spectra]] = createMassSpectrum(mass = cardinal_mzs, intensity = iData(msidata)[,number_spectra])}
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104 coordinates_info = cbind(cardinal_coordinates, c(1:length(maldi_data)))
1
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105 }else{
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106 peaks = list()
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107 for (spectra in 1:ncol(msidata))
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108 {
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109 single_peaks = createMassPeaks(Cardinal::mz(msidata), Cardinal::spectra(msidata)[,spectra], snr=as.numeric(rep("NA", nrow(msidata))))
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110 peaks[[spectra]] = single_peaks
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111 }
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112 coordinates_info = cbind(cardinal_coordinates, c(1:length(peaks)))}
0
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113 #end if
1
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114 #end if
0
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115
1
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116 ## default summarized = FALSE
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117 summarized_spectra = FALSE
0
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118
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119 ## Quality control plots during peak detection
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120 pdf("peaks_qc_plot.pdf", fonts = "Times", pointsize = 12)
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121 plot(0,type='n',axes=FALSE,ann=FALSE)
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122
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123 ## if no filename is given, name of file in Galaxy history is used
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124 #set $filename = $infile.display_name
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125
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126 title(main=paste("$filename"))
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127
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128 ## plot input file spectrum:
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129 #if $centroids:
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130 ## Choose random spectra for QC plots
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131 print(length(peaks))
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132 random_spectra = sample(1:length(peaks), 4, replace=FALSE)
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133 random_spectra_name = pixelnames[random_spectra]
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134 par(mfrow = c(2, 2), oma=c(0,0,2,0))
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135 for (random_sample in random_spectra){
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136 plot(peaks[[random_sample]],sub="", main=paste0("spectrum ", pixelnames[random_sample]))}
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137 title("Input spectra", outer=TRUE, line=0)
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138
1
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139 #else
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140 ## Choose random spectra for QC plots
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141 random_spectra = sample(1:length(maldi_data), 4, replace=FALSE)
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142 par(mfrow = c(2, 2), oma=c(0,0,2,0))
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143 for (random_sample in random_spectra){
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144 plot(maldi_data[[random_sample]],sub="", main=paste0("spectrum ", pixelnames[random_sample]))
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145 }
3
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146 title("Input spectra", outer=TRUE, line=0)
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147 #end if
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148
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149
1
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150 ## QC numbers for input file
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151 #if str($centroids) == "TRUE"
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152 pixel_number = length(peaks)
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153 minmz = round(min(unlist(lapply(peaks,mass))), digits=4)
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154 maxmz = round(max(unlist(lapply(peaks,mass))), digits=4)
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155 mean_features = round(length(unlist(lapply(peaks,mass)))/length(peaks), digits=2)
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156 medint = round(median(unlist(lapply(peaks,intensity))), digits=2)
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157 number_features = length(unique(unlist(lapply(peaks,mass))))
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158 inputdata = c(minmz, maxmz,number_features,mean_features, medint)
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159 QC_numbers= data.frame(inputdata = c(minmz, maxmz,number_features, mean_features, medint))
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160 vectorofactions = "inputdata"
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161 #else
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162 pixel_number = length(maldi_data)
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163 minmz = round(min(unlist(lapply(maldi_data,mass))), digits=4)
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164 maxmz = round(max(unlist(lapply(maldi_data,mass))), digits=4)
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165 mean_features = round(length(unlist(lapply(maldi_data,mass)))/length(maldi_data), digits=2)
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166 medint = round(median(unlist(lapply(maldi_data,intensity))), digits=2)
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167 number_features = length(unique(unlist(lapply(maldi_data,mass))))
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168 inputdata = c(minmz, maxmz,number_features,mean_features, medint)
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169 QC_numbers= data.frame(inputdata = c(minmz, maxmz,number_features, mean_features, medint))
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170 vectorofactions = "inputdata"
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171 #end if
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172
0
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173 #if str($tabular_annotation.load_annotation) == 'yes_annotation':
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174
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175 ## read and extract x,y,annotation information
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176 input_tabular = read.delim("$tabular_annotation.annotation_file", header = $tabular_annotation.tabular_header, stringsAsFactors = FALSE)
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177 annotation_input = input_tabular[,c($tabular_annotation.column_x, $tabular_annotation.column_y, $tabular_annotation.column_names)]
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178 colnames(annotation_input) = c("x", "y", "annotation") ## rename annotations header to default name "annotation"
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179
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180 ## merge provided annotation with coordinate information of MSI data
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181 colnames(coordinates_info)[3] = "pixel_index"
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182 merged_annotation = merge(coordinates_info, annotation_input, by=c("x", "y"), all.x=TRUE)
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183 merged_annotation[is.na(merged_annotation)] = "NA"
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184 ## order coordinate information according to pixel index to make sure that the order stays the same
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185 merged_annotation = merged_annotation[order(merged_annotation\$pixel_index),]
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186 samples = as.factor(merged_annotation\$annotation)
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187
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188 ## print annotation overview into PDF output
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189
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190 combine_plot = ggplot(merged_annotation, aes(x=x, y=y, fill=annotation))+
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191 geom_tile() +
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192 coord_fixed()+
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193 ggtitle("Spatial orientation of annotated data")+
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194 theme_bw()+
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195 theme(plot.title = element_text(hjust = 0.5))+
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196 theme(text=element_text(family="ArialMT", face="bold", size=12))+
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197 theme(legend.position="bottom",legend.direction="vertical")+
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198 theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = 8))+
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199 theme(legend.position="bottom",legend.direction="vertical")+
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200 guides(fill=guide_legend(ncol=4,byrow=TRUE))
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201
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202 print(combine_plot)
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203
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204 #end if
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205
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206 #################### Preprocessing methods #####################################
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207
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208 #for $method in $methods:
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209
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210 #if str( $method.methods_conditional.method ) == 'Peak_detection':
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211 print('peak detection')
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212 ##peak detection
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213
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214 #if $method.methods_conditional.use_annotations:
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215 maldi_data <- averageMassSpectra(maldi_data, labels=samples,method="mean") ## use average spectra for peak picking
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216 pixelnames = levels(samples)
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217 summarized_spectra = TRUE
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218 random_spectra = sample(1:length(maldi_data), 4, replace=TRUE)
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219 #end if
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220
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221 peaks <- detectPeaks(maldi_data, method="$method.methods_conditional.peak_method",
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222 halfWindowSize=$method.methods_conditional.halfWindowSize,SNR=$method.methods_conditional.snr)
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223
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224 ## QC plot and numbers
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225 ## plot old spectra with baseline in blue and picked peaks in green
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226 par(mfrow = c(2, 2), oma=c(0,0,2,0))
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227 for (random_sample in random_spectra){
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228 noise = estimateNoise(maldi_data[[random_sample]], method= "$method.methods_conditional.peak_method")
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229 plot(maldi_data[[random_sample]], sub="", main=paste0("spectrum ", pixelnames[random_sample]))
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230 lines(noise[,1], noise[,2]*$method.methods_conditional.snr, col="blue")
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231 points(peaks[[random_sample]], col="green", pch=20)}
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232 title("S/N in blue and picked peaks in green", outer=TRUE, line=0)
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233
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234 ## plot new spectrum
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235 par(mfrow = c(2, 2), oma=c(0,0,2,0))
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236 for (random_sample in random_spectra){
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237 plot(peaks[[random_sample]], sub="", main=paste0("spectrum ", pixelnames[random_sample]))}
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238 title("Picked peaks", outer=TRUE, line=0)
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239
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240 pixel_number = length(peaks)
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241 minmz = round(min(unlist(lapply(peaks,mass))), digits=4)
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242 maxmz = round(max(unlist(lapply(peaks,mass))), digits=4)
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243 mean_features = round(length(unlist(lapply(peaks,mass)))/length(peaks), digits=2)
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244 medint = round(median(unlist(lapply(peaks,intensity))), digits=2)
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245 number_features = length(unique(unlist(lapply(peaks,mass))))
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246 peaks_picked = c(minmz, maxmz,number_features,mean_features, medint)
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247 QC_numbers= cbind(QC_numbers, peaks_picked)
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248 vectorofactions = append(vectorofactions, "peaks_picked")
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249
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250 if (length(peaks[!sapply(peaks, isEmpty)])>0){
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251 featureMatrix <- intensityMatrix(peaks)
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252 #if $infile.ext == 'imzml'
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253 #if str($centroids) == "FALSE"
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254 featureMatrix <- intensityMatrix(peaks, maldi_data)
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255 #end if
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256 #end if
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257 featureMatrix2 =cbind(pixelnames, featureMatrix)
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258 colnames(featureMatrix2)[1] = c("mz")
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259 featureMatrix2 = t(featureMatrix2)
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260 write.table(featureMatrix2, file="$intensity_matrix", quote = FALSE, row.names = TRUE, col.names=FALSE, sep = "\t")
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261 }else{print("There are no spectra with peaks left")}
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262
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263
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264 #elif str( $method.methods_conditional.method ) == 'monoisotopic_peaks':
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265
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266 print('monoisotopic peaks')
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267 ##monoisotopic peaks
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268
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269 ## keep peaks to plot them with monoisotopic peaks
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270 picked_peaks = peaks
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271
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272 peaks = monoisotopicPeaks(peaks, minCor=$method.methods_conditional.minCor,
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273 tolerance=$method.methods_conditional.tolerance,
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274 distance=c($method.methods_conditional.distance),
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275 size=$method.methods_conditional.size)
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276
2
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277 ## plot old spectrum with picked isotopes as green dots
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278 par(mfrow = c(2, 2), oma=c(0,0,2,0))
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279 for (random_sample in random_spectra){
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280 plot(picked_peaks[[random_sample]], sub="", main=paste0("spectrum ", pixelnames[random_sample]))
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281 points(peaks[[random_sample]], col="green", pch=20)}
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282 title(paste0("Monoisotopic peaks in green"), outer=TRUE, line=0)
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283
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284
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285 par(mfrow = c(2, 2), oma=c(0,0,2,0))
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286 for (random_sample in random_spectra){
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287 plot(peaks[[random_sample]], sub="", main=paste0("spectrum ", pixelnames[random_sample]))}
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288 title("Monoisotopic peaks", outer=TRUE, line=0)
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289
1
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290 minmz = round(min(unlist(lapply(peaks,mass))), digits=4)
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291 maxmz = round(max(unlist(lapply(peaks,mass))), digits=4)
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292 mean_features = round(length(unlist(lapply(peaks,mass)))/length(peaks), digits=2)
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293 medint = round(median(unlist(lapply(peaks,intensity))), digits=2)
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294 number_features = length(unique(unlist(lapply(peaks,mass))))
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295 monoisotopes = c(minmz, maxmz,number_features,mean_features, medint)
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296 QC_numbers= cbind(QC_numbers, monoisotopes)
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297 vectorofactions = append(vectorofactions, "monoisotopes")
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298
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299 if (length(peaks[!sapply(peaks, isEmpty)])>0){
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300 featureMatrix <- intensityMatrix(peaks)
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301 ## only for profile imzML file: featurematrix is overwritten:
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302 #if $infile.ext == 'imzml'
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303 #if str($centroids) == "FALSE"
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304 featureMatrix <- intensityMatrix(peaks, maldi_data)
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305 #end if
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306 #end if
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307 featureMatrix2 =cbind(pixelnames, featureMatrix)
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308 colnames(featureMatrix2)[1] = c("mz")
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309 featureMatrix2 = t(featureMatrix2)
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310 write.table(featureMatrix2, file="$intensity_matrix", quote = FALSE, row.names = TRUE, col.names=FALSE, sep = "\t")
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311 }else{print("There are no spectra with peaks left")}
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312
3
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313
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314
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315 #elif str( $method.methods_conditional.method ) == 'Align':
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316
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317 print('align')
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318 ##align spectra with 2 separate functions
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319
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320
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321 #if str($method.methods_conditional.reference_for_alignment.align_ref) == 'no_reference':
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322 ## 1) calculate warping:
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323 warping_function <- determineWarpingFunctions(peaks,
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324 tolerance=$method.methods_conditional.tolerance, method="$method.methods_conditional.warping_method",
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325 allowNoMatches=$method.methods_conditional.allow_nomatch, minFrequency = $method.methods_conditional.reference_for_alignment.min_frequency)
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326 ## 2) warp spectra:
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327 peaks = warpMassPeaks(peaks, warping_function, emptyNoMatches=$method.methods_conditional.empty_nomatch)
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328
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329
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330 #elif str($method.methods_conditional.reference_for_alignment.align_ref) == 'yes_reference':
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331
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332 ## create reference mass_vector from tabular file
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333 mass_vector = read.delim("$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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334 int_vector = rep(1,length(mass_vector))
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335 mass_list = createMassPeaks(mass_vector, int_vector)
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336
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337 #if str($method.methods_conditional.reference_for_alignment.separate_alignment) == "FALSE"
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338 print('default alignment')
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339
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340 ## 1) calculate warping:
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341 warping_function <- determineWarpingFunctions(peaks,
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342 tolerance=$method.methods_conditional.tolerance, method="$method.methods_conditional.warping_method",
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343 allowNoMatches=$method.methods_conditional.allow_nomatch, reference = mass_list)
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344 ## 2) warp spectra:
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345 peaks = warpMassPeaks(peaks, warping_function, emptyNoMatches=$method.methods_conditional.empty_nomatch)
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346
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347 #elif str($method.methods_conditional.reference_for_alignment.separate_alignment) == "TRUE"
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348 print('spectra wise alignment')
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349
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350 peaks_new_list =list()
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351
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352 for (pixelnb in 1:length(peaks))
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353 {
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354
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355 ## 1) calculate warping:
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356 warping_function <- determineWarpingFunctions(peaks[[pixelnb]],
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357 tolerance=$method.methods_conditional.tolerance, method="$method.methods_conditional.warping_method",
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358 allowNoMatches=$method.methods_conditional.allow_nomatch, reference = mass_list)
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359 ## 2) warp spectra:
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360 peaks_new_list = warpMassPeaks(list(peaks[[pixelnb]]), warping_function, emptyNoMatches=$method.methods_conditional.empty_nomatch)
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361 }
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362 peaks_new = peaks_new_list
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363
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364 #end if
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365
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366 #end if
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367
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368 ## QC plot and numbers
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369 par(mfrow = c(2, 2), oma=c(0,0,2,0))
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370 for (random_sample in random_spectra){
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371 plot(peaks[[random_sample]], sub="", main=paste0("spectrum ", pixelnames[random_sample]))}
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372 title("Aligned spectra", outer=TRUE, line=0)
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373 minmz = round(min(unlist(lapply(peaks,mass))), digits=4)
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374 maxmz = round(max(unlist(lapply(peaks,mass))), digits=4)
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375 mean_features = round(length(unlist(lapply(peaks,mass)))/length(peaks), digits=2)
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376 medint = round(median(unlist(lapply(peaks,intensity))), digits=2)
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377 number_features = length(unique(unlist(lapply(peaks,mass))))
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378 aligned = c(minmz, maxmz,number_features,mean_features, medint)
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379 QC_numbers= cbind(QC_numbers, aligned)
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380 vectorofactions = append(vectorofactions, "aligned")
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381
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382 if (length(peaks[!sapply(peaks, isEmpty)])>0){
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383 featureMatrix <- intensityMatrix(peaks)
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384 ## only for profile imzML file: featurematrix is overwritten:
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385 #if $infile.ext == 'imzml'
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386 #if str($centroids) == "FALSE"
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387 featureMatrix <- intensityMatrix(peaks, maldi_data)
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388 #end if
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389 #end if
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390 featureMatrix2 =cbind(pixelnames, featureMatrix)
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391 colnames(featureMatrix2)[1] = c("mz")
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392 featureMatrix2 = t(featureMatrix2)
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393 write.table(featureMatrix2, file="$intensity_matrix", quote = FALSE, row.names = TRUE, col.names=FALSE, sep = "\t")
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394 }else{print("There are no spectra with peaks left")}
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395
0
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396 #elif str( $method.methods_conditional.method ) == 'Binning':
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397
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398 print('binning')
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399 ##m/z binning
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400
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401 peaks <- binPeaks(peaks, tolerance=$method.methods_conditional.bin_tolerance, method="$method.methods_conditional.bin_method")
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402
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403 ## QC plot and numbers
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404 par(mfrow = c(2, 2), oma=c(0,0,2,0))
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405 for (random_sample in random_spectra){
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406 plot(peaks[[random_sample]], sub="", main=paste0("spectrum ", pixelnames[random_sample]))}
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407 title("Binned spectra", outer=TRUE, line=0)
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408 minmz = round(min(unlist(lapply(peaks,mass))), digits=4)
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409 maxmz = round(max(unlist(lapply(peaks,mass))), digits=4)
2
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
410 mean_features = round(length(unlist(lapply(peaks,mass)))/length(peaks), digits=2)
1
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
411 medint =round( median(unlist(lapply(peaks,intensity))), digits=2)
2
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
412 number_features = length(unique(unlist(lapply(peaks,mass))))
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
413 binned = c(minmz, maxmz,number_features,mean_features, medint)
1
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
414 QC_numbers= cbind(QC_numbers, binned)
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
415 vectorofactions = append(vectorofactions, "binned")
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
416
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
417 if (length(peaks[!sapply(peaks, isEmpty)])>0){
2
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
418 featureMatrix <- intensityMatrix(peaks)
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
419 #if $infile.ext == 'imzml'
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
420 #if str($centroids) == "FALSE"
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
421 featureMatrix <- intensityMatrix(peaks, maldi_data)
2
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
422 #elif str($centroids) == "TRUE"
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
423 featureMatrix <- intensityMatrix(peaks)
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
424 #end if
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
425 #end if
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
426 featureMatrix2 =cbind(pixelnames, featureMatrix)
1
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
427 colnames(featureMatrix2)[1] = c("mz")
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
428 featureMatrix2 = t(featureMatrix2)
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
429 write.table(featureMatrix2, file="$intensity_matrix", quote = FALSE, row.names = TRUE, col.names=FALSE, sep = "\t")
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
430 }else{print("There are no spectra with peaks left")}
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
431
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
432
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
433 #elif str( $method.methods_conditional.method ) == 'Filtering':
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
434
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
435 print('filtering')
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
436 ##m/z filtering
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
437
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
438 ## filtering on all pixels or on pixel groups:
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
439 #if str($method.methods_conditional.filter_annot_groups ) == 'FALSE':
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
440
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
441 peaks <- filterPeaks(peaks,
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
442 minFrequency=$method.methods_conditional.minFrequency,
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
443 minNumber=$method.methods_conditional.minNumber,
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
444 mergeWhitelists=$method.methods_conditional.mergeWhitelists)
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
445
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
446 #elif str( $method.methods_conditional.filter_annot_groups ) == 'TRUE':
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
447
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
448 peaks <- filterPeaks(peaks,
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
449 minFrequency=$method.methods_conditional.minFrequency,
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
450 minNumber=$method.methods_conditional.minNumber,
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
451 mergeWhitelists=$method.methods_conditional.mergeWhitelists, label = samples)
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
452 #end if
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
453
1
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
454 ##QC plot and numbers
3
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
455 par(mfrow = c(2, 2), oma=c(0,0,2,0))
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
456 for (random_sample in random_spectra){
4
c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
457 plot(peaks[[random_sample]], sub="", main=paste0("spectrum ", pixelnames[random_sample]))}
3
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
458 title("Filtered spectra", outer=TRUE, line=0)
1
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
459 minmz = round(min(unlist(lapply(peaks,mass))), digits=4)
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
460 maxmz = round(max(unlist(lapply(peaks,mass))), digits=4)
2
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
461 mean_features = round(length(unlist(lapply(peaks,mass)))/length(peaks), digits=2)
1
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
462 medint = round(median(unlist(lapply(peaks,intensity))), digits=2)
2
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
463 number_features = length(unique(unlist(lapply(peaks,mass))))
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
464 filtered = c(minmz, maxmz,number_features,mean_features, medint)
1
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
465 QC_numbers= cbind(QC_numbers, filtered)
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
466 vectorofactions = append(vectorofactions, "filtered")
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
467
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
468 if (length(peaks[!sapply(peaks, isEmpty)])>0){
2
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
469 featureMatrix <- intensityMatrix(peaks)
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
470 #if $infile.ext == 'imzml'
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
471 #if str($centroids) == "FALSE"
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
472 featureMatrix <- intensityMatrix(peaks, maldi_data)
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
473 #end if
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
474 #end if
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
475 featureMatrix2 =cbind(pixelnames, featureMatrix)
1
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
476 colnames(featureMatrix2)[1] = c("mz")
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
477 featureMatrix2 = t(featureMatrix2)
1
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
478 }else{print("There are no spectra with peaks left")
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
479 featureMatrix2 = matrix(0, ncol=1, nrow=1)}
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
480 write.table(featureMatrix2, file="$intensity_matrix", quote = FALSE, row.names = TRUE, col.names=FALSE, sep = "\t")
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
481 #end if
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
482 #end for
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
483
1
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
484 if (length(peaks[!sapply(peaks, isEmpty)])>0){
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
485 ## mass peaks output
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
486 mass_peaks = data.frame(matrix(,ncol=3, nrow=0))
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
487 for (spectrum in 1:length(peaks)){
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
488 spectrum_df = data.frame(peaks[[spectrum]]@snr, peaks[[spectrum]]@mass, peaks[[spectrum]]@intensity)
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
489 spectrum_df\$spectrum_id = rep(pixelnames[[spectrum]], length(peaks[[spectrum]]@mass))
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
490 mass_peaks = rbind(mass_peaks,spectrum_df)
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
491 }
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
492 colnames(mass_peaks) = c("snr", "mass", "intensity", "spectrum")
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
493 write.table(mass_peaks, file="$masspeaks", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
494 }else{print("There are no spectra with peaks left")}
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
495
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
496 ## print table with QC values
3
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497 rownames(QC_numbers) = c("min m/z", "max mz", "# features", "median \n# peaks (int.>0)", "median\nintensity")
1
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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498 plot(0,type='n',axes=FALSE,ann=FALSE)
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
499 grid.table(t(QC_numbers))
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
500
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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diff changeset
501 dev.off()
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
502
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
503 if (summarized_spectra == FALSE){
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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parents:
diff changeset
504 #if $infile.ext == 'imzml'
3
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
505 MALDIquantForeign::exportImzMl(peaks, file="out.imzMl", processed=TRUE)
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
506 #elif $infile.ext == 'tabular'
1
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
507 masspeaks_coordinates = matrix(unlist(strsplit(as.character(pixelnames), "\\_")), ncol=3, byrow=TRUE)
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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diff changeset
508 ## extract x and y values and create the coordinate matrix in case tabular was input
1
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
509 peaklist_coordinates = unique(cbind(as.numeric(masspeaks_coordinates[,2]), as.numeric(masspeaks_coordinates[,3])))
3
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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diff changeset
510 exportImzMl(peaks, file="out.imzMl", processed=TRUE, coordinates=peaklist_coordinates)
1
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
511 #elif $infile.ext == 'rdata'
3
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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diff changeset
512 MALDIquantForeign::exportImzMl(peaks, file="out.imzMl", processed=TRUE, coordinates=cardinal_coordinates)
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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diff changeset
513 #end if
1
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
514
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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diff changeset
515 }
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
516
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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diff changeset
517 ]]>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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diff changeset
518 </configfile>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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diff changeset
519 </configfiles>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
520 <inputs>
3
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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diff changeset
521 <param name="infile" type="data" format="imzml,tabular,rdata" label="MSI data" help="Input file as imzML (composite upload), tabular peaklist or Cardinal MSImageSet saved as RData (regular upload)"/>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
522 <param name="centroids" type="boolean" label="Centroided input" help="Choose Yes if peak detection has already been done. Peak detection cannot be run again on centroided data" truevalue="TRUE" falsevalue="FALSE"/>
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
523 <conditional name="restriction_conditional">
3
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
524 <param name="restriction" type="select" label="Use only spectra of interest" help="This option only works for imzML files">
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
525 <option value="no_restriction" selected="True">No, calculate on entire file</option>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
526 <option value="restrict">Yes, restrict to spectra of interest</option>
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
527 </param>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
528 <when value="restrict">
3
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
529 <param name="coordinates_file" type="data" format="tabular" label="Tabular file with coordinates"/>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
530 <param name="column_x" data_ref="coordinates_file" label="Column with x values" type="data_column"/>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
531 <param name="column_y" data_ref="coordinates_file" label="Column with y values" type="data_column"/>
2
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
532 <param name="coordinates_header" type="boolean" label="File contains a header line" truevalue="TRUE" falsevalue="FALSE"/>
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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diff changeset
533 </when>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
534 <when value="no_restriction"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
535 </conditional>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
536
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
537 <conditional name="tabular_annotation">
3
c42549f04fdd 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 name="load_annotation" type="select" label="Spectra annotations" help="Annotations can be used for group wise peak detection or filtering">
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
539 <option value="no_annotation" selected="True">No</option>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
540 <option value="yes_annotation">Yes</option>
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
541 </param>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
542 <when value="yes_annotation">
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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parents:
diff changeset
543 <param name="annotation_file" type="data" format="tabular" label="Use annotations from tabular file"
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
544 help="Tabular file with three columns: x values, y values and pixel annotations"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
545 <param name="column_x" data_ref="annotation_file" label="Column with x values" type="data_column"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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diff changeset
546 <param name="column_y" data_ref="annotation_file" label="Column with y values" type="data_column"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
547 <param name="column_names" data_ref="annotation_file" label="Column with pixel annotations" type="data_column"/>
2
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galaxyp
parents: 1
diff changeset
548 <param name="tabular_header" type="boolean" label="File contains a header line" truevalue="TRUE" falsevalue="FALSE"/>
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
549 </when>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
550 <when value="no_annotation"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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diff changeset
551 </conditional>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
552 <repeat name="methods" title="Method" min="1">
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
553 <conditional name="methods_conditional">
1
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
554 <param name="method" type="select" label="Select a method">
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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parents:
diff changeset
555 <option value="Peak_detection">Peak detection</option>
4
c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
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diff changeset
556 <option value="monoisotopic_peaks">Monoisotopic peaks</option>
3
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
557 <option value="Align">Align Spectra (warping/phase correction)</option>
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
558 <option value="Binning">Binning</option>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
559 <option value="Filtering">Filtering</option>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
560 </param>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
561 <when value="Peak_detection">
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
562 <param name="peak_method" type="select" label="Noise estimation function">
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
563 <option value="MAD" selected="True">MAD</option>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
564 <option value="SuperSmoother">SuperSmoother</option>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
565 </param>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
566 <param name="halfWindowSize" type="integer" value="20"
2
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galaxyp
parents: 1
diff changeset
567 label="Half window size (number of data points)"
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
568 help="The resulting window reaches from
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
569 mass[currentIndex-halfWindowSize] to mass[currentIndex+halfWindowSize]
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
570 (window size is 2*halfWindowSize+1).
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
571 The best size differs depending on the selected smoothing method."/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
572 <param name="snr" type="integer" value="2" label="Signal-to-noise-ratio" help=""/>
2
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
573 <param name="use_annotations" type="boolean" label="Detect peaks on average mass spectra" help="Spectra with same annotation are averaged before peak detection, no imzML output" truevalue="TRUE" falsevalue="FALSE"/>
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
574 </when>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
575 <when value="monoisotopic_peaks">
2
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
576 <param name="minCor" type="float" value="0.95" label="Minimal correlation"
4
c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
577 help="Minimal correlation between the peak pattern generated by the model and the experimental peaks in the MassPeaks object to be recognized as isotopic pattern."/>
c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
578 <param name="tolerance" type="float" label="Tolerance" value="0.0001"
c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
579 help="Maximal relative deviation of a peak position (m/z) to be considered as identical: abs(((mass[i]+distance)-mass[i+1])/mass[i]) smaller than 'tolerance'. For 100ppm use 0.0001" />
c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
580 <param name="distance" type="text" label="Distance" value="1.00235" help="Distance between two consecutive peaks in an isotopic pattern. 1.00235 is average distance for polypeptides. Multiple values can be used to find multiple charged pattern e.g. 1, 0.5 ,0.33">
c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
581 <sanitizer invalid_char="">
c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
582 <valid initial="string.digits">
c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
583 <add value="," />
c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
584 <add value=":" />
c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
585 <add value="." />
c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
586 </valid>
c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
587 </sanitizer>
c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
588 </param>
c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
589 <param name="size" type="text" label="Size" value="3:10" help="Size (length) of isotopic pattern, longer patterns are prefered over shorter ones, min size is 2, a range can be used.">
c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
590 <sanitizer invalid_char="">
c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
591 <valid initial="string.digits">
c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
592 <add value=":" />
c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
593 </valid>
c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
594 </sanitizer>
c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
595 </param>
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
596 </when>
3
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
597
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
598 <when value="Align">
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
599 <param name="warping_method" type="select" label="Warping methods">
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
600 <option value="lowess" selected="True">Lowess</option>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
601 <option value="linear">Linear</option>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
602 <option value="quadratic">Quadratic</option>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
603 <option value="cubic">Cubic</option>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
604 </param>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
605 <param name="tolerance" type="float" value="0.00005"
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
606 label="Tolerance = abs(mz1 - mz2)/mz2"
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
607 help="Maximal relative deviation of a peak position (m/z) to be considered as identical. For 50ppm use 0.00005 or 5e-5" />
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
608 <param name="allow_nomatch" type="boolean" label="Don't throw an error when less than 2 reference m/z were found in a spectrum" truevalue="TRUE" falsevalue="FALSE"/>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
609 <param name="empty_nomatch" type="boolean" label="If TRUE the intensity values of MassSpectrum or MassPeaks objects with missing (NA) warping functions are set to zero" truevalue="TRUE" falsevalue="FALSE"/>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
610 <param name="remove_empty" type="boolean" label="Should empty spectra be removed" truevalue="TRUE" falsevalue="FALSE" help="For Cardinal RData files this step can only be performed if pixel annotations were provided"/>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
611
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
612 <conditional name="reference_for_alignment">
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
613 <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">
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
614 <option value="no_reference" selected="True">no reference</option>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
615 <option value="yes_reference">reference from tabular file</option>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
616 </param>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
617 <when value="no_reference">
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
618 <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"/>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
619 </when>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
620 <when value="yes_reference">
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
621 <param name="reference_file" type="data" format="tabular"
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
622 label="Reference m/z values"
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
623 help="Tabular file"/>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
624 <param name="mz_column" data_ref="reference_file" label="Column with m/z values" type="data_column"/>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
625 <param name="reference_header" type="boolean" label="File contains a header line" truevalue="TRUE" falsevalue="FALSE"/>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
626 <param name="separate_alignment" type="boolean" label="Spectrum wise alignment" help="Internal binning is omitted to avoid interaction between spectra" truevalue="TRUE" falsevalue="FALSE"/>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
627 </when>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
628 </conditional>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
629 </when>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
630
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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diff changeset
631 <when value="Binning">
3
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
632 <param name="bin_tolerance" type="float" value="0.002" label="Tolerance"
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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diff changeset
633 help="After the alignment the peak positions (mass) are very similar but not identical. The binning is needed to make similar peak mass values identical."/>
4
c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
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parents: 3
diff changeset
634 <param name="bin_method" display="radio" type="select" label="Bin creation rule" help="strict - creates bins never containing two or more peaks of the same sample. relaxed - allows multiple peaks of the same sample in one bin.">
2
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
635 <option value="strict" selected="True" >strict</option>
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
636 <option value="relaxed" >relaxed</option>
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
637 </param>
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
638 </when>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
639 <when value="Filtering">
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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parents:
diff changeset
640 <param name="minFrequency" type="float" value="0.25"
2
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
641 label="Removal of all peaks which occur in less than minFrequency spectra" help="Relative threshold. The higher value from relative and absolute threshold is taken. Set one value to zero to be sure it will not be used."/>
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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parents:
diff changeset
642 <param name="minNumber" type="float" value="1.0"
2
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
643 label="Removal of all peaks which occur in less than minNumber spectra" help="Absolute threshold. The higher value from relative and absolute threshold is taken. Set one value to zero to be sure it will not be used."/>
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
644 <param name="filter_annot_groups" type="boolean" label="Group wise filtering with pixel annotations." help="If not specified a single group is assumed or when filtering has been done group wise it will automatically be group wise when selecting filtering on all pixel" truevalue="TRUE" falsevalue="FALSE"/>
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
645 <param name="mergeWhitelists" type="boolean" truevalue="TRUE" falsevalue="FALSE"
2
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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diff changeset
646 label="mergeWhitelists" help="Yes means that peaks that survive the filtering in one annotation group are also kept in other groups regardless if the filtering criteria are met in these groups"/>
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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diff changeset
647 </when>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
648 </conditional>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
649 </repeat>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
650 </inputs>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
651 <outputs>
3
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
652 <data format="imzml" name="outfile_imzml" label="${tool.name} on ${on_string}: imzml">
2
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
653 <!--filter>methods_conditional['method'] == 'Peak_detection'</filter-->
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
654 </data>
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
655 <data format="pdf" name="plots" from_work_dir="peaks_qc_plot.pdf" label = "${tool.name} on ${on_string}: QC"/>
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
656 <data format="tabular" name="masspeaks" label="${tool.name} on ${on_string}: peaklist"/>
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
657 <data format="tabular" name="intensity_matrix" label="${tool.name} on ${on_string}: intensity_matrix"/>
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
658 </outputs>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
659 <tests>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
660 <test>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
661 <param name="infile" value="" ftype="imzml">
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
662 <composite_data value="Example_Continuous.imzML"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
663 <composite_data value="Example_Continuous.ibd"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
664 </param>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
665 <conditional name="tabular_annotation">
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
666 <param name="load_annotation" value="yes_annotation"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
667 <param name="annotation_file" value="pixel_annotations.tabular"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
668 <param name="column_x" value="1"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
669 <param name="column_y" value="2"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
670 <param name="column_names" value="3"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
671 <param name="tabular_header" value="TRUE"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
672 </conditional>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
673 <repeat name="methods">
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
674 <conditional name="methods_conditional">
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
675 <param name="method" value="Peak_detection"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
676 <param name="peak_method" value="SuperSmoother"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
677 <param name="halfWindowSize" value="1"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
678 <param name="snr" value="5"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
679 <param name="use_annotations" value="TRUE"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
680 </conditional>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
681 </repeat>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
682 <output name="plots" file="peakdetection1_QC.pdf" compare="sim_size"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
683 <output name="masspeaks" file="masspeaks1.tabular"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
684 <output name="intensity_matrix" file="int1.tabular"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
685 </test>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
686 <test>
1
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
687 <param name="infile" value="masspeaks3_forinput.tabular"/>
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
688 <param name="centroids" value="TRUE"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
689 <repeat name="methods">
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
690 <conditional name="methods_conditional">
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
691 <param name="method" value="monoisotopic_peaks"/>
2
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
692 <param name="tolerance" value="0.0004"/>
4
c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
693 <param name="size" value="3"/>
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
694 </conditional>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
695 </repeat>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
696 <output name="plots" file="peakdetection2_QC.pdf" compare="sim_size"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
697 <output name="masspeaks" file="masspeaks2.tabular"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
698 <output name="intensity_matrix" file="int2.tabular"/>
3
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
699 <output name="outfile_imzml" ftype="imzml" file="peak_detection2.imzml.txt" lines_diff="4">
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
700 <extra_files type="file" file="peak_detection2.imzml" name="imzml" lines_diff="6"/>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
701 <extra_files type="file" file="peak_detection2.ibd" name="ibd" compare="sim_size"/>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
702 </output>
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
703 </test>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
704 <test>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
705 <param name="infile" value="" ftype="imzml">
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
706 <composite_data value="Example_Continuous.imzML"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
707 <composite_data value="Example_Continuous.ibd"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
708 </param>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
709 <conditional name="tabular_annotation">
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
710 <param name="load_annotation" value="yes_annotation"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
711 <param name="annotation_file" value="pixel_annotations.tabular"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
712 <param name="column_x" value="1"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
713 <param name="column_y" value="2"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
714 <param name="column_names" value="3"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
715 <param name="tabular_header" value="TRUE"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
716 </conditional>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
717 <repeat name="methods">
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
718 <conditional name="methods_conditional">
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
719 <param name="method" value="Peak_detection"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
720 <param name="peak_method" value="MAD"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
721 <param name="halfWindowSize" value="1"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
722 <param name="snr" value="2"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
723 </conditional>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
724 </repeat>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
725 <repeat name="methods">
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
726 <conditional name="methods_conditional">
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
727 <param name="method" value="Binning"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
728 <param name="bin_tolerance" value="0.01"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
729 </conditional>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
730 </repeat>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
731 <repeat name="methods">
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
732 <conditional name="methods_conditional">
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
733 <param name="method" value="Filtering"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
734 <param name="minFrequency" value="0.5"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
735 <param name="minNumber" value="3"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
736 <param name="filter_annot_groups" value="TRUE"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
737 <param name="mergeWhitelists" value="FALSE"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
738 </conditional>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
739 </repeat>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
740 <output name="plots" file="peakdetection3_QC.pdf" compare="sim_size"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
741 <output name="intensity_matrix" file="intensity_matrix3.tabular"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
742 <output name="masspeaks" file="masspeaks3.tabular"/>
3
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
743 <output name="outfile_imzml" ftype="imzml" file="peak_detection3.imzml.txt" lines_diff="4">
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
744 <extra_files type="file" file="peak_detection3.imzml" name="imzml" lines_diff="6"/>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
745 <extra_files type="file" file="peak_detection3.ibd" name="ibd" compare="sim_size"/>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
746 </output>
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
747 </test>
2
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
748 <test>
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
749 <param name="infile" value="testfile_squares.rdata" ftype="rdata"/>
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
750 <param name="method" value="Peak_detection"/>
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
751 <param name="peak_method" value="MAD"/>
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
752 <param name="halfWindowSize" value="20"/>
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
753 <param name="snr" value="2"/>
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
754 <output name="plots" file="peakdetection4_QC.pdf" compare="sim_size"/>
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
755 <output name="intensity_matrix" file="intensity_matrix4.tabular"/>
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
756 <output name="masspeaks" file="masspeaks4.tabular"/>
3
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
757 <output name="outfile_imzml" ftype="imzml" file="peak_detection4.imzml.txt" lines_diff="4">
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
758 <extra_files type="file" file="peak_detection4.imzml" name="imzml" lines_diff="6"/>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
759 <extra_files type="file" file="peak_detection4.ibd" name="ibd" compare="sim_size"/>
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
760 </output>
2
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
761 </test>
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
762 </tests>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
763 <help>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
764 <![CDATA[
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
765
1
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
766 @MADLI_QUANT_DESCRIPTION@
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
767
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
768 -----
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
769
1
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
770 **Input data**
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
771
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
772 - MSI data: 3 types of input data can be used:
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
773
1
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
774 - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/wp/imzml/>`_
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
775 - Cardinal "MSImageSet" data saved as .RData
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
776 - MSI data as peak list (tabular file) with the columns named "snr", "mass", "intensity" and "spectrum". The spectrum has to be in the following format: xy_1_1 (for pixel coordinates x1y1). The header must have exactly the four column names.
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
777
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
778 ::
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
779
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
780 snr mass intensity spectrum
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
781 5.34 304.16 0.10 xy_1_1
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
782 12.09 305 0.2 xy_1_1
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
783 6.80 306.25 0.133 xy_1_1
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
784 ...
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
785 ...
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
786
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
787
3
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
788 - 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.
1
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
789
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
790 ::
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
791
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
792 x_coord y_coord
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
793 1 1
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
794 2 1
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
795 3 1
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
796 ...
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
797 ...
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
798
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
799
2
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
800 - Optional: Tabular file(s) containing pixel coordinates and annotation. X and y values in separate columns and the corresponding annotation in a third column. Tabular files with any header name or no header at all are supported. The annotations can be used to either detect peak on the average mass spectrum of each annotation group ('Detect peaks on average mass spectra') or to filter for peaks within pixel groups ('Group wise filtering'). This option is not compatible with tabular peak list inputs.
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
801
1
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
802 ::
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
803
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
804 x_coord y_coord annotation
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
805 1 1 healthy
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
806 2 1 healthy
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
807 3 1 disease
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
808 ...
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
809 ...
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
810
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
811 **Options**
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
812
2
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
813 - Peak detection: detection of peaks, only possible with profile mode input. A peak is a local maximum above a user defined noise threshold.
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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parents: 1
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814
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
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diff changeset
815 - Two functions exist to estimate the noise: MAD and supersmoother.
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
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diff changeset
816 - SNR is an abbreviation for signal-to-noise-ratio. A local maximum has to be higher than SNR*noise to be recognize as peak.
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
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817 - 'halfWindowSize': The resulting window reaches from mass[currentIndex-halfWindowSize] to mass[currentIndex+halfWindowSize]. A local maximum has to be the highest one in the given window to be recognized as peak.
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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diff changeset
818 - Detect peaks on average mass spectra: Spectra with the same annotation (taken from the annotation tabular input) are averaged and peak picking is performed on the average spectrum of each annotation group. The exported imzML is empty and cannot be used for further analysis steps. The peaklist and intensity matrix outputs contain the annotation group names with their averaged intensity values. Filtering steps have to be done in the same run as the peak picking.
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
819
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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diff changeset
820
3
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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diff changeset
821 - Monoisotopic peaks: Keeps only the monoisotopic peaks
2
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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822
4
c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
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diff changeset
823 - Based on poisson model for isotopic patterns as decribed in (`Breen et al. <https://doi.org/10.1002/1522-2683(20000601)21:11%3C2243::AID-ELPS2243%3E3.0.CO;2-K>`_)
c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
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diff changeset
824 - Isotopic pattern can be characterized and recognized by
c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
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parents: 3
diff changeset
825
c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
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diff changeset
826 - the similarity of the experimental pattern with the modelled pattern
c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
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diff changeset
827 - the distance between consecutive isotopic peaks. For polypeptides the average distance is 1.00235 (`Park et al. <https://pubs.acs.org/doi/abs/10.1021/ac800913b>`_). Multiply charged analytes have smaller distances between the peaks (e.g. z = 1 distance = ~1; z = 2: distance = ~0.5; z = 3: distance = ~0.3333) To search for differently charged isotopic pattern multiple distances can be applied - the order matters because the first distance that matches is reported (1, 0.5, 0.3333).
c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
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diff changeset
828 - the size (length) of the pattern, multiple values can be applied, longer patterns are prefered over shorter ones.
c6b47c89a2f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
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diff changeset
829
2
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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parents: 1
diff changeset
830
3
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
831 - Spectra alignment (warping): alignment for (re)calibration of m/z values.
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
832
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
833 - without external reference m/z: internal reference is obtained by filtering (default 90%) and binning the peaks to find landmark peaks and their average m/z
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
834 - with external reference m/z: the m/z provided in a tabular file are used as a reference, at least 10 reference values are recommended
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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diff changeset
835 - non linear warping (parametric time warping plus binning) to match the reference peaks (internal or external) to the peaks with the given tolerance. At least two m/z per spectrum are needed for the alignment. This requirement can be skipped by setting "Don't throw an error when less than 2 reference m/z were found in a spectrum" 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.
2
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
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diff changeset
836
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
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diff changeset
837
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
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838 - Peak binning: After the alignment the peak positions (m/z) are very similar but not identical. The binning is needed to make similar peak m/z values identical. The algorithm is based on the following workflow:
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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839
3
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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diff changeset
840 1. Put all m/z in a sorted vector.
2
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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841 2. Calculate differences between each neighbor.
3
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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842 3. Divide the m/z vector at the largest gap (largest difference) and form a left and a right bin.
2
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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843 4. Rerun step 3 for the left and/or the right bin if they don't fulfill the following criteria:
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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844
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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845 - All peaks in a bin are near to the mean (abs(mass-meanMass)/meanMass < tolerance).
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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846 - method == "strict": The bin doesn't contain two or more peaks of the same sample.
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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847
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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848
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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849 - Peak filtering: Removal of less frequent m/z features:
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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850
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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851 - minFrequency : between 0 and 1: m/z has to occur in 0 - 100% of all spectra; minNumber: m/z has to occur in at least this amount of spectra --> out of those two criteria the stricter value will be used
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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852 - Group wise filtering with pixel annotations: 'Yes' means that the filtering criteria are applied for each annotation group separately.
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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853 - mergeWhitelists: 'Yes' means that peaks that survive the filtering in one annotation group are also kept in other groups regardless if the filtering criteria are met in these groups
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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854 - To filter data that was averaged before peak detection: Filtering has to be done in the same tool run as the peak detection. The filtering criteria are automatically applied per annotation group (Group wise filtering can be 'No') and not per pixel. Example: to keep only m/z that were detected in at least half of all annotation groups set minFrequency to 0.5.
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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855
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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856
1
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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857 **Output**
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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858
3
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859 - centroided, processed imzML file, imzML file is empty when 'Detect peaks on average mass spectra' is chosen.
c42549f04fdd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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860 - pdf with mass spectra plots of four random spectra and a table with key values after each preprocessing step
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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861 - peak list (tabular file) with the columns "snr", "mass", "intensity" and "spectrum"
2
41c148280a08 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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862 - tabular file with intensity matrix (m/z in rows and spectra in columns). If the input file was imzML in profile mode the intensities before peak picking are also stored in the matrix . For all other inputs not picked values are set to NA. For peak picking on the average of multiple spectra, each spectra group is a column with mean intensities for each m/z.
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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863
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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864 .. _MALDIquant: http://strimmerlab.org/software/maldiquant/
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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865
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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866 ]]>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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867 </help>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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868 <expand macro="citation"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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869 </tool>