Mercurial > repos > galaxyp > maldi_quant_peak_detection

annotate maldi_quant_peakdetection.xml @ 1:96264fce1847 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
author galaxyp
date Mon, 01 Oct 2018 01:03:26 -0400
parents 3a8a502fbbc1
children 41c148280a08
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96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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1 <tool id="maldi_quant_peak_detection" name="MALDIquant peak detection" version="@VERSION@.1">
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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 &&
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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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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36 #if $restriction_conditional.restriction == 'restrict':
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38 print('Reading mask region')
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40 ## Import imzML file
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41 coordinate_matrix = as.matrix(read.delim("$restriction_conditional.coordinates_file", header = $restriction_conditional.coordinates_header, stringsAsFactors = FALSE))[,1:2]
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43 maldi_data <- importImzMl('infile.imzML',
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44 coordinates = coordinate_matrix, centroided = $centroids)
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45 pixelnames = paste("xy", coordinates(maldi_data)[,1],coordinates(maldi_data)[,2], sep="_")
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46
0
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48 #else:
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50 print('Reading entire file')
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51 ## Import imzML file
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53 #if $infile.ext == 'imzml'
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54 print('imzML file')
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55 #if str($centroids) == "TRUE"
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56 peaks <- importImzMl('infile.imzML', centroided = $centroids)
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57 pixelnames = paste("xy", coordinates(maldi_data)[,1],coordinates(maldi_data)[,2], sep="_")
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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 #end if
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62 coordinates_info = cbind(coordinates(maldi_data)[,1:2], c(1:length(maldi_data)))
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63
0
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64 #elif $infile.ext == 'tabular'
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65 print('tabular file')
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66 #set $centroids = "TRUE" ## will be used in some if conditions
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67 peak_tabular = read.delim("$infile", header = TRUE, stringsAsFactors = FALSE)
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68 peak_list = split(peak_tabular, f = peak_tabular\$spectrum) ## will be ordered according to spectrum
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69 pixelnames = unique(peak_tabular\$spectrum)
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70
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71 peaks = list()
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72 for (spectra in 1:length(peak_list))
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73 {
1
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74 single_peaks = createMassPeaks(peak_list[[spectra]]\$mass, peak_list[[spectra]]\$intensity, snr=peak_list[[spectra]]\$snr)
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75 peaks[[spectra]] = single_peaks
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76 }
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77
1
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78 #else
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79 print('rdata file')
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80 loadRData <- function(fileName){
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81 #loads an RData file, and returns it
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82 load(fileName)
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83 get(ls()[ls() != "fileName"])
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84 }
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85 msidata = loadRData('infile.RData')
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86 centroided(msidata) = $centroids
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87 pixelnames = gsub(", y = ", "_", names(Cardinal::pixels(msidata)))
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88 pixelnames = gsub(" = ", "y_", pixelnames)
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89
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90 cardinal_coordinates = as.matrix(Cardinal::coord(msidata)[,1:2])
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91
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92 if (centroided(msidata) == FALSE){
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93 ## create mass spectrum object
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94 cardinal_mzs = Cardinal::mz(msidata)
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95 maldi_data = list()
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96 for(number_spectra in 1:ncol(msidata)){
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97 maldi_data[[number_spectra]] = createMassSpectrum(mass = cardinal_mzs, intensity = iData(msidata)[,number_spectra])
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98 coordinates_info = cbind(cardinal_coordinates, c(1:length(maldi_data)))}
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99 coordinates_info = cbind(cardinal_coordinates, c(1:length(maldi_data)))
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100 }else{
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101 peaks = list()
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102 for (spectra in 1:ncol(msidata))
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103 {
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104 single_peaks = createMassPeaks(Cardinal::mz(msidata), Cardinal::spectra(msidata)[,spectra], snr=as.numeric(rep("NA", nrow(msidata))))
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105 peaks[[spectra]] = single_peaks
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106 }}
0
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107 #end if
1
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108 #end if
0
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109
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110
1
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111
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112
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113
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114
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115
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116
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117
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118
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119 ## default summarized = FALSE
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120 summarized_spectra = FALSE
0
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121
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122 ## Quality control plots during peak detection
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123 pdf("peaks_qc_plot.pdf", fonts = "Times", pointsize = 12)
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124 plot(0,type='n',axes=FALSE,ann=FALSE)
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125
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126 ## if no filename is given, name of file in Galaxy history is used
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127 #set $filename = $infile.display_name
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128
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129 title(main=paste("$filename"))
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130
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131 ## plot input file spectrum:
1
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132 #if str($centroids) == "TRUE"
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133 plot(peaks[[1]], main="First spectrum of input file")
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134 #else
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135 avgSpectra <- averageMassSpectra(maldi_data,method="mean")
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136 plot(avgSpectra, main="Average spectrum of input file")
0
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137 #end if
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138
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139
1
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140
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141
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142
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143
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144
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145
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146
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147 ## QC numbers for input file
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148 #if str($centroids) == "TRUE"
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149 pixel_number = length(peaks)
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150 minmz = round(min(unlist(lapply(peaks,mass))), digits=4)
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151 maxmz = round(max(unlist(lapply(peaks,mass))), digits=4)
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152 maxfeatures = round(length(unlist(lapply(peaks,mass)))/length(peaks), digits=2)
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153 medint = round(median(unlist(lapply(peaks,intensity))), digits=2)
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154 inputdata = c(minmz, maxmz,maxfeatures, medint)
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155 QC_numbers= data.frame(inputdata = c(minmz, maxmz,maxfeatures, medint))
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156 vectorofactions = "inputdata"
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157 #else
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158 pixel_number = length(maldi_data)
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159 minmz = round(min(unlist(lapply(maldi_data,mass))), digits=4)
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160 maxmz = round(max(unlist(lapply(maldi_data,mass))), digits=4)
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161 maxfeatures = round(length(unlist(lapply(maldi_data,mass)))/length(maldi_data), digits=2)
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162 medint = round(median(unlist(lapply(maldi_data,intensity))), digits=2)
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163 inputdata = c(minmz, maxmz,maxfeatures, medint)
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164 QC_numbers= data.frame(inputdata = c(minmz, maxmz,maxfeatures, medint))
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165 vectorofactions = "inputdata"
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166 #end if
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167
0
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168 #if str($tabular_annotation.load_annotation) == 'yes_annotation':
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169
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170 ## read and extract x,y,annotation information
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171 input_tabular = read.delim("$tabular_annotation.annotation_file", header = $tabular_annotation.tabular_header, stringsAsFactors = FALSE)
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172 annotation_input = input_tabular[,c($tabular_annotation.column_x, $tabular_annotation.column_y, $tabular_annotation.column_names)]
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173 colnames(annotation_input) = c("x", "y", "annotation") ## rename annotations header to default name "annotation"
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174
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175 ## merge with coordinate information of MSI data
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176 colnames(coordinates_info)[3] = "pixel_index"
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177 merged_annotation = merge(coordinates_info, annotation_input, by=c("x", "y"), all.x=TRUE)
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178 merged_annotation[is.na(merged_annotation)] = "NA"
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179 merged_annotation = merged_annotation[order(merged_annotation\$pixel_index),]
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180 samples = as.factor(merged_annotation\$annotation)
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181
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182 ## print annotation overview into PDF output
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183
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184 ## the more annotation groups a file has the smaller will be the legend
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185 number_combined = length(levels(as.factor(merged_annotation\$annotation)))
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186 if (number_combined<20){
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187 legend_size = 10
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188 }else if (number_combined>20 && number_combined<40){
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189 legend_size = 9
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190 }else if (number_combined>40 && number_combined<60){
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191 legend_size = 8
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192 }else if (number_combined>60 && number_combined<100){
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193 legend_size = 7
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194 }else{
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195 legend_size = 6
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196 }
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197
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198 combine_plot = ggplot(merged_annotation, aes(x=x, y=y, fill=annotation))+
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199 geom_tile() +
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200 coord_fixed()+
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201 ggtitle("Spatial orientation of annotated data")+
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202 theme_bw()+
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203 theme(plot.title = element_text(hjust = 0.5))+
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204 theme(text=element_text(family="ArialMT", face="bold", size=12))+
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205 theme(legend.position="bottom",legend.direction="vertical")+
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206 theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = legend_size))+
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207 guides(fill=guide_legend(ncol=5,byrow=TRUE))
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208
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209 print(combine_plot)
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210
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211 #end if
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212
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213
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214 #################### Preprocessing methods #####################################
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215
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216 #for $method in $methods:
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217
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218 #if str( $method.methods_conditional.method ) == 'Peak_detection':
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219 print('peak detection')
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220 ##peak detection
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221
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222 #if $method.methods_conditional.use_annotations:
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223 maldi_data <- averageMassSpectra(maldi_data, labels=samples,method="mean") ## use average spectra for peak picking
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224 pixelnames = levels(samples)
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225 summarized_spectra = TRUE
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226
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227 #end if
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228
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229 peaks <- detectPeaks(maldi_data, method="$method.methods_conditional.peak_method",
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230 halfWindowSize=$method.methods_conditional.halfWindowSize,SNR=$method.methods_conditional.snr)
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231
1
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232 ## QC plot and numbers
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233 plot(peaks[[1]], main="First spectrum after peak detection")
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234 pixel_number = length(peaks)
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235 minmz = round(min(unlist(lapply(peaks,mass))), digits=4)
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236 maxmz = round(max(unlist(lapply(peaks,mass))), digits=4)
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237 maxfeatures = round(length(unlist(lapply(peaks,mass)))/length(peaks), digits=2)
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238 medint = round(median(unlist(lapply(peaks,intensity))), digits=2)
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239 peaks_picked = c(minmz, maxmz,maxfeatures, medint)
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240 QC_numbers= cbind(QC_numbers, peaks_picked)
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241 vectorofactions = append(vectorofactions, "peaks_picked")
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242
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243 if (length(peaks[!sapply(peaks, isEmpty)])>0){
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244 #if $infile.ext == 'imzml'
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245 #if str($centroids) == "FALSE"
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246 featureMatrix <- intensityMatrix(peaks, maldi_data)
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247 #end if
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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248 #else
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249 featureMatrix <- intensityMatrix(peaks)
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250 #end if
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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251 featureMatrix2 =cbind(pixelnames, featureMatrix)
1
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252 colnames(featureMatrix2)[1] = c("mz")
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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253 featureMatrix2 = t(featureMatrix2)
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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254 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
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255 }else{print("There are no spectra with peaks left")}
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256
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257
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258 #elif str( $method.methods_conditional.method ) == 'monoisotopic_peaks':
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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259
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260 print('monoisotopic peaks')
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261 ##monoisotopic peaks
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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262
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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263 peaks = monoisotopicPeaks(peaks, minCor=$method.methods_conditional.minCor, tolerance=$method.methods_conditional.tolerance, distance=$method.methods_conditional.distance, size=$method.methods_conditional.size)
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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264
1
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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265 ## QC plot and numbers
0
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266 plot(peaks[[1]], main="First spectrum after monoisotopic peaks detection")
1
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267 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
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268 maxmz = round(max(unlist(lapply(peaks,mass))), digits=4)
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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269 maxfeatures = round(length(unlist(lapply(peaks,mass)))/length(peaks), digits=2)
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270 medint = round(median(unlist(lapply(peaks,intensity))), digits=2)
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271 monoisotopes = c(minmz, maxmz,maxfeatures, medint)
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272 QC_numbers= cbind(QC_numbers, monoisotopes)
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273 vectorofactions = append(vectorofactions, "monoisotopes")
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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274
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275 if (length(peaks[!sapply(peaks, isEmpty)])>0){
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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276 #if $infile.ext == 'imzml'
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277 #if str($centroids) == "FALSE"
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278 featureMatrix <- intensityMatrix(peaks, maldi_data)
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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279 #end if
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280 #else
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281 featureMatrix <- intensityMatrix(peaks)
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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282 #end if
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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283 featureMatrix2 =cbind(pixelnames, featureMatrix)
1
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284 colnames(featureMatrix2)[1] = c("mz")
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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285 featureMatrix2 = t(featureMatrix2)
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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286 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
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287 }else{print("There are no spectra with peaks left")}
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288
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289 #elif str( $method.methods_conditional.method ) == 'Binning':
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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290
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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291 print('binning')
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292 ##m/z binning
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293
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294 peaks <- binPeaks(peaks, tolerance=$method.methods_conditional.bin_tolerance)
1
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295
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296 ## QC plot and numbers
0
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297 plot(peaks[[1]], main="First spectrum after binning")
1
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298 minmz = round(min(unlist(lapply(peaks,mass))), digits=4)
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299 maxmz = round(max(unlist(lapply(peaks,mass))), digits=4)
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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300 maxfeatures = round(length(unlist(lapply(peaks,mass)))/length(peaks), digits=2)
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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301 medint =round( median(unlist(lapply(peaks,intensity))), digits=2)
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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302 binned = c(minmz, maxmz,maxfeatures, medint)
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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303 QC_numbers= cbind(QC_numbers, binned)
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304 vectorofactions = append(vectorofactions, "binned")
0
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305
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306 if (length(peaks[!sapply(peaks, isEmpty)])>0){
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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307 #if $infile.ext == 'imzml'
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308 #if str($centroids) == "FALSE"
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309 featureMatrix <- intensityMatrix(peaks, maldi_data)
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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310 #end if
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311 #if str($centroids) == "TRUE"
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312 featureMatrix <- intensityMatrix(peaks)
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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313 #end if
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314 #else
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315 featureMatrix <- intensityMatrix(peaks)
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316 #end if
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317 featureMatrix2 =cbind(pixelnames, featureMatrix)
1
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diff changeset
318 colnames(featureMatrix2)[1] = c("mz")
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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319 featureMatrix2 = t(featureMatrix2)
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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320 write.table(featureMatrix2, file="$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
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diff changeset
321 }else{print("There are no spectra with peaks left")}
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322
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323
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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324 #elif str( $method.methods_conditional.method ) == 'Filtering':
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325
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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326 print('filtering')
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327 ##m/z filtering
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328
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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329 ## filtering on all pixels or on pixel groups:
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330 #if str($method.methods_conditional.filter_annot_groups ) == 'FALSE':
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331
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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332 peaks <- filterPeaks(peaks,
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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333 minFrequency=$method.methods_conditional.minFrequency,
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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334 minNumber=$method.methods_conditional.minNumber,
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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335 mergeWhitelists=$method.methods_conditional.mergeWhitelists)
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336
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337 #elif str( $method.methods_conditional.filter_annot_groups ) == 'TRUE':
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338
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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339 peaks <- filterPeaks(peaks,
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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340 minFrequency=$method.methods_conditional.minFrequency,
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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341 minNumber=$method.methods_conditional.minNumber,
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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342 mergeWhitelists=$method.methods_conditional.mergeWhitelists, label = samples)
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343 #end if
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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344
1
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345 ##QC plot and numbers
0
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346 plot(peaks[[1]], main="First spectrum after m/z filtering")
1
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347 minmz = round(min(unlist(lapply(peaks,mass))), digits=4)
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348 maxmz = round(max(unlist(lapply(peaks,mass))), digits=4)
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349 maxfeatures = round(length(unlist(lapply(peaks,mass)))/length(peaks), digits=2)
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350 medint = round(median(unlist(lapply(peaks,intensity))), digits=2)
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351 filtered = c(minmz, maxmz,maxfeatures, medint)
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352 QC_numbers= cbind(QC_numbers, filtered)
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353 vectorofactions = append(vectorofactions, "filtered")
0
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354
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355 if (length(peaks[!sapply(peaks, isEmpty)])>0){
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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356 #if $infile.ext == 'imzml'
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357 #if str($centroids) == "FALSE"
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358 featureMatrix <- intensityMatrix(peaks, maldi_data)
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359 #end if
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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360 #else
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361 featureMatrix <- intensityMatrix(peaks)
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362 #end if
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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363 featureMatrix2 =cbind(pixelnames, featureMatrix)
1
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364 colnames(featureMatrix2)[1] = c("mz")
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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365 featureMatrix2 = t(featureMatrix2)
1
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366 }else{print("There are no spectra with peaks left")
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367 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
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368 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
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369 #end if
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370 #end for
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371
1
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372 if (length(peaks[!sapply(peaks, isEmpty)])>0){
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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373 ## mass peaks output
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374 mass_peaks = data.frame(matrix(,ncol=3, nrow=0))
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375 for (spectrum in 1:length(peaks)){
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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376 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
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377 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
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378 mass_peaks = rbind(mass_peaks,spectrum_df)
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379 }
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380 colnames(mass_peaks) = c("snr", "mass", "intensity", "spectrum")
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381 write.table(mass_peaks, file="$masspeaks", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
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382 }else{print("There are no spectra with peaks left")}
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383
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384 ## print table with QC values
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385 rownames(QC_numbers) = c("min m/z", "max mz", "# features", "median\nintensity")
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386 plot(0,type='n',axes=FALSE,ann=FALSE)
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387 grid.table(t(QC_numbers))
0
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388
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389 dev.off()
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390
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391 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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392 #if $infile.ext == 'imzml'
1
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393 MALDIquantForeign::exportImzMl(peaks, file="out.imzMl", processed=$export_processed)
0
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394 #elif $infile.ext == 'tabular'
1
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395 masspeaks_coordinates = matrix(unlist(strsplit(as.character(pixelnames), "\\_")), ncol=3, byrow=TRUE)
0
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396 ## extract x and y values and create the coordinate matrix in case tabular was input
1
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397 peaklist_coordinates = unique(cbind(as.numeric(masspeaks_coordinates[,2]), as.numeric(masspeaks_coordinates[,3])))
0
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398 exportImzMl(peaks, file="out.imzMl", processed=$export_processed, coordinates=peaklist_coordinates)
1
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399 #elif $infile.ext == 'rdata'
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400 MALDIquantForeign::exportImzMl(peaks, file="out.imzMl", processed=$export_processed, coordinates=cardinal_coordinates)
0
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401 #end if
1
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402
0
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403 }
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404
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405 ]]>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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406 </configfile>
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407 </configfiles>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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parents:
diff changeset
408 <inputs>
1
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
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409 <param name="infile" type="data" format="imzml,tabular,rdata" label="Inputfile as imzML or Cardinal MSImageSet saved as RData" help="This file is in imzML or tabular format (peak list, peak detection cannot be run again) or Cardinal MSImageSet 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
410 <param name="centroids" type="boolean" label="Is the imzML/RData data centroided (picked)" help="Choose Yes if peak detection has already been done. Peak detection cannot be run again on centroided data" truevalue="TRUE" falsevalue="FALSE"/>
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
411 <conditional name="restriction_conditional">
1
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
412 <param name="restriction" type="select" label="Read in only spectra of interest" help="This option only works for imzML files">
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
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413 <option value="no_restriction" selected="True">Calculate on entire file</option>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
414 <option value="restrict">Restrict to coordinates of interest</option>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
415 </param>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
416 <when value="restrict">
1
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
417 <param name="coordinates_file" type="data" format="tabular" label="Tabular file with coordinates" help="x-values in first column, y-values in second column"/>
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
418 <param name="coordinates_header" type="boolean" label="Tabular 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
419 </when>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
420 <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
421 </conditional>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
422
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
423 <conditional name="tabular_annotation">
1
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
424 <param name="load_annotation" type="select" label="Use pixel annotation from tabular file - select in peak detection or filtering step where annotation should be used">
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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425 <option value="no_annotation" selected="True">pixels belong into one group only</option>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
426 <option value="yes_annotation">use pixel annotation from a tabular file</option>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
427 </param>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
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428 <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
429 <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
430 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
431 <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
parents:
diff changeset
432 <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
433 <param name="column_names" data_ref="annotation_file" label="Column with pixel annotations" type="data_column"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
434 <param name="tabular_header" type="boolean" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
435 </when>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
436 <when value="no_annotation"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
437 </conditional>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
438 <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
439 <conditional name="methods_conditional">
1
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
440 <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
galaxyp
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diff changeset
441 <option value="Peak_detection">Peak detection</option>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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442 <option value="monoisotopic_peaks">Keep only monoisotopic peaks</option>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
443 <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
444 <option value="Filtering">Filtering</option>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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diff changeset
445 </param>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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diff changeset
446 <when value="Peak_detection">
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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447 <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
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448 <option value="MAD" selected="True">MAD</option>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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449 <option value="SuperSmoother">SuperSmoother</option>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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diff changeset
450 </param>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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diff changeset
451 <param name="halfWindowSize" type="integer" value="20"
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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diff changeset
452 label="Half window size"
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
453 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
454 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
455 (window size is 2*halfWindowSize+1).
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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diff changeset
456 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
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diff changeset
457 <param name="snr" type="integer" value="2" label="Signal-to-noise-ratio" help=""/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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458 <param name="use_annotations" type="boolean" label="Generate average mass spectra for each annotation group" help="Spectra with same annotation are summarized, no imzML export possible" truevalue="TRUE" falsevalue="FALSE"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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diff changeset
459 </when>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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460 <when value="monoisotopic_peaks">
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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461 <param name="minCor" type="float" value="0.95" label="minimal correlation"
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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462 help="double , minimal correlation between the peak pattern generated by the model and the experimental peaks in the MassPeaks object to be recognized as isotopic pattern"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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463 <param name="tolerance" type="float" label="tolerance" value="0.0004"
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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464 help="double, maximal relative deviation of peaks position (mass) to be considered as isotopic distance"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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465 <param name="distance" type="float" label="distance" value="1.00235" help="double, distance between two consecutive peaks in an isotopic pattern"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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466 <param name="size" type="integer" label="size" value="3" help="double, size (length) of isotopic pattern, longer patterns are prefered over shorter ones"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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diff changeset
467 </when>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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diff changeset
468 <when value="Binning">
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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469 <param name="bin_tolerance" type="float" value="0.002" label="Peak binning tolerance"
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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470 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."/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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diff changeset
471 </when>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
472 <when value="Filtering">
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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473 <param name="minFrequency" type="float" value="0.25"
1
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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parents: 0
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474 label="Removal of all peaks which occur in less than minFrequency spectra" help="It is a relative threshold. The higher value from relative and absolute threshold is taken. Set one value to zero to be sure it will not be sure."/>
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
475 <param name="minNumber" type="float" value="1.0"
1
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
476 label="Removal of all peaks which occur in less than minNumber spectra" help="It is an absolute threshold. The higher value from relative and absolute threshold is taken. Set one value to zero to be sure it will not be sure."/>
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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477 <param name="filter_annot_groups" type="boolean" label="Group wise filtering with pixel annotations. 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"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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diff changeset
478 <param name="mergeWhitelists" type="boolean" truevalue="TRUE" falsevalue="FALSE"
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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479 label="mergeWhitelists" help="if FALSE the filtering criteria are applied groupwise. If TRUE peaks that survive the filtering in one group (level of labels) these peaks are also kept in other groups even if their frequencies are below minFrequency"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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diff changeset
480 </when>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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diff changeset
481 </conditional>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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diff changeset
482 </repeat>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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parents:
diff changeset
483 <param name="export_processed" type="boolean" label="Export file as processed imzML" help="otherwise continuous imzML will be exported" checked="true" truevalue="TRUE" falsevalue="FALSE"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
484 </inputs>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
485 <outputs>
1
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
486 <data format="imzml" name="outfile_imzml" label="$infile.display_name peaks"/>
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
487 <data format="pdf" name="plots" from_work_dir="peaks_qc_plot.pdf" label = "$infile.display_name peakdetection QC"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
488 <data format="tabular" name="masspeaks" label="$infile.display_name mass_peaks"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
489 <data format="tabular" name="intensity_matrix" label="intensity_matrix"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
490 </outputs>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
491 <tests>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
492 <test>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
493 <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
494 <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
495 <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
496 </param>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
497 <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
498 <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
499 <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
500 <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
501 <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
502 <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
503 <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
504 </conditional>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
505 <repeat name="methods">
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
506 <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
507 <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
508 <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
509 <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
510 <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
511 <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
512 </conditional>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
513 </repeat>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
514 <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
515 <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
516 <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
517 </test>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
518 <test>
1
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
519 <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
520 <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
521 <repeat name="methods">
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
522 <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
523 <param name="method" value="monoisotopic_peaks"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
524 </conditional>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
525 </repeat>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
526 <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
527 <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
528 <output name="intensity_matrix" file="int2.tabular"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
529 </test>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
530 <test>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
531 <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
532 <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
533 <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
534 </param>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
535 <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
536 <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
537 <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
538 <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
539 <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
540 <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
541 <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
542 </conditional>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
543 <repeat name="methods">
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
544 <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
545 <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
546 <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
547 <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
548 <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
549 </conditional>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
550 </repeat>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
551 <repeat name="methods">
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
552 <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
553 <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
554 <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
555 </conditional>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
556 </repeat>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
557 <repeat name="methods">
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
558 <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
559 <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
560 <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
561 <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
562 <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
563 <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
564 </conditional>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
565 </repeat>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
566 <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
567 <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
568 <output name="masspeaks" file="masspeaks3.tabular"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
569 </test>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
570 </tests>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
571 <help>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
572 <![CDATA[
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
573
1
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
574 @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
575
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
576 -----
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
577
1
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
578 **Input data**
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
579
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
580 - 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
581
1
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
582 - 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
583 - 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
584 - 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
585
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
586 ::
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
587
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
588 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
589 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
590 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
591 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
592 ...
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
593 ...
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
594
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
595
1
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
596 - Optional: Tabular file with pixel coordinates to restrict reading of imzML files to coordinates of interest. The file has to contain x values in the first column and y values in the second columns. Further columns are allowed. Tabular files with any header name or no header at all are supported.
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
597
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
598 ::
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
599
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
600 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
601 1 1
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
602 2 1
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
603 3 1
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
604 ...
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
605 ...
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
606
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
607
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
608 - 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 summarize pixels of an imzML file which belong to the same group and detect peaks on average spectra, further steps will be done on average spectra as well and average spectra are exported. If this option was not chosen the filtering tool can use the annotations to filter for peaks within pixel groups (select "Group wise filtering").
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
609
1
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
610 ::
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
611
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
612 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
613 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
614 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
615 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
616 ...
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
617 ...
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
618
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
619
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
620 **Options**
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
621
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
622 - Peak detection: detection of peaks, only possible with profile mode input
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
623 - Monoisotopic peaks: detection of monoisotopic peaks
1
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
624 - 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.
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
625 - Peak filtering: Removal of less frequent peaks (either with a minimum ratio or with an absolute minimum number of spectra in which the peak has to occur)
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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diff changeset
626
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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diff changeset
627
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
628 **Output**
0
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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diff changeset
629
1
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
630 - centroided imzML file (processed or continuous), except for peak picking on the average of multiple spectra
96264fce1847 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
631 - pdf with mass spectra plots after each preprocessing step
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
632 - peak list (tabular file) with the columns "snr", "mass", "intensity" and "spectrum"
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
633 - 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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diff changeset
634
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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diff changeset
635 .. _MALDIquant: http://strimmerlab.org/software/maldiquant/
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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diff changeset
636
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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diff changeset
637 ]]>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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diff changeset
638 </help>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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diff changeset
639 <expand macro="citation"/>
3a8a502fbbc1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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640 </tool>