Mercurial > repos > galaxyp > maldi_quant_peak_detection

annotate maldi_quant_peakdetection.xml @ 0:01212bf66f61 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
author galaxyp
date Wed, 22 Aug 2018 11:49:29 -0400
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01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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1 <tool id="maldi_quant_peak_detection" name="MALDIquant peak detection" version="1.18.0.0">
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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 #end if
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19 Rscript '${maldi_quant_peak_detection}'&&
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20 mkdir $outfile_imzml.files_path &&
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21 mv ./out.imzMl "${os.path.join($outfile_imzml.files_path, 'imzml')}" | true &&
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22 mv ./out.ibd "${os.path.join($outfile_imzml.files_path, 'ibd')}" | true &&
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23 echo "imzML file:" > $outfile_imzml &&
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24 ls -l "$outfile_imzml.files_path" >> $outfile_imzml
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25 ]]>
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26 </command>
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27 <configfiles>
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28 <configfile name="maldi_quant_peak_detection"><![CDATA[
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30 @R_IMPORTS@
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32 summarized_spectra = FALSE
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33
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34 #if $restriction_conditional.restriction == 'restrict':
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35
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36 print('Reading mask region')
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37 ## Import imzML file
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38 coordinate_matrix = as.matrix(read.delim("$restriction_conditional.coordinates_file", header = FALSE, stringsAsFactors = FALSE))[,1:2]
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39
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40 maldi_data <- importImzMl('infile.imzML',
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41 coordinates = coordinate_matrix, centroided = $centroids)
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42 pixelnames = paste0("x = ", coordinates(maldi_data)[,1],", y = ", coordinates(maldi_data)[,2])
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43
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44 #else:
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45
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46 print('Reading entire file')
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47 ## Import imzML file
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49
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50 #if $infile.ext == 'imzml'
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51
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52 #if str($centroids) == "TRUE"
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53 peaks <- importImzMl('infile.imzML', centroided = $centroids)
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54 pixelnames = paste0("x = ", coordinates(peaks)[,1],", y = ", coordinates(peaks)[,2])
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55
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56 #else
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57 maldi_data <- importImzMl('infile.imzML', centroided = $centroids)
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58 pixelnames = paste0("x = ", coordinates(maldi_data)[,1],", y = ", coordinates(maldi_data)[,2])
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59 #end if
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60 #elif $infile.ext == 'tabular'
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61
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62 peak_tabular = read.delim("$infile", header = TRUE, stringsAsFactors = FALSE)
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63 peak_list = split(peak_tabular, f = peak_tabular\$spectrum) ## will be ordered according to spectrum
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64 pixelnames = unique(peak_tabular\$spectrum)
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65
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66 peaks = list()
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67 for (spectra in 1:length(peak_list))
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68 {
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69 single_peaks = createMassPeaks(peak_list[[spectra]]\$mass, peak_list[[spectra]]\$intensity, snr=peak_list[[spectra]]\$snr)
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70 peaks[[spectra]] = single_peaks
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71 }
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73 #end if
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76 #end if
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78 ## Quality control plots during peak detection
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80 pdf("peaks_qc_plot.pdf", fonts = "Times", pointsize = 12)
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81 plot(0,type='n',axes=FALSE,ann=FALSE)
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83 ## if no filename is given, name of file in Galaxy history is used
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84 #set $filename = $infile.display_name
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85
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86 title(main=paste("$filename"))
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87
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88 ## plot input file spectrum:
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89 #if $infile.ext == 'imzml'
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90
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91 #if str($centroids) == "TRUE"
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92 plot(peaks[[1]], main="First spectrum of input file")
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93 #else
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94 avgSpectra <- averageMassSpectra(maldi_data,method="mean")
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95 plot(avgSpectra, main="Average spectrum of input file")
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96 #end if
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97 #elif $infile.ext == 'tabular'
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98 plot(peaks[[1]], main="First spectrum of input file")
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99 #end if
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100
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101
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102 #if str($tabular_annotation.load_annotation) == 'yes_annotation':
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103
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104 ## read and extract x,y,annotation information
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105 input_tabular = read.delim("$tabular_annotation.annotation_file", header = $tabular_annotation.tabular_header, stringsAsFactors = FALSE)
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106 annotation_input = input_tabular[,c($tabular_annotation.column_x, $tabular_annotation.column_y, $tabular_annotation.column_names)]
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107 colnames(annotation_input) = c("x", "y", "annotation") ## rename annotations header to default name "annotation"
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108
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109 ## merge with coordinate information of MSI data
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110
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111 coordinates_st = cbind(coordinates(maldi_data)[,1:2], c(1:length(maldi_data)))
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112 colnames(coordinates_st)[3] = "pixel_index"
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113 merged_annotation = merge(coordinates_st, annotation_input, by=c("x", "y"), all.x=TRUE)
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114 merged_annotation[is.na(merged_annotation)] = "NA"
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115 merged_annotation = merged_annotation[order(merged_annotation\$pixel_index),]
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116 samples = as.factor(merged_annotation\$annotation)
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117
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118 ## print annotation overview into PDF output
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119
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120 ## the more annotation groups a file has the smaller will be the legend
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121 number_combined = length(levels(as.factor(merged_annotation\$annotation)))
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122 if (number_combined<20){
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123 legend_size = 10
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124 }else if (number_combined>20 && number_combined<40){
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125 legend_size = 9
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126 }else if (number_combined>40 && number_combined<60){
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127 legend_size = 8
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128 }else if (number_combined>60 && number_combined<100){
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129 legend_size = 7
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130 }else{
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131 legend_size = 6
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132 }
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133
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134 combine_plot = ggplot(merged_annotation, aes(x=x, y=y, fill=annotation))+
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135 geom_tile() +
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136 coord_fixed()+
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137 ggtitle("Spatial orientation of annotated data")+
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138 theme_bw()+
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139 theme(plot.title = element_text(hjust = 0.5))+
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140 theme(text=element_text(family="ArialMT", face="bold", size=12))+
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141 theme(legend.position="bottom",legend.direction="vertical")+
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142 theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = legend_size))+
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143 guides(fill=guide_legend(ncol=5,byrow=TRUE))
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144
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145 print(combine_plot)
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146
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147 #end if
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148
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149
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150 #################### Preprocessing methods #####################################
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151
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152 #for $method in $methods:
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153
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154
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155 #if str( $method.methods_conditional.method ) == 'Peak_detection':
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156 print('peak detection')
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157 ##peak detection
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158
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159 #if $method.methods_conditional.use_annotations:
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160 maldi_data <- averageMassSpectra(maldi_data, labels=samples,method="mean") ## use average spectra for peak picking
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161 pixelnames = merged_annotation\$annotation
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162 summarized_spectra = TRUE
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163
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164 #end if
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165
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166 peaks <- detectPeaks(maldi_data, method="$method.methods_conditional.peak_method",
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167 halfWindowSize=$method.methods_conditional.halfWindowSize,SNR=$method.methods_conditional.snr)
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168
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169 ## QC plot
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170 plot(peaks[[1]], main="First spectrum after peak detection")
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171
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172 if (length(peaks[!sapply(peaks, isEmpty)])>0){
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173 #if $infile.ext == 'imzml'
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galaxyp
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174 #if str($centroids) == "FALSE"
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175 featureMatrix <- intensityMatrix(peaks, maldi_data)
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176 #end if
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177 #else
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178 featureMatrix <- intensityMatrix(peaks)
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179 #end if
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180 featureMatrix2 =cbind(pixelnames, featureMatrix)
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181 colnames(featureMatrix2)[1] = c("mz | spectra")
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182 featureMatrix2 = t(featureMatrix2)
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183 write.table(featureMatrix2, file="$intensity_matrix", quote = FALSE, row.names = TRUE, col.names=FALSE, sep = "\t")
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184 }else{print("There are no spectra with peaks left")}
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185
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186
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187 #elif str( $method.methods_conditional.method ) == 'monoisotopic_peaks':
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188
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189 print('monoisotopic peaks')
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190 ##monoisotopic peaks
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191
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192 peaks = monoisotopicPeaks(peaks, minCor=$method.methods_conditional.minCor, tolerance=$method.methods_conditional.tolerance, distance=$method.methods_conditional.distance, size=$method.methods_conditional.size)
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193
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194 ## QC plot
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195 plot(peaks[[1]], main="First spectrum after monoisotopic peaks detection")
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196
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197 if (length(peaks[!sapply(peaks, isEmpty)])>0){
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198 #if $infile.ext == 'imzml'
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199 #if str($centroids) == "FALSE"
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200 featureMatrix <- intensityMatrix(peaks, maldi_data)
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201 #end if
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202 #else
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203 featureMatrix <- intensityMatrix(peaks)
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204 #end if
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205 featureMatrix2 =cbind(pixelnames, featureMatrix)
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206 colnames(featureMatrix2)[1] = c("mz | spectra")
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207 featureMatrix2 = t(featureMatrix2)
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galaxyp
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208 write.table(featureMatrix2, file="$intensity_matrix", quote = FALSE, row.names = TRUE, col.names=FALSE, sep = "\t")
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209 }else{print("There are no spectra with peaks left")}
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210
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211 #elif str( $method.methods_conditional.method ) == 'Binning':
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212
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213 print('binning')
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214 ##m/z binning
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215
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216 peaks <- binPeaks(peaks, tolerance=$method.methods_conditional.bin_tolerance)
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217 ## QC plot
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218 plot(peaks[[1]], main="First spectrum after binning")
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219
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220 if (length(peaks[!sapply(peaks, isEmpty)])>0){
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221 #if $infile.ext == 'imzml'
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222 #if str($centroids) == "FALSE"
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223 featureMatrix <- intensityMatrix(peaks, maldi_data)
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224 #end if
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225 #if str($centroids) == "TRUE"
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226 featureMatrix <- intensityMatrix(peaks)
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227 #end if
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228 #else
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229 featureMatrix <- intensityMatrix(peaks)
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230 #end if
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231 featureMatrix2 =cbind(pixelnames, featureMatrix)
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232 colnames(featureMatrix2)[1] = c("mz | spectra")
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233 featureMatrix2 = t(featureMatrix2)
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234 write.table(featureMatrix2, file="$intensity_matrix", quote = FALSE, row.names = TRUE, col.names=FALSE, sep = "\t")
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235 }else{print("There are no spectra with peaks left")}
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236
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237
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238 #elif str( $method.methods_conditional.method ) == 'Filtering':
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239
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240 print('filtering')
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241 ##m/z filtering
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242
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243 ## filtering on all pixels or on pixel groups:
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244 #if str($method.methods_conditional.filter_annot_groups ) == 'FALSE':
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245
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246 peaks <- filterPeaks(peaks,
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247 minFrequency=$method.methods_conditional.minFrequency,
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248 minNumber=$method.methods_conditional.minNumber,
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249 mergeWhitelists=$method.methods_conditional.mergeWhitelists)
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250
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galaxyp
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251 #elif str( $method.methods_conditional.filter_annot_groups ) == 'TRUE':
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252
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253 peaks <- filterPeaks(peaks,
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254 minFrequency=$method.methods_conditional.minFrequency,
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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255 minNumber=$method.methods_conditional.minNumber,
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256 mergeWhitelists=$method.methods_conditional.mergeWhitelists, label = samples)
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257 #end if
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258
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259 ##QC plot
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260 plot(peaks[[1]], main="First spectrum after m/z filtering")
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261
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262 if (length(peaks[!sapply(peaks, isEmpty)])>0){
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263 #if $infile.ext == 'imzml'
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264 #if str($centroids) == "FALSE"
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265 featureMatrix <- intensityMatrix(peaks, maldi_data)
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266 #end if
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267 #else
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268 featureMatrix <- intensityMatrix(peaks)
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269 #end if
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270 featureMatrix2 =cbind(pixelnames, featureMatrix)
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271 colnames(featureMatrix2)[1] = c("mz | spectra")
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272 featureMatrix2 = t(featureMatrix2)
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273 write.table(featureMatrix2, file="$intensity_matrix", quote = FALSE, row.names = TRUE, col.names=FALSE, sep = "\t")
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274 }else{print("There are no spectra with peaks left")}
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275
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276 #end if
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277 #end for
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278
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279 if (length(peaks[!sapply(peaks, isEmpty)])>0){
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280 ## mass peaks output
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281 mass_peaks = data.frame(matrix(,ncol=3, nrow=0))
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282 for (spectrum in 1:length(peaks)){
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283 spectrum_df = data.frame(peaks[[spectrum]]@snr, peaks[[spectrum]]@mass, peaks[[spectrum]]@intensity)
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284 spectrum_df\$spectrum_id = rep(pixelnames[[spectrum]], length(peaks[[spectrum]]@mass))
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285 mass_peaks = rbind(mass_peaks,spectrum_df)
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286 }
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287 colnames(mass_peaks) = c("snr", "mass", "intensity", "spectrum")
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288 write.table(mass_peaks, file="$masspeaks", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
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289 }else{print("There are no spectra with peaks left")}
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290
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291 dev.off()
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292
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293 if (summarized_spectra == FALSE){
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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294 #if $infile.ext == 'imzml'
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295 exportImzMl(peaks, file="out.imzMl", processed=$export_processed)
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296 #elif $infile.ext == 'tabular'
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297 masspeaks_coordinates = matrix(unlist(strsplit(as.character(pixelnames), "\\,")), ncol=2, byrow=TRUE)
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298 ## extract x and y values and create the coordinate matrix in case tabular was input
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299 peaklist_coordinates = unique(cbind(as.numeric(substring(masspeaks_coordinates[,1], 5, last = 1000000L)), as.numeric(substring(masspeaks_coordinates[,2], 5, last = 1000000L))))
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300 exportImzMl(peaks, file="out.imzMl", processed=$export_processed, coordinates=peaklist_coordinates)
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301 #end if
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302 }
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303
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304 ]]>
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305 </configfile>
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306 </configfiles>
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307 <inputs>
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308 <param name="infile" type="data" format="imzml,tabular" label="MS metadata" help="This file is in imzML or tabular format (peak list, peak detection cannot be run again)"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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309 <param name="centroids" type="boolean" label="Is the imzML 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"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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310 <conditional name="restriction_conditional">
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311 <param name="restriction" type="select" label="Restrict the preprocessing to coordinates of interest">
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312 <option value="no_restriction" selected="True">Calculate on entire file</option>
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313 <option value="restrict">Restrict to coordinates of interest</option>
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314 </param>
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315 <when value="restrict">
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316 <param name="coordinates_file" type="data" format="tabular" label="Tabular file with coordinates which should be read" help="x-values in first column, y-values in second column"/>
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317 </when>
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318 <when value="no_restriction"/>
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319 </conditional>
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320
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321 <conditional name="tabular_annotation">
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322 <param name="load_annotation" type="select" label="Use pixel annotation from tabular file - select in peak detection or filtering step where you want to apply the annotation information">
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323 <option value="no_annotation" selected="True">pixels belong into one group only</option>
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324 <option value="yes_annotation">use pixel annotation from a tabular file</option>
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diff changeset
325 </param>
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326 <when value="yes_annotation">
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327 <param name="annotation_file" type="data" format="tabular" label="Use annotations from tabular file"
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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328 help="Tabular file with three columns: x values, y values and pixel annotations"/>
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329 <param name="column_x" data_ref="annotation_file" label="Column with x values" type="data_column"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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330 <param name="column_y" data_ref="annotation_file" label="Column with y values" type="data_column"/>
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331 <param name="column_names" data_ref="annotation_file" label="Column with pixel annotations" type="data_column"/>
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332 <param name="tabular_header" type="boolean" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/>
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333 </when>
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334 <when value="no_annotation"/>
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335 </conditional>
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336 <repeat name="methods" title="Method" min="1">
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galaxyp
parents:
diff changeset
337 <conditional name="methods_conditional">
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
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338 <param name="method" type="select" label="Select the method you want to apply">
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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339 <option value="Peak_detection">Peak detection</option>
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galaxyp
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340 <option value="monoisotopic_peaks">Keep only monoisotopic peaks</option>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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341 <option value="Binning">Binning</option>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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342 <option value="Filtering">Filtering</option>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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diff changeset
343 </param>
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galaxyp
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344 <when value="Peak_detection">
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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345 <param name="peak_method" type="select" label="Noise estimation function">
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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346 <option value="MAD" selected="True">MAD</option>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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347 <option value="SuperSmoother">SuperSmoother</option>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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348 </param>
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galaxyp
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349 <param name="halfWindowSize" type="integer" value="20"
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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diff changeset
350 label="Half window size"
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galaxyp
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351 help="The resulting window reaches from
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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352 mass[currentIndex-halfWindowSize] to mass[currentIndex+halfWindowSize]
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galaxyp
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353 (window size is 2*halfWindowSize+1).
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galaxyp
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354 The best size differs depending on the selected smoothing method."/>
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galaxyp
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355 <param name="snr" type="integer" value="2" label="Signal-to-noise-ratio" help=""/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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356 <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"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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357 </when>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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358 <when value="monoisotopic_peaks">
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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359 <param name="minCor" type="float" value="0.95" label="minimal correlation"
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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360 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"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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361 <param name="tolerance" type="float" label="tolerance" value="0.0004"
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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362 help="double, maximal relative deviation of peaks position (mass) to be considered as isotopic distance"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
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363 <param name="distance" type="float" label="distance" value="1.00235" help="double, distance between two consecutive peaks in an isotopic pattern"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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diff changeset
364 <param name="size" type="integer" label="size" value="3" help="double, size (length) of isotopic pattern, longer patterns are prefered over shorter ones"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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diff changeset
365 </when>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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366 <when value="Binning">
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galaxyp
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367 <param name="bin_tolerance" type="float" value="0.002" label="Peak binning tolerance"
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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368 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."/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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369 </when>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
370 <when value="Filtering">
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galaxyp
parents:
diff changeset
371 <param name="minFrequency" type="float" value="0.25"
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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diff changeset
372 label="Remove all peaks which occur in less than minFrequency spectra" help="It is a relative threshold."/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
373 <param name="minNumber" type="float" value="1.0"
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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diff changeset
374 label="remove all peaks which occur in less than minNumber spectra" help="It is an absolute threshold."/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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diff changeset
375 <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"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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diff changeset
376 <param name="mergeWhitelists" type="boolean" truevalue="TRUE" falsevalue="FALSE"
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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377 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"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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diff changeset
378 </when>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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diff changeset
379 </conditional>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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diff changeset
380 </repeat>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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diff changeset
381 <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"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
382 </inputs>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
383 <outputs>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
384 <data format="imzml" name="outfile_imzml" label="$infile.display_name peaks" />
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
385 <data format="pdf" name="plots" from_work_dir="peaks_qc_plot.pdf" label = "$infile.display_name peakdetection QC"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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diff changeset
386 <data format="tabular" name="masspeaks" label="$infile.display_name mass_peaks"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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diff changeset
387 <data format="tabular" name="intensity_matrix" label="intensity_matrix"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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diff changeset
388 </outputs>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
389 <tests>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
390 <test>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
391 <param name="infile" value="" ftype="imzml">
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
392 <composite_data value="Example_Continuous.imzML"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
393 <composite_data value="Example_Continuous.ibd"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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diff changeset
394 </param>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
395 <conditional name="tabular_annotation">
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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diff changeset
396 <param name="load_annotation" value="yes_annotation"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
397 <param name="annotation_file" value="pixel_annotations.tabular"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
398 <param name="column_x" value="1"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
399 <param name="column_y" value="2"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
400 <param name="column_names" value="3"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
401 <param name="tabular_header" value="TRUE"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
402 </conditional>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
403 <repeat name="methods">
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
404 <conditional name="methods_conditional">
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
405 <param name="method" value="Peak_detection"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
406 <param name="peak_method" value="SuperSmoother"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
407 <param name="halfWindowSize" value="1"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
408 <param name="snr" value="5"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
409 <param name="use_annotations" value="TRUE"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
410 </conditional>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
411 </repeat>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
412 <output name="plots" file="peakdetection1_QC.pdf" compare="sim_size"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
413 <output name="masspeaks" file="masspeaks1.tabular"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
414 <output name="intensity_matrix" file="int1.tabular"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
415 </test>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
416 <test>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
417 <param name="infile" value="masspeaks1_forinput.tabular"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
418 <param name="centroids" value="TRUE"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
419 <repeat name="methods">
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
420 <conditional name="methods_conditional">
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
421 <param name="method" value="monoisotopic_peaks"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
422 <param name="minCor" value="0.60"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
423 <param name="tolerance" value="0.0001"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
424 </conditional>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
425 </repeat>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
426 <output name="plots" file="peakdetection2_QC.pdf" compare="sim_size"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
427 <output name="masspeaks" file="masspeaks2.tabular"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
428 <output name="intensity_matrix" file="int2.tabular"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
429 </test>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
430 <test>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
431 <param name="infile" value="" ftype="imzml">
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
432 <composite_data value="Example_Continuous.imzML"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
433 <composite_data value="Example_Continuous.ibd"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
434 </param>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
435 <conditional name="tabular_annotation">
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
436 <param name="load_annotation" value="yes_annotation"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
437 <param name="annotation_file" value="pixel_annotations.tabular"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
438 <param name="column_x" value="1"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
439 <param name="column_y" value="2"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
440 <param name="column_names" value="3"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
441 <param name="tabular_header" value="TRUE"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
442 </conditional>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
443 <repeat name="methods">
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
444 <conditional name="methods_conditional">
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
445 <param name="method" value="Peak_detection"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
446 <param name="peak_method" value="MAD"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
447 <param name="halfWindowSize" value="1"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
448 <param name="snr" value="2"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
449 </conditional>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
450 </repeat>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
451 <repeat name="methods">
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
452 <conditional name="methods_conditional">
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
453 <param name="method" value="Binning"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
454 <param name="bin_tolerance" value="0.01"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
455 </conditional>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
456 </repeat>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
457 <repeat name="methods">
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
458 <conditional name="methods_conditional">
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
459 <param name="method" value="Filtering"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
460 <param name="bin_tolerance" value="0.01"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
461 <param name="minFrequency" value="0.5"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
462 <param name="minNumber" value="3"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
463 <param name="filter_annot_groups" value="TRUE"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
464 <param name="mergeWhitelists" value="FALSE"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
465 </conditional>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
466 </repeat>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
467 <output name="plots" file="peakdetection3_QC.pdf" compare="sim_size"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
468 <output name="intensity_matrix" file="intensity_matrix3.tabular"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
469 <output name="masspeaks" file="masspeaks3.tabular"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
470 </test>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
471 </tests>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
472 <help>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
473 <![CDATA[
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
474
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
475 MALDIquant_ provides a complete analysis pipeline for MALDI-TOF and other mass spectrometry data. So far we have only implemented the functionalities for mass spectrometry imaging data.
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
476
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
477 Input data:
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
478
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
479 - MSI data as imzML or file (upload via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/wp/imzml/>`_
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
480 - or MSI data as peak list (tabular file) with the columns named "snr", "mass", "intensity" and "spectrum". To obtain a valid imzML output file spectrum should contain the pixel coordinates in the format: "x = 1, y = 1"
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
481 - optinal tabular file with pixel coordinates to restrict reading of imzML file to coordinates of interest
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
482 - optional tabular file with pixel annotations. 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")
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
483
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
484
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
485 Options:
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
486
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
487 - Peak detection: detection of peaks, only possible with imzML input
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
488 - Monoisotopic peaks: detection of monoisotopic peaks
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
489 - Peak binning: After the alignment the peak positions (mass) are very similar but not identical. The binning is needed to make similar peak mass values identical.
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
490 - 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)
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
491
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
492
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
493 Output:
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
494
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
495 - centroided processed or continuous imzML file
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
496 - pdf with mass spectra after each preprocessing step
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
497 - peak list (tabular file) with the columns "snr", "mass", "intensity" and "spectrum"
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
498 - 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.
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
499
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
500 .. _MALDIquant: http://strimmerlab.org/software/maldiquant/
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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501
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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502 ]]>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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503 </help>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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504 <expand macro="citation"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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505 </tool>