Mercurial > repos > galaxyp > maldi_quant_peak_detection

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
author galaxyp
date Sat, 04 Mar 2023 19:14:04 +0000
parents d286ff4600dd
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7
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1 <tool id="maldi_quant_peak_detection" name="MALDIquant peak detection" version="@VERSION@.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 cat '${maldi_quant_peak_detection}' &&
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20 Rscript '${maldi_quant_peak_detection}' &&
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21 mkdir $outfile_imzml.files_path &&
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22 mv ./out.imzMl "${os.path.join($outfile_imzml.files_path, 'imzml')}" | true &&
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23 mv ./out.ibd "${os.path.join($outfile_imzml.files_path, 'ibd')}" | true &&
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24 echo "imzML file:" > $outfile_imzml &&
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25 ls -l "$outfile_imzml.files_path" >> $outfile_imzml
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26 ]]>
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27 </command>
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28 <configfiles>
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29 <configfile name="maldi_quant_peak_detection"><![CDATA[
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30
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31 @R_IMPORTS@
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32
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33 #if $restriction_conditional.restriction == 'restrict':
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34
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35 print('Reading mask region')
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36
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37 ## Import imzML file
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38 coordinate_matrix = read.delim("$restriction_conditional.coordinates_file", header = $restriction_conditional.coordinates_header, stringsAsFactors = FALSE)
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39 coordinate_matrix = coordinate_matrix[,c($restriction_conditional.column_x, $restriction_conditional.column_y)]
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40 #if str($centroids) == "TRUE"
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41 peaks <- importImzMl('infile.imzML',
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42 coordinates = as.matrix(coordinate_matrix), centroided = $centroids)
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43 pixelnames = paste("xy", coordinates(peaks)[,1],coordinates(peaks)[,2], sep="_")
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44 #else
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45 maldi_data <- importImzMl('infile.imzML',
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46 coordinates = as.matrix(coordinate_matrix), centroided = $centroids)
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47 pixelnames = paste("xy", coordinates(maldi_data)[,1],coordinates(maldi_data)[,2], sep="_")
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48 #end if
0
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49
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50 #else:
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51
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52 print('Reading entire file')
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53 ## Import imzML file
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54
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55 #if $infile.ext == 'imzml'
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56 print('imzML file')
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57 #if str($centroids) == "TRUE"
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58 peaks <- importImzMl('infile.imzML', centroided = $centroids)
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59 pixelnames = paste("xy", coordinates(peaks)[,1],coordinates(peaks)[,2], sep="_")
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60 coordinates_info = cbind(coordinates(peaks)[,1:2], c(1:length(peaks)))
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61 #else
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62 maldi_data <- importImzMl('infile.imzML', centroided = $centroids)
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63 pixelnames = paste("xy", coordinates(maldi_data)[,1],coordinates(maldi_data)[,2], sep="_")
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64 coordinates_info = cbind(coordinates(maldi_data)[,1:2], c(1:length(maldi_data)))
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65 #end if
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66
1
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67
0
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68 #elif $infile.ext == 'tabular'
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69 print('tabular file')
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70 #set $centroids = "TRUE" ## will be used in some if conditions
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71 peak_tabular = read.delim("$infile", header = TRUE, stringsAsFactors = FALSE)
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72 peak_list = split(peak_tabular, f = peak_tabular\$spectrum) ## will be ordered according to spectrum
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73 pixelnames = unique(peak_tabular\$spectrum)
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74
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75 peaks = list()
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76 for (spectra in 1:length(peak_list))
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77 {
1
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78 single_peaks = createMassPeaks(peak_list[[spectra]]\$mass, peak_list[[spectra]]\$intensity, snr=peak_list[[spectra]]\$snr)
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79 peaks[[spectra]] = single_peaks
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80 }
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81
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82 #end if
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83 #end if
0
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84
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85 ## default summarized = FALSE
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86 summarized_spectra = FALSE
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87
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88 ## Quality control plots during peak detection
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89 pdf("peaks_qc_plot.pdf", fonts = "Times", pointsize = 12)
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90 plot(0,type='n',axes=FALSE,ann=FALSE)
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91
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92 ## if no filename is given, name of file in Galaxy history is used
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93 #set $filename = $infile.display_name
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94
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95 title(main=paste("$filename"))
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96
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97 ## plot input file spectrum:
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98 #if $centroids:
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99 ## Choose random spectra for QC plots
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100 random_spectra = sample(1:length(peaks), size=4, replace=length(peaks)<4)## in case dataset has less than 4 spectra, same spetra are allowed to be sampled
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101 random_spectra_name = pixelnames[random_spectra]
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102 par(mfrow = c(2, 2), oma=c(0,0,2,0))
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103 for (random_sample in random_spectra){
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104 plot(peaks[[random_sample]],sub="", main=paste0("spectrum ", pixelnames[random_sample]))}
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105 title("Input spectra", outer=TRUE, line=0)
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106
1
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107 #else
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108 ## Choose random spectra for QC plots
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109 random_spectra = sample(1:length(maldi_data), size=4, replace=length(maldi_data)<4)## in case dataset has less than 4 spectra, same spetra are allowed to be sampled
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110 par(mfrow = c(2, 2), oma=c(0,0,2,0))
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111 for (random_sample in random_spectra){
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112 plot(maldi_data[[random_sample]],sub="", main=paste0("spectrum ", pixelnames[random_sample]))
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113 }
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114 title("Input spectra", outer=TRUE, line=0)
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115 #end if
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116
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117 ## QC numbers for input file
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118 #if str($centroids) == "TRUE"
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119 pixel_number = length(peaks)
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120 minmz = round(min(unlist(lapply(peaks,mass))), digits=4)
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121 maxmz = round(max(unlist(lapply(peaks,mass))), digits=4)
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122 mean_features = round(length(unlist(lapply(peaks,mass)))/length(peaks), digits=2)
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123 medint = round(median(unlist(lapply(peaks,intensity))), digits=2)
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124 number_features = length(unique(unlist(lapply(peaks,mass))))
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125 number_spectra = length(peaks)
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126 inputdata = c(minmz, maxmz,number_features,mean_features, medint, number_spectra)
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127 QC_numbers= data.frame(inputdata = c(minmz, maxmz,number_features, mean_features, medint, number_spectra))
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128 vectorofactions = "inputdata"
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129 #else
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130 pixel_number = length(maldi_data)
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131 minmz = round(min(unlist(lapply(maldi_data,mass))), digits=4)
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132 maxmz = round(max(unlist(lapply(maldi_data,mass))), digits=4)
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133 mean_features = round(length(unlist(lapply(maldi_data,mass)))/length(maldi_data), digits=2)
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134 medint = round(median(unlist(lapply(maldi_data,intensity))), digits=2)
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135 number_features = length(unique(unlist(lapply(maldi_data,mass))))
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136 number_spectra = length(maldi_data)
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137 inputdata = c(minmz, maxmz,number_features,mean_features, medint, number_spectra)
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138 QC_numbers= data.frame(inputdata = c(minmz, maxmz,number_features, mean_features, medint, number_spectra))
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139 vectorofactions = "inputdata"
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140 #end if
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141
0
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142 #if str($tabular_annotation.load_annotation) == 'yes_annotation':
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143
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144 ## read and extract x,y,annotation information
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145 input_tabular = read.delim("$tabular_annotation.annotation_file", header = $tabular_annotation.tabular_header, stringsAsFactors = FALSE)
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146 annotation_input = input_tabular[,c($tabular_annotation.column_x, $tabular_annotation.column_y, $tabular_annotation.column_names)]
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147 annotation_input[,3] <- as.character(annotation_input[,3]) ## make sure annotations are character
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148 colnames(annotation_input) = c("x", "y", "annotation") ## rename annotations header to default name "annotation"
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149
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150 ## merge provided annotation with coordinate information of MSI data
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151 colnames(coordinates_info)[3] = "pixel_index"
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152 merged_annotation = merge(coordinates_info, annotation_input, by=c("x", "y"), all.x=TRUE)
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153 merged_annotation[is.na(merged_annotation)] = "NA"
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154 ## order coordinate information according to pixel index to make sure that the order stays the same
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155 merged_annotation = merged_annotation[order(merged_annotation\$pixel_index),]
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156 samples = as.factor(merged_annotation\$annotation)
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157
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158 ## print annotation overview into PDF output
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159
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160 combine_plot = ggplot(merged_annotation, aes(x=x, y=y, fill=annotation))+
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161 geom_tile() +
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162 coord_fixed()+
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163 ggtitle("Spatial orientation of annotated data")+
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164 theme_bw()+
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165 theme(plot.title = element_text(hjust = 0.5))+
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166 theme(text=element_text(family="ArialMT", face="bold", size=12))+
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167 theme(legend.position="bottom",legend.direction="vertical")+
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168 theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = 8))+
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169 theme(legend.position="bottom",legend.direction="vertical")+
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170 guides(fill=guide_legend(ncol=4,byrow=TRUE))
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171
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172 print(combine_plot)
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173
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174 #end if
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175
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176 #################### Preprocessing methods #####################################
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177
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178 #for $method in $methods:
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179
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180 #if str( $method.methods_conditional.method ) == 'Peak_detection':
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181 print('peak detection')
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182 ##peak detection
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183
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184 #if $method.methods_conditional.use_annotations:
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185 maldi_data <- averageMassSpectra(maldi_data, labels=samples,method="mean") ## use average spectra for peak picking
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186 pixelnames = levels(samples)
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187 summarized_spectra = TRUE
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188 random_spectra = sample(1:length(maldi_data), 4, replace=TRUE)
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189 #end if
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190
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191 peaks <- detectPeaks(maldi_data, method="$method.methods_conditional.peak_method",
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192 halfWindowSize=$method.methods_conditional.halfWindowSize,SNR=$method.methods_conditional.snr)
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193
1
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194 ## QC plot and numbers
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195 ## plot old spectra with baseline in blue and picked peaks in green
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196 par(mfrow = c(2, 2), oma=c(0,0,2,0))
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197 for (random_sample in random_spectra){
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198 noise = estimateNoise(maldi_data[[random_sample]], method= "$method.methods_conditional.peak_method")
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199 plot(maldi_data[[random_sample]], sub="", main=paste0("spectrum ", pixelnames[random_sample]))
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200 lines(noise[,1], noise[,2]*$method.methods_conditional.snr, col="blue")
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201 points(peaks[[random_sample]], col="green", pch=20)}
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202 title("S/N in blue and picked peaks in green", outer=TRUE, line=0)
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203
2
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204 ## plot new spectrum
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205 par(mfrow = c(2, 2), oma=c(0,0,2,0))
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206 for (random_sample in random_spectra){
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207 plot(peaks[[random_sample]], sub="", main=paste0("spectrum ", pixelnames[random_sample]))}
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208 title("Picked peaks", outer=TRUE, line=0)
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209
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210 pixel_number = length(peaks)
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211 minmz = round(min(unlist(lapply(peaks,mass))), digits=4)
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212 maxmz = round(max(unlist(lapply(peaks,mass))), digits=4)
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213 mean_features = round(length(unlist(lapply(peaks,mass)))/length(peaks), digits=2)
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214 medint = round(median(unlist(lapply(peaks,intensity))), digits=2)
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215 number_features = length(unique(unlist(lapply(peaks,mass))))
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216 number_spectra = length(peaks)
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217 peaks_picked = c(minmz, maxmz,number_features,mean_features, medint, number_spectra)
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218 QC_numbers= cbind(QC_numbers, peaks_picked)
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219 vectorofactions = append(vectorofactions, "peaks_picked")
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220
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221 if (length(peaks[!sapply(peaks, isEmpty)])>0){
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222 featureMatrix <- intensityMatrix(peaks)
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223 #if $infile.ext == 'imzml'
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224 #if str($centroids) == "FALSE"
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225 featureMatrix <- intensityMatrix(peaks, maldi_data)
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226 #end if
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227 #end if
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228 featureMatrix2 =cbind(pixelnames, featureMatrix)
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229 colnames(featureMatrix2)[1] = c("mz")
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230 featureMatrix2 = t(featureMatrix2)
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231 write.table(featureMatrix2, file="$intensity_matrix", quote = FALSE, row.names = TRUE, col.names=FALSE, sep = "\t")
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232 }else{print("There are no spectra with peaks left")}
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233
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234
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235 #elif str( $method.methods_conditional.method ) == 'monoisotopic_peaks':
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236
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237 print('monoisotopic peaks')
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238 ##monoisotopic peaks
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239
3
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240 ## keep peaks to plot them with monoisotopic peaks
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241 picked_peaks = peaks
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242
3
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243 peaks = monoisotopicPeaks(peaks, minCor=$method.methods_conditional.minCor,
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244 tolerance=$method.methods_conditional.tolerance,
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245 distance=c($method.methods_conditional.distance),
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246 size=$method.methods_conditional.size)
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247
2
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248 ## plot old spectrum with picked isotopes as green dots
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249 par(mfrow = c(2, 2), oma=c(0,0,2,0))
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250 for (random_sample in random_spectra){
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251 plot(picked_peaks[[random_sample]], sub="", main=paste0("spectrum ", pixelnames[random_sample]))
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252 points(peaks[[random_sample]], col="green", pch=20)}
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253 title(paste0("Monoisotopic peaks in green"), outer=TRUE, line=0)
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254
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255
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256 par(mfrow = c(2, 2), oma=c(0,0,2,0))
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257 for (random_sample in random_spectra){
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258 plot(peaks[[random_sample]], sub="", main=paste0("spectrum ", pixelnames[random_sample]))}
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259 title("Monoisotopic peaks", outer=TRUE, line=0)
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260
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261 minmz = round(min(unlist(lapply(peaks,mass))), digits=4)
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262 maxmz = round(max(unlist(lapply(peaks,mass))), digits=4)
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263 mean_features = round(length(unlist(lapply(peaks,mass)))/length(peaks), digits=2)
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264 medint = round(median(unlist(lapply(peaks,intensity))), digits=2)
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265 number_features = length(unique(unlist(lapply(peaks,mass))))
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266 number_spectra = length(peaks)
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267 monoisotopes = c(minmz, maxmz,number_features,mean_features, medint, number_spectra)
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268 QC_numbers= cbind(QC_numbers, monoisotopes)
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269 vectorofactions = append(vectorofactions, "monoisotopes")
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270
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271 if (length(peaks[!sapply(peaks, isEmpty)])>0){
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272 featureMatrix <- intensityMatrix(peaks)
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273 ## only for profile imzML file: featurematrix is overwritten:
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274 #if $infile.ext == 'imzml'
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275 #if str($centroids) == "FALSE"
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276 featureMatrix <- intensityMatrix(peaks, maldi_data)
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277 #end if
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278 #end if
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279 featureMatrix2 =cbind(pixelnames, featureMatrix)
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280 colnames(featureMatrix2)[1] = c("mz")
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281 featureMatrix2 = t(featureMatrix2)
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282 write.table(featureMatrix2, file="$intensity_matrix", quote = FALSE, row.names = TRUE, col.names=FALSE, sep = "\t")
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283 }else{print("There are no spectra with peaks left")}
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284
3
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285
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286
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287 #elif str( $method.methods_conditional.method ) == 'Align':
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288
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289 print('align')
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290 ##align spectra with 2 separate functions
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291
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292
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293 #if str($method.methods_conditional.reference_for_alignment.align_ref) == 'no_reference':
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294 ## 1) calculate warping:
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295 warping_function <- determineWarpingFunctions(peaks,
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296 tolerance=$method.methods_conditional.tolerance, method="$method.methods_conditional.warping_method",
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297 allowNoMatches=$method.methods_conditional.allow_nomatch, minFrequency = $method.methods_conditional.reference_for_alignment.min_frequency)
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298 ## 2) warp spectra:
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299 peaks = warpMassPeaks(peaks, warping_function, emptyNoMatches=$method.methods_conditional.empty_nomatch)
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300
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301
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302 #elif str($method.methods_conditional.reference_for_alignment.align_ref) == 'yes_reference':
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303
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304 ## create reference mass_vector from tabular file
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305 mass_vector = read.delim("$method.methods_conditional.reference_for_alignment.reference_file", header = $method.methods_conditional.reference_for_alignment.reference_header, stringsAsFactors = FALSE)[,$method.methods_conditional.reference_for_alignment.mz_column]
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306 int_vector = rep(1,length(mass_vector))
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307 mass_list = createMassPeaks(mass_vector, int_vector)
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308
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309 #if str($method.methods_conditional.reference_for_alignment.separate_alignment) == "FALSE"
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310 print('default alignment')
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311
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312 ## 1) calculate warping:
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313 warping_function <- determineWarpingFunctions(peaks,
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314 tolerance=$method.methods_conditional.tolerance, method="$method.methods_conditional.warping_method",
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315 allowNoMatches=$method.methods_conditional.allow_nomatch, reference = mass_list)
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316 ## 2) warp spectra:
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317 peaks = warpMassPeaks(peaks, warping_function, emptyNoMatches=$method.methods_conditional.empty_nomatch)
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318
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319 #elif str($method.methods_conditional.reference_for_alignment.separate_alignment) == "TRUE"
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320 print('spectra wise alignment')
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321
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322 peaks_new_list =list()
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323
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324 for (pixelnb in 1:length(peaks))
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325 {
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326
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327 ## 1) calculate warping:
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328 warping_function <- determineWarpingFunctions(peaks[[pixelnb]],
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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329 tolerance=$method.methods_conditional.tolerance, method="$method.methods_conditional.warping_method",
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330 allowNoMatches=$method.methods_conditional.allow_nomatch, reference = mass_list)
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331 ## 2) warp spectra:
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332 peaks_new_list = warpMassPeaks(list(peaks[[pixelnb]]), warping_function, emptyNoMatches=$method.methods_conditional.empty_nomatch)
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333 }
5
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334 peaks = peaks_new_list
3
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335
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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336 #end if
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337
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338 #end if
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339
5
e66f552a3c47 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 218c44b9ba1b5f0f47edb743ed70075fb661386e"
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340 #if $method.methods_conditional.remove_empty:
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341 print(paste(length(findEmptyMassObjects(peaks)), " empty spectra were removed", sep=" "))
e66f552a3c47 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 218c44b9ba1b5f0f47edb743ed70075fb661386e"
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342
e66f552a3c47 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 218c44b9ba1b5f0f47edb743ed70075fb661386e"
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343 ## only if there are empty spectra to remove
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344
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345 if (length(findEmptyMassObjects(peaks))>0)
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346
e66f552a3c47 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 218c44b9ba1b5f0f47edb743ed70075fb661386e"
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347 {
e66f552a3c47 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 218c44b9ba1b5f0f47edb743ed70075fb661386e"
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348
e66f552a3c47 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 218c44b9ba1b5f0f47edb743ed70075fb661386e"
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349 peaks = removeEmptyMassObjects(peaks)
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350 pixelnames = paste("xy", coordinates(peaks)[,1],coordinates(peaks)[,2], sep="_")
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351 }
e66f552a3c47 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 218c44b9ba1b5f0f47edb743ed70075fb661386e"
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352 #end if
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353
3
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354 ## QC plot and numbers
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355 par(mfrow = c(2, 2), oma=c(0,0,2,0))
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356
3
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357 for (random_sample in random_spectra){
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358
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359 tryCatch(
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360 {
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361 plot(peaks[[random_sample]], sub="", main=paste0("spectrum ", pixelnames[random_sample]))
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362 },error=function(cond)
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363 {
d286ff4600dd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 8c5cd26641af4b6206662ee525c1e7bd4205d96e"
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364 plot(NULL, xlim=c(0,0), ylim=c(0,0), ylab="intensity", xlab="m/z")
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365 }
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366 )
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367 }
5
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368
3
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369 title("Aligned spectra", outer=TRUE, line=0)
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370 minmz = round(min(unlist(lapply(peaks,mass))), digits=4)
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371 maxmz = round(max(unlist(lapply(peaks,mass))), digits=4)
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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372 mean_features = round(length(unlist(lapply(peaks,mass)))/length(peaks), digits=2)
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373 medint = round(median(unlist(lapply(peaks,intensity))), digits=2)
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374 number_features = length(unique(unlist(lapply(peaks,mass))))
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375 number_spectra = length(peaks)
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376 aligned = c(minmz, maxmz,number_features,mean_features, medint, number_spectra)
3
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377 QC_numbers= cbind(QC_numbers, aligned)
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378 vectorofactions = append(vectorofactions, "aligned")
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379
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380 if (length(peaks[!sapply(peaks, isEmpty)])>0){
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381 featureMatrix <- intensityMatrix(peaks)
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382 ## only for profile imzML file: featurematrix is overwritten:
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383 #if $infile.ext == 'imzml'
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384 #if str($centroids) == "FALSE"
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385 featureMatrix <- intensityMatrix(peaks, maldi_data)
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386 #end if
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387 #end if
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388
3
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389 featureMatrix2 =cbind(pixelnames, featureMatrix)
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390 colnames(featureMatrix2)[1] = c("mz")
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391 featureMatrix2 = t(featureMatrix2)
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392 write.table(featureMatrix2, file="$intensity_matrix", quote = FALSE, row.names = TRUE, col.names=FALSE, sep = "\t")
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393 }else{print("There are no spectra with peaks left")}
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394
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395
0
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396 #elif str( $method.methods_conditional.method ) == 'Binning':
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397
7
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398
0
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399 print('binning')
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400 ##m/z binning
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401
2
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402 peaks <- binPeaks(peaks, tolerance=$method.methods_conditional.bin_tolerance, method="$method.methods_conditional.bin_method")
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403
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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404 ## QC plot and numbers
3
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405 par(mfrow = c(2, 2), oma=c(0,0,2,0))
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406
3
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407 for (random_sample in random_spectra){
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408
d286ff4600dd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 8c5cd26641af4b6206662ee525c1e7bd4205d96e"
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409 tryCatch(
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410 {
d286ff4600dd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 8c5cd26641af4b6206662ee525c1e7bd4205d96e"
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diff changeset
411 plot(peaks[[random_sample]], sub="", main=paste0("spectrum ", pixelnames[random_sample]))
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412 },error=function(cond)
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diff changeset
413 {
d286ff4600dd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 8c5cd26641af4b6206662ee525c1e7bd4205d96e"
galaxyp
parents: 5
diff changeset
414 plot(NULL, xlim=c(0,0), ylim=c(0,0), ylab="intensity", xlab="m/z")
d286ff4600dd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 8c5cd26641af4b6206662ee525c1e7bd4205d96e"
galaxyp
parents: 5
diff changeset
415 }
d286ff4600dd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 8c5cd26641af4b6206662ee525c1e7bd4205d96e"
galaxyp
parents: 5
diff changeset
416 )
d286ff4600dd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 8c5cd26641af4b6206662ee525c1e7bd4205d96e"
galaxyp
parents: 5
diff changeset
417 }
d286ff4600dd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 8c5cd26641af4b6206662ee525c1e7bd4205d96e"
galaxyp
parents: 5
diff changeset
418
3
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
419 title("Binned spectra", outer=TRUE, line=0)
1
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
420 minmz = round(min(unlist(lapply(peaks,mass))), digits=4)
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
421 maxmz = round(max(unlist(lapply(peaks,mass))), digits=4)
2
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
422 mean_features = round(length(unlist(lapply(peaks,mass)))/length(peaks), digits=2)
1
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
423 medint =round( median(unlist(lapply(peaks,intensity))), digits=2)
2
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
424 number_features = length(unique(unlist(lapply(peaks,mass))))
7
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
425 number_spectra = length(peaks)
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
426 binned = c(minmz, maxmz,number_features,mean_features, medint, number_spectra)
1
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
427 QC_numbers= cbind(QC_numbers, binned)
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
428 vectorofactions = append(vectorofactions, "binned")
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
429
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
430 if (length(peaks[!sapply(peaks, isEmpty)])>0){
2
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
431 featureMatrix <- intensityMatrix(peaks)
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
432 #if $infile.ext == 'imzml'
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
433 #if str($centroids) == "FALSE"
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
434 featureMatrix <- intensityMatrix(peaks, maldi_data)
2
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
435 #elif str($centroids) == "TRUE"
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
436 featureMatrix <- intensityMatrix(peaks)
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
437 #end if
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
438 #end if
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
439 featureMatrix2 =cbind(pixelnames, featureMatrix)
1
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
440 colnames(featureMatrix2)[1] = c("mz")
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
441 featureMatrix2 = t(featureMatrix2)
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
442 write.table(featureMatrix2, file="$intensity_matrix", quote = FALSE, row.names = TRUE, col.names=FALSE, sep = "\t")
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
443 }else{print("There are no spectra with peaks left")}
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
444
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
445
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
446 #elif str( $method.methods_conditional.method ) == 'Filtering':
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
447
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
448 print('filtering')
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
449 ##m/z filtering
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
450
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
451
7
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
452 peaks <- filterPeaks(peaks
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
453 #if str( $method.methods_conditional.filter_type.filter_params ) != 'min_Number':
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
454 ,minFrequency=$method.methods_conditional.filter_type.minFrequency
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
455 #end if
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
456 #if str( $method.methods_conditional.filter_type.filter_params ) != 'min_Frequency':
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
457 ,minNumber=$method.methods_conditional.filter_type.minNumber
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
458 #end if
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
459 ## in case of group wise filtering set grouping conditions
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
460 #if str( $method.methods_conditional.filter_groups.filter_annot_groups ) == 'yes_grouping':
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
461 ,mergeWhitelists=$method.methods_conditional.filter_groups.mergeWhitelists, label = samples
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
462 #end if
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
463 ) ## finishes filterPeaks function
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
464
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
465
1
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
466 ##QC plot and numbers
3
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
467 par(mfrow = c(2, 2), oma=c(0,0,2,0))
6
d286ff4600dd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 8c5cd26641af4b6206662ee525c1e7bd4205d96e"
galaxyp
parents: 5
diff changeset
468
3
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
469 for (random_sample in random_spectra){
6
d286ff4600dd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 8c5cd26641af4b6206662ee525c1e7bd4205d96e"
galaxyp
parents: 5
diff changeset
470
d286ff4600dd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 8c5cd26641af4b6206662ee525c1e7bd4205d96e"
galaxyp
parents: 5
diff changeset
471 tryCatch(
d286ff4600dd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 8c5cd26641af4b6206662ee525c1e7bd4205d96e"
galaxyp
parents: 5
diff changeset
472 {
d286ff4600dd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 8c5cd26641af4b6206662ee525c1e7bd4205d96e"
galaxyp
parents: 5
diff changeset
473 plot(peaks[[random_sample]], sub="", main=paste0("spectrum ", pixelnames[random_sample]))
d286ff4600dd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 8c5cd26641af4b6206662ee525c1e7bd4205d96e"
galaxyp
parents: 5
diff changeset
474 },error=function(cond)
d286ff4600dd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 8c5cd26641af4b6206662ee525c1e7bd4205d96e"
galaxyp
parents: 5
diff changeset
475 {
d286ff4600dd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 8c5cd26641af4b6206662ee525c1e7bd4205d96e"
galaxyp
parents: 5
diff changeset
476 plot(NULL, xlim=c(0,0), ylim=c(0,0), ylab="intensity", xlab="m/z")
d286ff4600dd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 8c5cd26641af4b6206662ee525c1e7bd4205d96e"
galaxyp
parents: 5
diff changeset
477 }
d286ff4600dd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 8c5cd26641af4b6206662ee525c1e7bd4205d96e"
galaxyp
parents: 5
diff changeset
478 )
d286ff4600dd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 8c5cd26641af4b6206662ee525c1e7bd4205d96e"
galaxyp
parents: 5
diff changeset
479 }
d286ff4600dd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 8c5cd26641af4b6206662ee525c1e7bd4205d96e"
galaxyp
parents: 5
diff changeset
480
7
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
481 ## QC numbers for filtered file
3
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
482 title("Filtered spectra", outer=TRUE, line=0)
1
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
483 minmz = round(min(unlist(lapply(peaks,mass))), digits=4)
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
484 maxmz = round(max(unlist(lapply(peaks,mass))), digits=4)
2
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
485 mean_features = round(length(unlist(lapply(peaks,mass)))/length(peaks), digits=2)
1
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
486 medint = round(median(unlist(lapply(peaks,intensity))), digits=2)
2
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
487 number_features = length(unique(unlist(lapply(peaks,mass))))
7
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
488 number_spectra = length(peaks)
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
489 filtered = c(minmz, maxmz,number_features,mean_features, medint, number_spectra)
1
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
490 QC_numbers= cbind(QC_numbers, filtered)
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
491 vectorofactions = append(vectorofactions, "filtered")
0
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 if (length(peaks[!sapply(peaks, isEmpty)])>0){
2
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
494 featureMatrix <- intensityMatrix(peaks)
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
495 #if $infile.ext == 'imzml'
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
496 #if str($centroids) == "FALSE"
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
497 featureMatrix <- intensityMatrix(peaks, maldi_data)
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
498 #end if
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
499 #end if
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
500 featureMatrix2 =cbind(pixelnames, featureMatrix)
1
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
501 colnames(featureMatrix2)[1] = c("mz")
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
502 featureMatrix2 = t(featureMatrix2)
1
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
503 }else{print("There are no spectra with peaks left")
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
504 featureMatrix2 = matrix(0, ncol=1, nrow=1)}
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
505 write.table(featureMatrix2, file="$intensity_matrix", quote = FALSE, row.names = TRUE, col.names=FALSE, sep = "\t")
7
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
506
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
507 #elif str( $method.methods_conditional.method ) == 'skip_preprocessing':
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
508 ##for now as option to filter large files
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
509
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
510 #end if
7
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
511
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
512 #end for
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
513
1
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
514 if (length(peaks[!sapply(peaks, isEmpty)])>0){
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
515 ## mass peaks output
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
516 mass_peaks = data.frame(matrix(,ncol=3, nrow=0))
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
517 for (spectrum in 1:length(peaks)){
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
518 spectrum_df = data.frame(peaks[[spectrum]]@snr, peaks[[spectrum]]@mass, peaks[[spectrum]]@intensity)
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
519 spectrum_df\$spectrum_id = rep(pixelnames[[spectrum]], length(peaks[[spectrum]]@mass))
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
520 mass_peaks = rbind(mass_peaks,spectrum_df)
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
521 }
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
522 colnames(mass_peaks) = c("snr", "mass", "intensity", "spectrum")
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
523 write.table(mass_peaks, file="$masspeaks", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
524 }else{print("There are no spectra with peaks left")}
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
525
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
526 ## print table with QC values
7
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
527 rownames(QC_numbers) = c("min m/z", "max mz", "# features", "median \n# peaks (int.>0)", "median\nintensity", "# spectra")
1
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
528 plot(0,type='n',axes=FALSE,ann=FALSE)
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
529 grid.table(t(QC_numbers))
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
530
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
531 dev.off()
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
532
7
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
533
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
534 if (summarized_spectra == FALSE){
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
535 #if $infile.ext == 'imzml'
3
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
536 MALDIquantForeign::exportImzMl(peaks, file="out.imzMl", processed=TRUE)
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
537 #elif $infile.ext == 'tabular'
1
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
538 masspeaks_coordinates = matrix(unlist(strsplit(as.character(pixelnames), "\\_")), ncol=3, byrow=TRUE)
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
539 ## extract x and y values and create the coordinate matrix in case tabular was input
1
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
540 peaklist_coordinates = unique(cbind(as.numeric(masspeaks_coordinates[,2]), as.numeric(masspeaks_coordinates[,3])))
3
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
541 exportImzMl(peaks, file="out.imzMl", processed=TRUE, coordinates=peaklist_coordinates)
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
542 #end if
1
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
543
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
544 }
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
545
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
546 ]]>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
547 </configfile>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
548 </configfiles>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
549 <inputs>
7
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
550 <param name="infile" type="data" format="imzml,tabular" label="MSI data" help="Input file as imzML (composite upload) or tabular peaklist (regular upload)"/>
3
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
551 <param name="centroids" type="boolean" label="Centroided input" help="Choose Yes if peak detection has already been done. Peak detection cannot be run again on centroided data" truevalue="TRUE" falsevalue="FALSE"/>
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
552 <conditional name="restriction_conditional">
3
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
553 <param name="restriction" type="select" label="Use only spectra of interest" help="This option only works for imzML files">
7
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
554 <option value="no_restriction" selected="True">No, use all spectra</option>
3
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
555 <option value="restrict">Yes, restrict to spectra of interest</option>
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
556 </param>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
557 <when value="restrict">
3
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
558 <param name="coordinates_file" type="data" format="tabular" label="Tabular file with coordinates"/>
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
559 <param name="column_x" data_ref="coordinates_file" label="Column with x values" type="data_column"/>
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
560 <param name="column_y" data_ref="coordinates_file" label="Column with y values" type="data_column"/>
2
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
561 <param name="coordinates_header" type="boolean" label="File contains a header line" truevalue="TRUE" falsevalue="FALSE"/>
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
562 </when>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
563 <when value="no_restriction"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
564 </conditional>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
565
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
566 <conditional name="tabular_annotation">
3
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
567 <param name="load_annotation" type="select" label="Spectra annotations" help="Annotations can be used for group wise peak detection or filtering">
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
568 <option value="no_annotation" selected="True">No</option>
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
569 <option value="yes_annotation">Yes</option>
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
570 </param>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
571 <when value="yes_annotation">
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
572 <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
galaxyp
parents:
diff changeset
573 help="Tabular file with three columns: x values, y values and pixel annotations"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
574 <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
galaxyp
parents:
diff changeset
575 <param name="column_y" data_ref="annotation_file" label="Column with y values" type="data_column"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
576 <param name="column_names" data_ref="annotation_file" label="Column with pixel annotations" type="data_column"/>
2
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
577 <param name="tabular_header" type="boolean" label="File contains a header line" truevalue="TRUE" falsevalue="FALSE"/>
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
578 </when>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
579 <when value="no_annotation"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
580 </conditional>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
581 <repeat name="methods" title="Method" min="1">
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
582 <conditional name="methods_conditional">
1
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
583 <param name="method" type="select" label="Select a method">
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
584 <option value="Peak_detection">Peak detection</option>
4
e9300ef37403 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
585 <option value="monoisotopic_peaks">Monoisotopic peaks</option>
3
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
586 <option value="Align">Align Spectra (warping/phase correction)</option>
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
587 <option value="Binning">Binning</option>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
588 <option value="Filtering">Filtering</option>
7
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
589 <option value="skip_preprocessing">No method</option>
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
590 </param>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
591 <when value="Peak_detection">
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
592 <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
parents:
diff changeset
593 <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
parents:
diff changeset
594 <option value="SuperSmoother">SuperSmoother</option>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
595 </param>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
596 <param name="halfWindowSize" type="integer" value="20"
2
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
597 label="Half window size (number of data points)"
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
598 help="The resulting window reaches from
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
599 mass[currentIndex-halfWindowSize] to mass[currentIndex+halfWindowSize]
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
600 (window size is 2*halfWindowSize+1).
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
601 The best size differs depending on the selected smoothing method."/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
602 <param name="snr" type="integer" value="2" label="Signal-to-noise-ratio" help=""/>
2
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
603 <param name="use_annotations" type="boolean" label="Detect peaks on average mass spectra" help="Spectra with same annotation are averaged before peak detection, no imzML output" truevalue="TRUE" falsevalue="FALSE"/>
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
604 </when>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
605 <when value="monoisotopic_peaks">
2
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
606 <param name="minCor" type="float" value="0.95" label="Minimal correlation"
4
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galaxyp
parents: 3
diff changeset
607 help="Minimal correlation between the peak pattern generated by the model and the experimental peaks in the MassPeaks object to be recognized as isotopic pattern."/>
e9300ef37403 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
608 <param name="tolerance" type="float" label="Tolerance" value="0.0001"
e9300ef37403 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
609 help="Maximal relative deviation of a peak position (m/z) to be considered as identical: abs(((mass[i]+distance)-mass[i+1])/mass[i]) smaller than 'tolerance'. For 100ppm use 0.0001" />
e9300ef37403 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
610 <param name="distance" type="text" label="Distance" value="1.00235" help="Distance between two consecutive peaks in an isotopic pattern. 1.00235 is average distance for polypeptides. Multiple values can be used to find multiple charged pattern e.g. 1, 0.5 ,0.33">
e9300ef37403 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
611 <sanitizer invalid_char="">
e9300ef37403 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
612 <valid initial="string.digits">
e9300ef37403 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
613 <add value="," />
e9300ef37403 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
614 <add value=":" />
e9300ef37403 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
615 <add value="." />
e9300ef37403 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
616 </valid>
e9300ef37403 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
617 </sanitizer>
e9300ef37403 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
618 </param>
e9300ef37403 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
619 <param name="size" type="text" label="Size" value="3:10" help="Size (length) of isotopic pattern, longer patterns are prefered over shorter ones, min size is 2, a range can be used.">
e9300ef37403 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
620 <sanitizer invalid_char="">
e9300ef37403 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
621 <valid initial="string.digits">
e9300ef37403 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
622 <add value=":" />
e9300ef37403 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
623 </valid>
e9300ef37403 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
624 </sanitizer>
e9300ef37403 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
625 </param>
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
626 </when>
3
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
627
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
628 <when value="Align">
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
629 <param name="warping_method" type="select" label="Warping methods">
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
630 <option value="lowess" selected="True">Lowess</option>
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
631 <option value="linear">Linear</option>
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
632 <option value="quadratic">Quadratic</option>
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
633 <option value="cubic">Cubic</option>
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
634 </param>
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
635 <param name="tolerance" type="float" value="0.00005"
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
636 label="Tolerance = abs(mz1 - mz2)/mz2"
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
637 help="Maximal relative deviation of a peak position (m/z) to be considered as identical. For 50ppm use 0.00005 or 5e-5" />
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
638 <param name="allow_nomatch" type="boolean" label="Don't throw an error when less than 2 reference m/z were found in a spectrum" truevalue="TRUE" falsevalue="FALSE"/>
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
639 <param name="empty_nomatch" type="boolean" label="If TRUE the intensity values of MassSpectrum or MassPeaks objects with missing (NA) warping functions are set to zero" truevalue="TRUE" falsevalue="FALSE"/>
7
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
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parents: 6
diff changeset
640 <param name="remove_empty" type="boolean" label="Should empty spectra be removed" truevalue="TRUE" falsevalue="FALSE"/>
3
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
641
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
642 <conditional name="reference_for_alignment">
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
643 <param name="align_ref" type="select" label="Reference" help="If given, samples will be aligned to reference, use internal calibrants to perform m/z calibration">
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
644 <option value="no_reference" selected="True">no reference</option>
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
645 <option value="yes_reference">reference from tabular file</option>
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
646 </param>
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
647 <when value="no_reference">
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
648 <param name="min_frequency" type="float" value="0.9" label = "minFrequency" help="Removal of all peaks which occur in less than minFrequency spectra to generate the reference m/z"/>
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
649 </when>
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
650 <when value="yes_reference">
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
651 <param name="reference_file" type="data" format="tabular"
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
652 label="Reference m/z values"
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
653 help="Tabular file"/>
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
654 <param name="mz_column" data_ref="reference_file" label="Column with m/z values" type="data_column"/>
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
655 <param name="reference_header" type="boolean" label="File contains a header line" truevalue="TRUE" falsevalue="FALSE"/>
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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diff changeset
656 <param name="separate_alignment" type="boolean" label="Spectrum wise alignment" help="Internal binning is omitted to avoid interaction between spectra" truevalue="TRUE" falsevalue="FALSE"/>
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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diff changeset
657 </when>
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
658 </conditional>
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
659 </when>
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
660
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
661 <when value="Binning">
3
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
662 <param name="bin_tolerance" type="float" value="0.002" label="Tolerance"
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
663 help="After the alignment the peak positions (mass) are very similar but not identical. The binning is needed to make similar peak mass values identical."/>
4
e9300ef37403 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
664 <param name="bin_method" display="radio" type="select" label="Bin creation rule" help="strict - creates bins never containing two or more peaks of the same sample. relaxed - allows multiple peaks of the same sample in one bin.">
2
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
665 <option value="strict" selected="True" >strict</option>
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
666 <option value="relaxed" >relaxed</option>
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
667 </param>
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
668 </when>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
669 <when value="Filtering">
7
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
670 <conditional name="filter_groups">
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
671 <param name="filter_annot_groups" type="select" label="m/z filtering parameters are applied to all spectra or groups of spectra" help="By default a single group is assumed and filtering will be done based on all pixels. To filter groups of spectra, an annotation annotation file has to be specified above">
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
672 <option value="no_grouping" selected="True">use single group</option>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
673 <option value="yes_grouping">use spectra groups from annotation file</option>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
674 </param>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
675 <when value="no_grouping"/>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
676 <when value="yes_grouping">
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
677 <param name="mergeWhitelists" type="boolean" truevalue="TRUE" falsevalue="FALSE"
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
678 label="mergeWhitelists" help="Yes means that peaks that survive the filtering in one annotation group are also kept in other groups regardless if the filtering criteria are met in these groups"/>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
679 </when>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
680 </conditional>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
681 <conditional name="filter_type">
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
682 <param name="filter_params" type="select" label="m/z filtering parameters" help="minFrequency: Removal of all peaks which occur in less than minFrequency spectra (relative treshold). minNumber: Removal of all peaks which ocur in lass than minNumber spectra (absolute threshold). If both are set the higher value from relative and absolute threshold is taken.">
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
683 <option value="min_Frequency" selected="True">minFrequency</option>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
684 <option value="min_Number">minNumber</option>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
685 <option value="both">both</option>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
686 </param>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
687 <when value="min_Frequency">
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
688 <param name="minFrequency" type="float" value="0.25" label="Removal of all peaks which occur in less than minFrequency spectra" />
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
689 </when>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
690 <when value="min_Number">
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
691 <param name="minNumber" type="float" value="1.0" label="Removal of all peaks which occur in less than minNumber spectra" />
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
692 </when>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
693 <when value="both">
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
694 <param name="minFrequency" type="float" value="0.25" label="Removal of all peaks which occur in less than minFrequency spectra" />
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
695 <param name="minNumber" type="float" value="1.0" label="Removal of all peaks which occur in less than minNumber spectra" />
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
696 </when>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
697 </conditional>
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
698 </when>
7
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
699 <when value="skip_preprocessing"/>
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
700 </conditional>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
701 </repeat>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
702 </inputs>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
703 <outputs>
3
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
704 <data format="imzml" name="outfile_imzml" label="${tool.name} on ${on_string}: imzml">
2
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
705 <!--filter>methods_conditional['method'] == 'Peak_detection'</filter-->
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
706 </data>
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
707 <data format="pdf" name="plots" from_work_dir="peaks_qc_plot.pdf" label = "${tool.name} on ${on_string}: QC"/>
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
708 <data format="tabular" name="masspeaks" label="${tool.name} on ${on_string}: peaklist"/>
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
709 <data format="tabular" name="intensity_matrix" label="${tool.name} on ${on_string}: intensity_matrix"/>
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
710 </outputs>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
711 <tests>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
712 <test>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
713 <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
714 <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
715 <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
716 </param>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
717 <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
718 <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
719 <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
720 <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
721 <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
722 <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
723 <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
724 </conditional>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
725 <repeat name="methods">
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
726 <conditional name="methods_conditional">
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
727 <param name="method" value="Peak_detection"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
728 <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
729 <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
730 <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
731 <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
732 </conditional>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
733 </repeat>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
734 <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
735 <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
736 <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
737 </test>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
738 <test>
1
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
739 <param name="infile" value="masspeaks3_forinput.tabular"/>
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
740 <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
741 <repeat name="methods">
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
742 <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
743 <param name="method" value="monoisotopic_peaks"/>
2
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
744 <param name="tolerance" value="0.0004"/>
4
e9300ef37403 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
745 <param name="size" value="3"/>
7
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
746 </conditional>
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
747 </repeat>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
748 <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
749 <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
750 <output name="intensity_matrix" file="int2.tabular"/>
3
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
751 <output name="outfile_imzml" ftype="imzml" file="peak_detection2.imzml.txt" lines_diff="4">
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
752 <extra_files type="file" file="peak_detection2.imzml" name="imzml" lines_diff="6"/>
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
753 <extra_files type="file" file="peak_detection2.ibd" name="ibd" compare="sim_size"/>
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
754 </output>
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
755 </test>
7
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
756 <test>
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
757 <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
758 <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
759 <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
760 </param>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
761 <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
762 <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
763 <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
764 <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
765 <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
766 <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
767 <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
768 </conditional>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
769 <repeat name="methods">
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
770 <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
771 <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
772 <param name="peak_method" value="MAD"/>
7
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
773 <param name="halfWindowSize" value="10"/>
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
774 <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
775 </conditional>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
776 </repeat>
7
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
777 <repeat name="methods">
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
778 <conditional name="methods_conditional">
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
779 <param name="method" value="Filtering"/>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
780 <conditional name="filter_groups">
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
781 <param name="filter_annot_groups" value="yes_grouping"/>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
782 <param name="mergeWhitelists" value="FALSE"/>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
783 </conditional>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
784 <conditional name="filter_type">
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
785 <param name="filter_params" value="min_Frequency"/>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
786 <param name="minFrequency" value="0.25"/>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
787 </conditional>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
788 </conditional>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
789 </repeat>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
790 <output name="plots" file="peakdetection3_QC.pdf" compare="sim_size"/>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
791 <output name="intensity_matrix" file="int3.tabular"/>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
792 <output name="masspeaks" file="masspeaks3.tabular"/>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
793 <output name="outfile_imzml" ftype="imzml" file="peak_detection3.imzml.txt" lines_diff="4">
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
794 <extra_files type="file" file="peak_detection3.imzml" name="imzml" lines_diff="6"/>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
795 <extra_files type="file" file="peak_detection3.ibd" name="ibd" compare="sim_size"/>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
796 </output>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
797 </test>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
798 <test>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
799 <param name="infile" value="" ftype="imzml">
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
800 <composite_data value="Example_Processed.imzML"/>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
801 <composite_data value="Example_Processed.ibd"/>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
802 </param>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
803 <repeat name="methods">
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
804 <conditional name="methods_conditional">
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
805 <param name="method" value="Peak_detection"/>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
806 <param name="peak_method" value="SuperSmoother"/>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
807 <param name="halfWindowSize" value="5"/>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
808 <param name="snr" value="3"/>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
809 </conditional>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
810 </repeat>
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
811 <repeat name="methods">
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
812 <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
813 <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
814 <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
815 </conditional>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
816 </repeat>
2
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
817 <output name="plots" file="peakdetection4_QC.pdf" compare="sim_size"/>
7
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
818 <output name="intensity_matrix" file="int4.tabular"/>
2
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
819 <output name="masspeaks" file="masspeaks4.tabular"/>
3
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
820 <output name="outfile_imzml" ftype="imzml" file="peak_detection4.imzml.txt" lines_diff="4">
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
821 <extra_files type="file" file="peak_detection4.imzml" name="imzml" lines_diff="6"/>
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
822 <extra_files type="file" file="peak_detection4.ibd" name="ibd" compare="sim_size"/>
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
823 </output>
2
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
824 </test>
7
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
825 <test>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
826 <param name="infile" value="" ftype="imzml">
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
827 <composite_data value="preprocessing_results3.imzML"/>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
828 <composite_data value="preprocessing_results3.ibd"/>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
829 </param>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
830 <param name="centroids" value="TRUE"/>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
831 <conditional name="restriction_conditional">
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
832 <param name="restriction" value="restrict"/>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
833 <param name="coordinates_file" value="annotations.tabular"/>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
834 <param name="column_x" value="1"/>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
835 <param name="column_y" value="2"/>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
836 <param name="coordinates_header" value="TRUE"/>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
837 </conditional>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
838 <repeat name="methods">
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
839 <conditional name="methods_conditional">
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
840 <param name="method" value="skip_preprocessing"/>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
841 </conditional>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
842 </repeat>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
843 <output name="plots" file="peakdetection5_QC.pdf" compare="sim_size"/>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
844 <output name="masspeaks" file="masspeaks5.tabular"/>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
845 <output name="outfile_imzml" ftype="imzml" file="peak_detection5.imzml.txt" lines_diff="4">
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
846 <extra_files type="file" file="peak_detection5.imzml" name="imzml" lines_diff="6"/>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
847 <extra_files type="file" file="peak_detection5.ibd" name="ibd" compare="sim_size"/>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
848 </output>
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
849 </test>
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
850 </tests>
7
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
851
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
852 <help>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
853 <![CDATA[
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
854
1
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
855 @MADLI_QUANT_DESCRIPTION@
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
856
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
857 -----
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
858
1
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
859 **Input data**
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
860
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
861 - MSI data: 3 types of input data can be used:
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
862
7
160538a890a6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
parents: 6
diff changeset
863 - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/imzml/>`_
1
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
864 - 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.
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
865
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
866 ::
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
867
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
868 snr mass intensity spectrum
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
869 5.34 304.16 0.10 xy_1_1
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
870 12.09 305 0.2 xy_1_1
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
871 6.80 306.25 0.133 xy_1_1
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
872 ...
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
873 ...
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
874
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
875
3
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
876 - Optional: Tabular file with pixel coordinates to restrict reading of imzML files to coordinates of interest. Tabular files with any header name or no header at all are supported.
1
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
877
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
878 ::
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
879
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
880 x_coord y_coord
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
881 1 1
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
882 2 1
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
883 3 1
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
884 ...
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
885 ...
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
886
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
887
2
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
888 - Optional: Tabular file(s) containing pixel coordinates and annotation. X and y values in separate columns and the corresponding annotation in a third column. Tabular files with any header name or no header at all are supported. The annotations can be used to either detect peak on the average mass spectrum of each annotation group ('Detect peaks on average mass spectra') or to filter for peaks within pixel groups ('Group wise filtering'). This option is not compatible with tabular peak list inputs.
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
889
1
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
890 ::
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
891
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
892 x_coord y_coord annotation
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
893 1 1 healthy
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
894 2 1 healthy
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
895 3 1 disease
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
896 ...
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
897 ...
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
898
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
899 **Options**
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
900
2
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
901 - Peak detection: detection of peaks, only possible with profile mode input. A peak is a local maximum above a user defined noise threshold.
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
902
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
903 - Two functions exist to estimate the noise: MAD and supersmoother.
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
904 - SNR is an abbreviation for signal-to-noise-ratio. A local maximum has to be higher than SNR*noise to be recognize as peak.
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
905 - 'halfWindowSize': The resulting window reaches from mass[currentIndex-halfWindowSize] to mass[currentIndex+halfWindowSize]. A local maximum has to be the highest one in the given window to be recognized as peak.
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
906 - Detect peaks on average mass spectra: Spectra with the same annotation (taken from the annotation tabular input) are averaged and peak picking is performed on the average spectrum of each annotation group. The exported imzML is empty and cannot be used for further analysis steps. The peaklist and intensity matrix outputs contain the annotation group names with their averaged intensity values. Filtering steps have to be done in the same run as the peak picking.
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
907
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
908
3
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
909 - Monoisotopic peaks: Keeps only the monoisotopic peaks
2
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
910
4
e9300ef37403 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
911 - Based on poisson model for isotopic patterns as decribed in (`Breen et al. <https://doi.org/10.1002/1522-2683(20000601)21:11%3C2243::AID-ELPS2243%3E3.0.CO;2-K>`_)
e9300ef37403 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
912 - Isotopic pattern can be characterized and recognized by
e9300ef37403 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
913
e9300ef37403 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
914 - the similarity of the experimental pattern with the modelled pattern
e9300ef37403 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
915 - the distance between consecutive isotopic peaks. For polypeptides the average distance is 1.00235 (`Park et al. <https://pubs.acs.org/doi/abs/10.1021/ac800913b>`_). Multiply charged analytes have smaller distances between the peaks (e.g. z = 1 distance = ~1; z = 2: distance = ~0.5; z = 3: distance = ~0.3333) To search for differently charged isotopic pattern multiple distances can be applied - the order matters because the first distance that matches is reported (1, 0.5, 0.3333).
e9300ef37403 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
916 - the size (length) of the pattern, multiple values can be applied, longer patterns are prefered over shorter ones.
e9300ef37403 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
917
2
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
918
3
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
919 - Spectra alignment (warping): alignment for (re)calibration of m/z values.
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
920
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
921 - without external reference m/z: internal reference is obtained by filtering (default 90%) and binning the peaks to find landmark peaks and their average m/z
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
922 - with external reference m/z: the m/z provided in a tabular file are used as a reference, at least 10 reference values are recommended
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
923 - non linear warping (parametric time warping plus binning) to match the reference peaks (internal or external) to the peaks with the given tolerance. At least two m/z per spectrum are needed for the alignment. This requirement can be skipped by setting "Don't throw an error when less than 2 reference m/z were found in a spectrum" to yes. If the not aligned spectra should be set to zero select yes in "If TRUE the intensity values of MassSpectrum or MassPeaks objects with missing (NA) warping functions are set to zero". In order to remove such empty spectra set "Should empty spectra be removed" to yes.
2
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
924
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
925
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
926 - Peak binning: After the alignment the peak positions (m/z) are very similar but not identical. The binning is needed to make similar peak m/z values identical. The algorithm is based on the following workflow:
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
927
3
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
928 1. Put all m/z in a sorted vector.
2
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
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diff changeset
929 2. Calculate differences between each neighbor.
3
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
930 3. Divide the m/z vector at the largest gap (largest difference) and form a left and a right bin.
2
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
931 4. Rerun step 3 for the left and/or the right bin if they don't fulfill the following criteria:
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
932
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
933 - All peaks in a bin are near to the mean (abs(mass-meanMass)/meanMass < tolerance).
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
934 - method == "strict": The bin doesn't contain two or more peaks of the same sample.
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
935
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
936
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
937 - Peak filtering: Removal of less frequent m/z features:
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
938
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
939 - minFrequency : between 0 and 1: m/z has to occur in 0 - 100% of all spectra; minNumber: m/z has to occur in at least this amount of spectra --> out of those two criteria the stricter value will be used
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
940 - Group wise filtering with pixel annotations: 'Yes' means that the filtering criteria are applied for each annotation group separately.
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
941 - mergeWhitelists: 'Yes' means that peaks that survive the filtering in one annotation group are also kept in other groups regardless if the filtering criteria are met in these groups
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
942 - To filter data that was averaged before peak detection: Filtering has to be done in the same tool run as the peak detection. The filtering criteria are automatically applied per annotation group (Group wise filtering can be 'No') and not per pixel. Example: to keep only m/z that were detected in at least half of all annotation groups set minFrequency to 0.5.
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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diff changeset
943
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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diff changeset
944
1
eaaa73b043e6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
945 **Output**
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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946
3
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 2
diff changeset
947 - centroided, processed imzML file, imzML file is empty when 'Detect peaks on average mass spectra' is chosen.
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
948 - pdf with mass spectra plots of four random spectra and a table with key values after each preprocessing step
0
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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diff changeset
949 - peak list (tabular file) with the columns "snr", "mass", "intensity" and "spectrum"
2
17c54820f3be planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
950 - 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
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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diff changeset
951
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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diff changeset
952 .. _MALDIquant: http://strimmerlab.org/software/maldiquant/
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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953
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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954 ]]>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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955 </help>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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diff changeset
956 <expand macro="citation"/>
01212bf66f61 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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957 </tool>