Mercurial > repos > galaxyp > maldi_quant_preprocessing

annotate maldi_quant_preprocessing.xml @ 0:e2aa05746a69 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
author galaxyp
date Wed, 22 Aug 2018 11:49:06 -0400
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children 0892a051eb17
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e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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1 <tool id="maldi_quant_preprocessing" name="MALDIquant preprocessing" version="1.18.0.0">
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2 <description>
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3 Preprocessing of mass-spectrometry imaging data
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4 </description>
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5 <macros>
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6 <import>maldi_macros.xml</import>
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7 </macros>
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8 <expand macro="requirements"/>
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9 <command detect_errors="exit_code">
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10 <![CDATA[
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11 #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 du infile.hdr &&
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19 du infile.img &&
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20 du -s -B1 infile.hdr &&
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21 #else
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22 ln -s $infile infile.RData &&
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23 #end if
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24 Rscript "${maldi_quant_preprocessing}" &&
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25 mkdir $outfile_imzml.files_path &&
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26 mv ./out.imzMl "${os.path.join($outfile_imzml.files_path, 'imzml')}" | true &&
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27 mv ./out.ibd "${os.path.join($outfile_imzml.files_path, 'ibd')}" | true &&
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28 echo "imzML file:" > $outfile_imzml &&
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29 ls -l "$outfile_imzml.files_path" >> $outfile_imzml
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30 ]]>
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31 </command>
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32 <configfiles>
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33 <configfile name="maldi_quant_preprocessing"><![CDATA[
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34
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35 @R_IMPORTS@
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36
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37 #if $restriction_conditional.restriction == 'restrict':
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38
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39 print('Reading mask region')
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40 ## Import imzML file
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41
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42 coordinate_matrix = as.matrix(read.delim("$restriction_conditional.coordinates_file", header = FALSE, stringsAsFactors = FALSE))[,1:2]
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43
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44 maldi_data = importImzMl('infile.imzML',
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45 coordinates = coordinate_matrix)
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46 pixelnames = paste0("x = ", coordinates(maldi_data)[,1],", y = ", coordinates(maldi_data)[,2])
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47
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48 #else:
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49
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50 print('Reading entire file')
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51 #if $infile.ext == 'imzml'
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52 ## Import imzML file
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53 maldi_data = import( 'infile.imzML', type="imzML" )
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54 #elif $infile.ext == 'analyze75'
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55 ## Import analyze7.5 file
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56 maldi_data = import( 'infile.hdr' )
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57 #else
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58 loadRData <- function(fileName){
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59 #loads an RData file, and returns it
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60 load(fileName)
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61 get(ls()[ls() != "fileName"])
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62 }
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63 msidata = loadRData('infile.RData')
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64
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65 ## save coordinates
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66 cardinal_coordinates = as.matrix(Cardinal::coord(msidata)[,1:2])
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67 ## save mz values
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68 cardinal_mzs = Cardinal::mz(msidata)
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69 ## create MALDIquant MassSpectrum object
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70 maldi_data = list()
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71 for(number_spectra in 1:ncol(msidata)){
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72 maldi_data[[number_spectra]] = createMassSpectrum(mass = cardinal_mzs, intensity = iData(msidata)[,number_spectra])
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73 }
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74
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75 #end if
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76
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77 #end if
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78
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79 ## Quality control plots during preprocessing
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80
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81 pdf("prepro_qc_plot.pdf", fonts = "Times", pointsize = 12)
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82 plot(0,type='n',axes=FALSE,ann=FALSE)
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83
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84 ## if no filename is given, name of file in Galaxy history is used
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85 #set $filename = $infile.display_name
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86 title(main=paste("$filename"))
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87
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88 #if str($tabular_annotation.load_annotation) == 'yes_annotation':
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89 print("use annotation file")
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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90 ## read and extract x,y,annotation information
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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91 input_tabular = read.delim("$tabular_annotation.annotation_file", header = $tabular_annotation.tabular_header, stringsAsFactors = FALSE)
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92 annotation_input = input_tabular[,c($tabular_annotation.column_x, $tabular_annotation.column_y, $tabular_annotation.column_names)]
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93 colnames(annotation_input) = c("x", "y", "annotation") ## rename annotations header to default name "annotation"
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94
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95 ## merge with coordinate information of MSI data
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96 coordinates_st = cbind(coordinates(maldi_data)[,1:2], c(1:length(maldi_data)))
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97 colnames(coordinates_st)[3] = "pixel_index"
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98 merged_annotation = merge(coordinates_st, annotation_input, by=c("x", "y"), all.x=TRUE)
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99 merged_annotation[is.na(merged_annotation)] = "NA"
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100 merged_annotation = merged_annotation[order(merged_annotation\$pixel_index),]
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101 samples = as.factor(merged_annotation\$annotation)
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102
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103 ## print annotation overview into PDF output
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104
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105 ## the more annotation groups a file has the smaller will be the legend
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106 number_combined = length(levels(as.factor(merged_annotation\$annotation)))
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107 if (number_combined<20){
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108 legend_size = 10
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109 }else if (number_combined>20 && number_combined<40){
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110 legend_size = 9
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111 }else if (number_combined>40 && number_combined<60){
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112 legend_size = 8
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113 }else if (number_combined>60 && number_combined<100){
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114 legend_size = 7
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115 }else{
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116 legend_size = 6
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117 }
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118
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119 combine_plot = ggplot(merged_annotation, aes(x=x, y=y, fill=annotation))+
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120 geom_tile() +
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121 coord_fixed()+
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122 ggtitle("Spatial orientation of annotated data")+
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123 theme_bw()+
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124 theme(plot.title = element_text(hjust = 0.5))+
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125 theme(text=element_text(family="ArialMT", face="bold", size=12))+
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126 theme(legend.position="bottom",legend.direction="vertical")+
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127 theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = legend_size))+
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128 guides(fill=guide_legend(ncol=5,byrow=TRUE))
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129
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130 print(combine_plot)
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131
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132 #end if
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133
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134 #################### Preprocessing methods #####################################
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135
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136 ## QC plot
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137 avgSpectra = averageMassSpectra(maldi_data,method="mean")
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138 plot(avgSpectra, main="Average spectrum for input file")
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139
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140 #for $method in $methods:
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141
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142 #if str( $method.methods_conditional.method ) == 'Transformation':
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143
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144 print('transforming')
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145 ##transformation
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146 maldi_data = transformIntensity(maldi_data, method="$method.methods_conditional.transform_method")
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147 ## QC plot
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148 avgSpectra = averageMassSpectra(maldi_data,method="mean")
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149 plot(avgSpectra, main="Average spectrum after transformation")
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150
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151
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152 #elif str( $method.methods_conditional.method ) == 'Smoothing':
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153
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154 print('smoothing')
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155 ##smoothing
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156
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157 #if str($method.methods_conditional.methods_for_smoothing.smooth_method ) == 'SavitzkyGolay':
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158 print('SavitzkyGolay')
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159
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160 maldi_data = smoothIntensity(maldi_data,
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161 method="SavitzkyGolay", polynomialOrder=$method.methods_conditional.methods_for_smoothing.polynomial,
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162 halfWindowSize=$method.methods_conditional.halfWindowSize)
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163
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164 #elif str($method.methods_conditional.methods_for_smoothing.smooth_method ) == 'MovingAverage':
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165 print('MovingAverage')
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166
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167 maldi_data = smoothIntensity(maldi_data,
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168 method="MovingAverage", weighted=$method.methods_conditional.methods_for_smoothing.weighted,
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169 halfWindowSize=$method.methods_conditional.halfWindowSize)
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170
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171 #end if
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172
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173 ## QC plot
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174 avgSpectra = averageMassSpectra(maldi_data,method="mean")
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175 plot(avgSpectra, main="Average spectrum after smoothing")
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176
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177
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178 #elif str( $method.methods_conditional.method ) == 'Baseline':
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179
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180 print('baseline removing')
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181 ## Remove baseline
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182
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183 maldi_data = removeBaseline(maldi_data,
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184 method="$method.methods_conditional.baseline_method",
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185 iterations=$method.methods_conditional.iterations)
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186 ## QC plot
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187 avgSpectra = averageMassSpectra(maldi_data,method="mean")
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188 plot(avgSpectra, main="Average spectrum after baseline removal")
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189
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190
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191 #elif str( $method.methods_conditional.method ) == 'Calibrate':
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192
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193 print('calibrate')
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194 ##calibrate
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195
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196 #if $method.methods_conditional.mass_start != 0 and $method.methods_conditional.mass_end != 0:
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197 ## calibrate only given m/z range
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198 maldi_data = calibrateIntensity(maldi_data,
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199 method="$method.methods_conditional.calibrate_method",
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200 range=c($method.methods_conditional.mass_start, $method.methods_conditional.mass_end))
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201 #else:
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202 maldi_data = calibrateIntensity(maldi_data,
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203 method="$method.methods_conditional.calibrate_method")
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204 #end if
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205 ## QC plot
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206 avgSpectra = averageMassSpectra(maldi_data,method="mean")
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207 plot(avgSpectra, main="Average spectrum after normalization")
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208
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209
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210 #elif str( $method.methods_conditional.method ) == 'Align':
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211
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212 print('align')
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213 ##align spectra
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214
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215 #if str($method.methods_conditional.reference_for_alignment.align_ref) == 'no_reference':
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216
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217 maldi_data = alignSpectra(maldi_data, halfWindowSize=$method.methods_conditional.halfWindowSize,
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218 SNR=$method.methods_conditional.snr,
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219 tolerance=$method.methods_conditional.tolerance,
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220 warpingMethod="$method.methods_conditional.warping_method")
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221
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222 #elif str($method.methods_conditional.reference_for_alignment.align_ref) == 'yes_reference':
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223
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224 ## create reference mass_vector from tabular file
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225 mass_vector = read.delim("$method.methods_conditional.reference_for_alignment.reference_file", header = FALSE, stringsAsFactors = FALSE)[,1]
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226 int_vector = rep(1,length(mass_vector))
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227 mass_list = createMassPeaks(mass_vector, int_vector)
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228
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229 maldi_data = alignSpectra(maldi_data, halfWindowSize=$method.methods_conditional.halfWindowSize,
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230 SNR=$method.methods_conditional.snr,
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231 tolerance=$method.methods_conditional.tolerance,
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232 warpingMethod="$method.methods_conditional.warping_method",
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233 reference = mass_list, allowNoMatches =$method.methods_conditional.reference_for_alignment.allow_nomatch, emptyNoMatches = $method.methods_conditional.reference_for_alignment.empty_nomatch)
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234
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235 #if $method.methods_conditional.reference_for_alignment.remove_empty:
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236
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237 #if $infile.ext == 'rdata'
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238 cardinal_coordinates = cardinal_coordinates[-findEmptyMassObjects(maldi_data),] ## remove coordinates of empty spectra for Cardinal RData input
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239 #end if
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240 #if str($tabular_annotation.load_annotation) == 'yes_annotation':
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241 merged_annotation = merged_annotation[-findEmptyMassObjects(maldi_data),] ## remove coordinate annotations for empty spectra
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242 #end if
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243 maldi_data = removeEmptyMassObjects(maldi_data)
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244 #end if
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245 #end if
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246
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247 ## QC plot
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248
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249 if (length(maldi_data)>0){
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250 avgSpectra = averageMassSpectra(maldi_data,method="mean")
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251 plot(avgSpectra, main="Average spectrum after alignment")
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252 }else{"All spectra are empty"}
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253
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254 #end if
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255 #end for
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256
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257 dev.off()
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258
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259 ## export imzML file
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260 if (length(maldi_data)>0){
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261 #if $infile.ext == 'rdata'
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262 MALDIquantForeign::exportImzMl(maldi_data, file="out.imzMl", processed=$export_processed, coordinates=cardinal_coordinates)
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263 #else
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264 MALDIquantForeign::exportImzMl(maldi_data, file="out.imzMl", processed=$export_processed)
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265 #end if
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266
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267 ## export annotation tabular file
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268 #if str($tabular_annotation.load_annotation) == 'yes_annotation':
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269 write.table(merged_annotation, file="$annotation_output", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
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270 #end if
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271 }else{"All spectra are empty, outputfiles will be empty,too."}
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272
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273 ]]>
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274 </configfile>
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275 </configfiles>
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276 <inputs>
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277 <param name="infile" type="data" format="imzml,rdata" label="MS metadata" help="This file is in imzML format or Cardinal MSImageSet saved as RData"/>
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278 <conditional name="restriction_conditional">
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279 <param name="restriction" type="select" label="Read in only spectra of interest" help="This option only works for imzML files">
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280 <option value="no_restriction" selected="True">Calculate on entire file</option>
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281 <option value="restrict">Restrict to coordinates of interest</option>
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282 </param>
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283 <when value="restrict">
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284 <param name="coordinates_file" type="data" format="tabular" label="Tabular file with coordinates which should be read" help="x-values in first column, y-values in second column"/>
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285 </when>
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286 <when value="no_restriction"/>
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287 </conditional>
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288 <conditional name="tabular_annotation">
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289 <param name="load_annotation" type="select" label="Use pixel annotation from tabular file to have updated annotation information in case empty spectra will be removed">
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290 <option value="no_annotation" selected="True">use no annotation</option>
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291 <option value="yes_annotation">use pixel annotation from a tabular file</option>
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292 </param>
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293 <when value="yes_annotation">
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294 <param name="annotation_file" type="data" format="tabular" label="Use annotations from tabular file"
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295 help="Tabular file with three columns: x values, y values and pixel annotations"/>
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296 <param name="column_x" data_ref="annotation_file" label="Column with x values" type="data_column"/>
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297 <param name="column_y" data_ref="annotation_file" label="Column with y values" type="data_column"/>
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298 <param name="column_names" data_ref="annotation_file" label="Column with pixel annotations" type="data_column"/>
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299 <param name="tabular_header" type="boolean" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/>
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300 </when>
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301 <when value="no_annotation"/>
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302 </conditional>
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303 <repeat name="methods" title="Method" min="1">
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304 <conditional name="methods_conditional">
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305 <param name="method" type="select" label="Select the method you want to apply">
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306 <option value="Transformation" selected="True">Transformation</option>
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307 <option value="Smoothing">Smoothing</option>
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308 <option value="Baseline">Baseline removal</option>
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309 <option value="Calibrate">Calibrate</option>
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310 <option value="Align">Align Spectra (warping/phase correction)</option>
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311 <validator type="empty_field" />
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312 </param>
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313 <when value="Transformation">
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314 <param name="transform_method" type="select" label="Select your transfprormation method">
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315 <option value="sqrt" selected="True">sqrt</option>
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316 <option value="log">log</option>
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317 <option value="log2">log2</option>
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318 <option value="log10">log10</option>
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319 <validator type="empty_field" />
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320 </param>
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321 </when>
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322 <when value="Smoothing">
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323 <conditional name="methods_for_smoothing">
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324 <param name="smooth_method" type="select" label="This method smoothes the intensity values of a MassSpectrum object">
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325 <option value="SavitzkyGolay" selected="True">SavitzkyGolay</option>
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326 <option value="MovingAverage">MovingAverage</option>
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327 </param>
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328 <when value="SavitzkyGolay">
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329 <param name="polynomial" value="3" type="text" label="PolynomialOrder argument to control the order of the filter"/>
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330 </when>
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331 <when value="MovingAverage">
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332 <param name="weighted" type="boolean" label="Weighted average" help = "indicates if the average should be equal weight or if it should have weights depending on the distance from the center as calculated as 1/2^abs(-halfWindowSize:halfWindowSize) with the sum of all weigths normalized to 1" truevalue="TRUE" falsevalue="FALSE"/>
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333 </when>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
334 </conditional>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
335 <param name="halfWindowSize" type="integer" value="10"
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
336 label="Half window size"
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
337 help="The resulting window reaches from
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
338 mass[currentIndex-halfWindowSize] to mass[currentIndex+halfWindowSize]
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
339 (window size is 2*halfWindowSize+1).
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
340 The best size differs depending on the selected smoothing method."/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
341 </when>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
342 <when value="Baseline">
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
343 <param name="baseline_method" type="select" label="Baseline removal method">
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
344 <option value="SNIP" selected="True">SNIP</option>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
345 <option value="TopHat">TopHat</option>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
346 <option value="ConvexHull">ConvexHull</option>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
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347 <option value="median">median</option>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
348 <validator type="empty_field" />
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
349 </param>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
350 <param name="iterations" type="integer" value="100"
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
351 label="Number of iterations"
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
352 help=""/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
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353 </when>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
354 <when value="Calibrate">
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
355 <param name="calibrate_method" type="select" label="Calibration method">
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
356 <option value="TIC" selected="True">TIC</option>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
357 <option value="PQN">PQN</option>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
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358 <option value="median">median</option>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
359 <validator type="empty_field" />
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
360 </param>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
361 <param name="mass_start" type="integer" value="0"
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
362 label="Start of m/z range, has to be inside m/z range"
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
363 help="Scaling factor is calculated on the mass range and applied to the whole spectrum"/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
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364 <param name="mass_end" type="integer" value="0"
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
365 label="End of m/z range, has to be inside m/z range"
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
366 help="The Start and End value needs to be different from 0 to be taken into account and."/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
367 </when>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
368 <when value="Align">
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
369 <param name="warping_method" type="select" label="Warping methods">
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
370 <option value="lowess" selected="True">Lowess</option>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
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371 <option value="linear">Linear</option>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
372 <option value="quadratic">Quadratic</option>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
373 <option value="cubic">Cubic</option>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
374 </param>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
375
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
376 <param name="tolerance" type="float" value="0.002"
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
377 label="Tolerance"
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
378 help="Double, maximal relative deviation of a peak position (m/z) to be considered as identical" />
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
379
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
380 <param name="halfWindowSize" type="integer" value="20"
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
381 label="Half window size"
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
382 help="The resulting window reaches from
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
383 mass[currentIndex-halfWindowSize] to mass[currentIndex+halfWindowSize]
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
384 (window size is 2*halfWindowSize+1).
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
385 The best size differs depending on the selected smoothing method."/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
386
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
387 <param name="snr" type="integer" value="2"
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
388 label="Signal-to-noise-ratio"
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
389 help=""/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
390
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
391 <conditional name="reference_for_alignment">
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
392 <param name="align_ref" type="select" label="Reference to which the samples should be aligned" help="Use internal calibrants to perform m/z calibration">
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
393 <option value="no_reference" selected="True">no reference</option>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
394 <option value="yes_reference">reference from tabular file</option>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
395 </param>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
396 <when value="no_reference"/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
397 <when value="yes_reference">
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
398 <param name="reference_file" type="data" format="tabular"
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
399 label="Tabular file with m/z of internal calibrants (MassPeaks) which should be used for spectra alignment"
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
400 help="calibration of m/z values to internal calibrants, at least 2 m/z per spectrum are needed"/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
401 <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"/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
402 <param name="empty_nomatch" type="boolean" label="logical, if TRUE the intensity values of MassSpectrum or MassPeaks objects with missing (NA) warping functions are set to zero" truevalue="TRUE" falsevalue="FALSE"/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
403 <param name="remove_empty" type="boolean" label="Should empty spectra be removed" truevalue="TRUE" falsevalue="FALSE"/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
404 </when>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
405 </conditional>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
406 </when>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
407 </conditional>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
408 </repeat>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
409 <param name="export_processed" type="boolean" label="Export file as processed imzML" help="otherwise continuous imzML will be exported" truevalue="TRUE" falsevalue="FALSE"/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
410 </inputs>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
411 <outputs>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
412 <data format="imzml" name="outfile_imzml" label="$infile.display_name processed" />
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
413 <data format="pdf" name="plots" from_work_dir="prepro_qc_plot.pdf" label="$infile.display_name preprocessed QC"/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
414 <data format="tabular" name="annotation_output" label="$infile.display_name annotations">
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
415 <filter>tabular_annotation["load_annotation"] == 'yes_annotation'</filter>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
416 </data>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
417 </outputs>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
418 <tests>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
419 <test>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
420 <param name="infile" value="" ftype="imzml">
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
421 <composite_data value="Example_Continuous.imzML"/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
422 <composite_data value="Example_Continuous.ibd"/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
423 </param>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
424 <conditional name="restriction_conditional">
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
425 <param name="restriction" value="restrict"/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
426 <param name="coordinates_file" value="restricted_pixels.tabular"/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
427 </conditional>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
428 <conditional name="methods_conditional">
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
429 <param name="method" value="Transformation"/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
430 <param name="transform_method" value="log2"/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
431 <param name="method" value="Smoothing"/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
432 <param name="smooth_method" value="SavitzkyGolay"/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
433 <param name="method" value="Basline"/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
434 <param name="baseline_method" value ="TopHat"/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
435 </conditional>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
436 <output name="outfile_imzml" file="outfile1.imzML" compare="sim_size"/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
437 <output name="outfile_imzml" file="outfile1.ibd" compare="sim_size"/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
438 <output name="plots" file="Preprocessing1_QC.pdf" compare="sim_size"/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
439 </test>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
440 <test>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
441 <param name="infile" value="msidata_1.RData" ftype="rdata"/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
442 <conditional name="methods_conditional">
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
443 <param name="method" value="Calibrate"/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
444 <param name="calibrate_method" value="PQN"/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
445 </conditional>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
446 <output name="outfile_imzml" file="outfile2.imzML" compare="sim_size"/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
447 <output name="outfile_imzml" file="outfile2.ibd" compare="sim_size"/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
448 <output name="plots" file="Preprocessing2_QC.pdf" compare="sim_size"/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
449 </test>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
450 <test>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
451 <param name="infile" value="" ftype="imzml">
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
452 <composite_data value="Example_Continuous.imzML"/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
453 <composite_data value="Example_Continuous.ibd"/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
454 </param>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
455 <conditional name="tabular_annotation">
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
456 <param name="load_annotation" value="yes_annotation"/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
457 <param name="annotation_file" value="pixel_annotations.tabular"/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
458 <param name="column_x" value="1"/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
459 <param name="column_y" value="2"/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
460 <param name="column_names" value="3"/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
461 <param name="tabular_header" value="TRUE"/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
462 </conditional>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
463 <conditional name="methods_conditional">
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
464 <param name="method" value="Align"/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
465 <param name="warping_method" value="linear"/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
466 <param name="halfWindowSize" value="1"/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
467 <conditional name="reference_for_alignment">
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
468 <param name="align_ref" value="yes_reference"/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
469 <param name="reference_file" value="align_reference_test2.tabular" ftype="tabular"/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
470 <param name="allow_nomatch" value="TRUE"/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
471 <param name="remove_empty" value="TRUE"/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
472 <param name="empty_nomatch" value="TRUE"/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
473 </conditional>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
474 </conditional>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
475 <output name="outfile_imzml" file="outfile3.imzML" compare="sim_size"/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
476 <output name="outfile_imzml" file="outfile3.ibd" compare="sim_size"/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
477 <output name="plots" file="Preprocessing3_QC.pdf" compare="sim_size"/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
478 <output name="annotation_output" file="annotations_output3.tabular"/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
479 </test>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
480 </tests>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
481 <help><![CDATA[
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
482
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
483 MALDIquant_ provides a complete analysis pipeline for MALDI-TOF and other mass spectrometry data. So far we have only implemented the functionalities for mass spectrometry imaging data.
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
484
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
485 Input data:
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
486
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
487 - MSI data as imzML file (upload via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/wp/imzml/>`_
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
488 - optinal tabular file with pixel coordinates to restrict reading of imzML file to coordinates of interest
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
489
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
490 Options:
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
491
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
492 - Transformation: transformation of intensities with log, log2, log10 and squareroot
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
493 - Smoothing: Smoothing of the peaks reduces noise and improves peak detection. Available smoothing methods are SavitzkyGolay and Moving Average
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
494 - Baseline reduction: Baseline reduction removes background intensity generated by chemical noise (common in MALDI datasets). Available methods are SNIP, TopHat,ConvexHull and median.
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
495 - Intensity calibration (normalization): Normalization of intensities to Total Ion Current (TIC), median spectrum, Probabilistic Quotient Normalization (PQN)
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
496 - Spectra alignment (warping):alignment for (re)calibration of m/z values
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
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497
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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498
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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499 Output:
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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500
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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501 - imzML file (imzML format can be continuous or processed)
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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502 - pdf with average mass spectra after each preprocessing step
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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503
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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504 .. _MALDIquant: http://strimmerlab.org/software/maldiquant/
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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505
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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506 ]]>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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507 </help>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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508 <expand macro="citation"/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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509 </tool>