Mercurial > repos > galaxyp > maldi_quant_preprocessing

annotate maldi_quant_preprocessing.xml @ 2:e754c2b545a9 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
author galaxyp
date Thu, 25 Oct 2018 07:31:55 -0400
parents 0892a051eb17
children 71411ac28268
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e754c2b545a9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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1 <tool id="maldi_quant_preprocessing" name="MALDIquant preprocessing" version="@VERSION@.2">
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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 cat '${maldi_quant_preprocessing}' &&
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12 #if $infile.ext == 'imzml'
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13 cp '${infile.extra_files_path}/imzml' infile.imzML &&
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14 cp '${infile.extra_files_path}/ibd' infile.ibd &&
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15 #elif $infile.ext == 'analyze75'
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16 cp '${infile.extra_files_path}/hdr' infile.hdr &&
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17 cp '${infile.extra_files_path}/img' infile.img &&
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18 cp '${infile.extra_files_path}/t2m' infile.t2m &&
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19 du infile.hdr &&
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20 du infile.img &&
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21 du -s -B1 infile.hdr &&
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22 #else
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23 ln -s $infile infile.RData &&
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24 #end if
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25 Rscript "${maldi_quant_preprocessing}" &&
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26
0
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27 mkdir $outfile_imzml.files_path &&
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28 mv ./out.imzMl "${os.path.join($outfile_imzml.files_path, 'imzml')}" | true &&
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29 mv ./out.ibd "${os.path.join($outfile_imzml.files_path, 'ibd')}" | true &&
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30 echo "imzML file:" > $outfile_imzml &&
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31 ls -l "$outfile_imzml.files_path" >> $outfile_imzml
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32 ]]>
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33 </command>
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34 <configfiles>
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35 <configfile name="maldi_quant_preprocessing"><![CDATA[
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36
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37 @R_IMPORTS@
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38
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39 #if $restriction_conditional.restriction == 'restrict':
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41 print('Reading mask region')
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42 ## Import imzML file
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43
1
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44 coordinate_matrix = as.matrix(read.delim("$restriction_conditional.coordinates_file", header = $restriction_conditional.coordinates_header, stringsAsFactors = FALSE))[,1:2]
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45
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46 maldi_data = importImzMl('infile.imzML',
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47 coordinates = coordinate_matrix)
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48 pixelnames = paste0("x = ", coordinates(maldi_data)[,1],", y = ", coordinates(maldi_data)[,2])
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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 #if $infile.ext == 'imzml'
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54 ## Import imzML file
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55 maldi_data = import( 'infile.imzML', type="imzML" )
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56 coordinates_info = cbind(coordinates(maldi_data)[,1:2], c(1:length(maldi_data)))
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57 #elif $infile.ext == 'analyze75'
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58 ## Import analyze7.5 file
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59 maldi_data = importAnalyze( 'infile.hdr' )
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60 coordinates_info = cbind(coordinates(maldi_data)[,1:2], c(1:length(maldi_data)))
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61 #else
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62 loadRData <- function(fileName){
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63 #loads an RData file, and returns it
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64 load(fileName)
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65 get(ls()[ls() != "fileName"])
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66 }
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67 msidata = loadRData('infile.RData')
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68 ## save coordinates
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69 cardinal_coordinates = as.matrix(Cardinal::coord(msidata)[,1:2])
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70 ## save mz values
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71 cardinal_mzs = Cardinal::mz(msidata)
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72 ## create MALDIquant MassSpectrum object
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73 maldi_data = list()
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74 for(number_spectra in 1:ncol(msidata)){
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75 maldi_data[[number_spectra]] = createMassSpectrum(mass = cardinal_mzs, intensity = iData(msidata)[,number_spectra])
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76 coordinates_info = cbind(cardinal_coordinates, c(1:length(maldi_data)))
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77 }
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78
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79 #end if
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81 #end if
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82
1
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83 ## Quality control plots during preprocessing
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84
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85 pdf("prepro_qc_plot.pdf", fonts = "Times", pointsize = 12)
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86 plot(0,type='n',axes=FALSE,ann=FALSE)
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87
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88 ## if no filename is given, name of file in Galaxy history is used
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89 #set $filename = $infile.display_name
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90 title(main=paste("$filename"))
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91
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92 #if str($tabular_annotation.load_annotation) == 'yes_annotation':
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93 print("use annotation file")
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94
0
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95 ## read and extract x,y,annotation information
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96 input_tabular = read.delim("$tabular_annotation.annotation_file", header = $tabular_annotation.tabular_header, stringsAsFactors = FALSE)
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97 annotation_input = input_tabular[,c($tabular_annotation.column_x, $tabular_annotation.column_y, $tabular_annotation.column_names)]
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98 colnames(annotation_input) = c("x", "y", "annotation") ## rename annotations header to default name "annotation"
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99
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100 ## merge with coordinate information (from above) of MSI data
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101 colnames(coordinates_info)[3] = "pixel_index"
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102 merged_annotation = merge(coordinates_info, annotation_input, by=c("x", "y"), all.x=TRUE)
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103 merged_annotation[is.na(merged_annotation)] = "NA"
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104 merged_annotation = merged_annotation[order(merged_annotation\$pixel_index),]
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105 samples = as.factor(merged_annotation\$annotation)
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106
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107 ## print annotation overview into PDF output
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108
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109 ## the more annotation groups a file has the smaller will be the legend
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110 number_combined = length(levels(as.factor(merged_annotation\$annotation)))
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111 if (number_combined<20){
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112 legend_size = 10
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113 }else if (number_combined>20 && number_combined<40){
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114 legend_size = 9
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115 }else if (number_combined>40 && number_combined<60){
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116 legend_size = 8
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117 }else if (number_combined>60 && number_combined<100){
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118 legend_size = 7
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119 }else{
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120 legend_size = 6
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121 }
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122
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123 combine_plot = ggplot(merged_annotation, aes(x=x, y=y, fill=annotation))+
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124 geom_tile() +
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125 coord_fixed()+
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126 ggtitle("Spatial orientation of annotated data")+
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127 theme_bw()+
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128 theme(plot.title = element_text(hjust = 0.5))+
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129 theme(text=element_text(family="ArialMT", face="bold", size=12))+
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130 theme(legend.position="bottom",legend.direction="vertical")+
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131 theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = legend_size))+
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132 guides(fill=guide_legend(ncol=5,byrow=TRUE))
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133
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134 print(combine_plot)
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135
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136 #end if
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137
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138 #################### Preprocessing methods #####################################
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139
1
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140 ## QC plot on input file
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141 avgSpectra = averageMassSpectra(maldi_data,method="mean")
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142 plot(avgSpectra, main="Average spectrum for input file")
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143
1
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144 pixel_number = length(maldi_data)
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145 minmz = round(min(unlist(lapply(maldi_data,mass))), digits=4)
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146 maxmz = round(max(unlist(lapply(maldi_data,mass))), digits=4)
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147 mean_features = round(length(unlist(lapply(maldi_data,mass)))/length(maldi_data), digits=2)
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148 number_features = length(unique(unlist(lapply(maldi_data,mass))))
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149 medint = round(median(unlist(lapply(maldi_data,intensity))), digits=2)
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150 inputdata = c(minmz, maxmz,number_features,mean_features, medint)
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151 QC_numbers= data.frame(inputdata = c(minmz, maxmz,number_features, mean_features, medint))
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152 vectorofactions = "inputdata"
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153
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154
0
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155 #for $method in $methods:
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156
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157 #if str( $method.methods_conditional.method ) == 'Transformation':
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158
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159 print('transforming')
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160 ##transformation
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161 maldi_data = transformIntensity(maldi_data, method="$method.methods_conditional.transform_method")
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162 ## QC plot and numbers
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163 avgSpectra = averageMassSpectra(maldi_data,method="mean")
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164 plot(avgSpectra, main="Average spectrum after transformation")
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165 pixel_number = length(maldi_data)
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166 minmz = round(min(unlist(lapply(maldi_data,mass))), digits=4)
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167 maxmz = round(max(unlist(lapply(maldi_data,mass))), digits=4)
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168 mean_features = round(length(unlist(lapply(maldi_data,mass)))/length(maldi_data), digits=2)
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169 medint = round(median(unlist(lapply(maldi_data,intensity))), digits=2)
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170 number_features = length(unique(unlist(lapply(maldi_data,mass))))
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171 transformed = c(minmz, maxmz,number_features,mean_features, medint)
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172 QC_numbers= cbind(QC_numbers, transformed)
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173 vectorofactions = append(vectorofactions, "transformed")
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174
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175
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176 #elif str( $method.methods_conditional.method ) == 'Smoothing':
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177
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178 print('smoothing')
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179 ##smoothing
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180
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181 #if str($method.methods_conditional.methods_for_smoothing.smooth_method ) == 'SavitzkyGolay':
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182 print('SavitzkyGolay')
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183
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184 maldi_data = smoothIntensity(maldi_data,
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185 method="SavitzkyGolay", polynomialOrder=$method.methods_conditional.methods_for_smoothing.polynomial,
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186 halfWindowSize=$method.methods_conditional.halfWindowSize)
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187
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188 #elif str($method.methods_conditional.methods_for_smoothing.smooth_method ) == 'MovingAverage':
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189 print('MovingAverage')
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190
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191 maldi_data = smoothIntensity(maldi_data,
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192 method="MovingAverage", weighted=$method.methods_conditional.methods_for_smoothing.weighted,
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193 halfWindowSize=$method.methods_conditional.halfWindowSize)
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194
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195 #end if
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196
1
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197 ## QC plot and numbers
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198 avgSpectra = averageMassSpectra(maldi_data,method="mean")
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199 plot(avgSpectra, main="Average spectrum after smoothing", sub="")
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200 pixel_number = length(maldi_data)
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201 minmz = round(min(unlist(lapply(maldi_data,mass))), digits=4)
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202 maxmz = round(max(unlist(lapply(maldi_data,mass))), digits=4)
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203 mean_features = round(length(unlist(lapply(maldi_data,mass)))/length(maldi_data), digits=2)
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204 medint = round(median(unlist(lapply(maldi_data,intensity))), digits=2)
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205 number_features = length(unique(unlist(lapply(maldi_data,mass))))
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206 smoothed = c(minmz, maxmz,number_features,mean_features, medint)
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207 QC_numbers= cbind(QC_numbers, smoothed)
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208 vectorofactions = append(vectorofactions, "smoothed")
0
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209
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210
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211 #elif str( $method.methods_conditional.method ) == 'Baseline':
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212
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213 print('baseline removing')
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214 ## Remove baseline
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215
1
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216 #if str($method.methods_conditional.methods_for_baseline.baseline_method ) == 'SNIP':
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217 print('SNIP')
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218 random_spectra = sample(1:length(maldi_data), 4, replace=FALSE)
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219 par(mfrow = c(2,2))
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220 for (random_sample in random_spectra){
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221 maldi_data_baseline = estimateBaseline(maldi_data[[random_sample]],
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222 method="SNIP", iterations=$method.methods_conditional.methods_for_baseline.iterations)
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223 plot(maldi_data[[random_sample]], sub="", main=paste0("Estimated baseline for spectrum ", random_sample))
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224 lines(maldi_data_baseline, col="blue", lwd=2)}
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225
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226 maldi_data = removeBaseline(maldi_data,
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227 method="SNIP",
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228 iterations=$method.methods_conditional.methods_for_baseline.iterations)
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229
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230 #elif str($method.methods_conditional.methods_for_baseline.baseline_method ) == 'TopHat':
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231 print('TopHat')
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232
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233 maldi_data = removeBaseline(maldi_data,
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234 method="TopHat",
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235 halfWindowSize=$method.methods_conditional.methods_for_baseline.tophat_halfWindowSize)
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236
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237 #elif str($method.methods_conditional.methods_for_baseline.baseline_method ) == 'ConvexHull':
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238 print('ConvexHull')
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239
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240 maldi_data = removeBaseline(maldi_data,
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241 method="ConvecHull")
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242
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243 #elif str($method.methods_conditional.methods_for_baseline.baseline_method ) == 'median':
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244 print('median')
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245
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246 maldi_data = removeBaseline(maldi_data,
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247 method="TopHat",
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248 halfWindowSize=$method.methods_conditional.methods_for_baseline.median_halfWindowSize)
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249
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250 #end if
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251
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252 ## QC plot and numbers
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253 par(mfrow = c(1,1))
0
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254 avgSpectra = averageMassSpectra(maldi_data,method="mean")
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255 plot(avgSpectra, main="Average spectrum after baseline removal")
1
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256 pixel_number = length(maldi_data)
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257 minmz = round(min(unlist(lapply(maldi_data,mass))), digits=4)
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258 maxmz = round(max(unlist(lapply(maldi_data,mass))), digits=4)
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259 mean_features = round(length(unlist(lapply(maldi_data,mass)))/length(maldi_data), digits=2)
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260 medint = round(median(unlist(lapply(maldi_data,intensity))), digits=2)
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261 number_features = length(unique(unlist(lapply(maldi_data,mass))))
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262 baseline_removed = c(minmz, maxmz,number_features,mean_features, medint)
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263 QC_numbers= cbind(QC_numbers, baseline_removed)
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264 vectorofactions = append(vectorofactions, "baseline_removed")
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265
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266
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267 #elif str( $method.methods_conditional.method ) == 'Calibrate':
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268
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269 print('calibrate')
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270 ##calibrate
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271
2
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272 #if str($method.methods_conditional.cond_calibration_range) == "yes":
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273 ## calibrate only given m/z range
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274 maldi_data = calibrateIntensity(maldi_data,
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275 method="$method.methods_conditional.calibrate_method",
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276 range=c($method.methods_conditional.cond_calibration_range.mass_start, $method.methods_conditional.cond_calibration_range.mass_end))
0
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277 #else:
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278 maldi_data = calibrateIntensity(maldi_data,
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279 method="$method.methods_conditional.calibrate_method")
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280 #end if
1
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281 ## QC plot and numbers
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282 avgSpectra = averageMassSpectra(maldi_data,method="mean")
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283 plot(avgSpectra, main="Average spectrum after normalization")
1
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284 pixel_number = length(maldi_data)
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285 minmz = round(min(unlist(lapply(maldi_data,mass))), digits=4)
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286 maxmz = round(max(unlist(lapply(maldi_data,mass))), digits=4)
2
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287 mean_features = round(length(unlist(lapply(maldi_data,mass)))/length(maldi_data), digits=2)
1
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288 medint = round(median(unlist(lapply(maldi_data,intensity))), digits=2)
2
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289 number_features = length(unique(unlist(lapply(maldi_data,mass))))
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290 intensity_calibrated = c(minmz, maxmz,number_features,mean_features, medint)
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291 QC_numbers= cbind(QC_numbers, intensity_calibrated)
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292 vectorofactions = append(vectorofactions, "intensity_calibrated ")
0
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293
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294
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295 #elif str( $method.methods_conditional.method ) == 'Align':
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296
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297 print('align')
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298 ##align spectra
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299
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300 #if str($method.methods_conditional.reference_for_alignment.align_ref) == 'no_reference':
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301 maldi_data = alignSpectra(maldi_data, halfWindowSize=$method.methods_conditional.halfWindowSize,
1
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302 SNR=$method.methods_conditional.snr, tolerance=$method.methods_conditional.tolerance,
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303 allowNoMatches =$method.methods_conditional.allow_nomatch, emptyNoMatches = $method.methods_conditional.empty_nomatch,
0
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304 warpingMethod="$method.methods_conditional.warping_method")
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305
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306 #elif str($method.methods_conditional.reference_for_alignment.align_ref) == 'yes_reference':
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307 ## create reference mass_vector from tabular file
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308 mass_vector = read.delim("$method.methods_conditional.reference_for_alignment.reference_file", header = $method.methods_conditional.reference_for_alignment.reference_header, stringsAsFactors = FALSE)[,1]
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309 int_vector = rep(1,length(mass_vector))
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310 mass_list = createMassPeaks(mass_vector, int_vector)
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311
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312 maldi_data = alignSpectra(maldi_data, halfWindowSize=$method.methods_conditional.halfWindowSize,
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313 SNR=$method.methods_conditional.snr,
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314 tolerance=$method.methods_conditional.tolerance,
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315 warpingMethod="$method.methods_conditional.warping_method",
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316 reference = mass_list, allowNoMatches =$method.methods_conditional.allow_nomatch, emptyNoMatches = $method.methods_conditional.empty_nomatch)
0
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317
1
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318 #end if
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319
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320 #if $method.methods_conditional.remove_empty:
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321 print("remove empty spectra")
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322
1
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323 #if $infile.ext == 'rdata'
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324 cardinal_coordinates = cardinal_coordinates[-findEmptyMassObjects(maldi_data),] ## remove coordinates of empty spectra for Cardinal RData input
0
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325 #end if
1
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326 #if str($tabular_annotation.load_annotation) == 'yes_annotation':
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327 merged_annotation = merged_annotation[-findEmptyMassObjects(maldi_data),] ## remove coordinate annotations for empty spectra
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328 #end if
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329 maldi_data = removeEmptyMassObjects(maldi_data)
0
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330 #end if
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331
1
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332
0
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333 ## QC plot
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334
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335 if (length(maldi_data)>0){
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336 avgSpectra = averageMassSpectra(maldi_data,method="mean")
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337 plot(avgSpectra, main="Average spectrum after alignment")
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338 }else{"All spectra are empty"}
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339
1
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340 pixel_number = length(maldi_data)
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341 minmz = round(min(unlist(lapply(maldi_data,mass))), digits=4)
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342 maxmz = round(max(unlist(lapply(maldi_data,mass))), digits=4)
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343 mean_features = round(length(unlist(lapply(maldi_data,mass)))/length(maldi_data), digits=2)
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344 medint = round(median(unlist(lapply(maldi_data,intensity))), digits=2)
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345 number_features = length(unique(unlist(lapply(maldi_data,mass))))
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346 spectra_aligned = c(minmz, maxmz,number_features,mean_features, medint)
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347 QC_numbers= cbind(QC_numbers, spectra_aligned)
1
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348 vectorofactions = append(vectorofactions, "spectra_aligned")
0
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349 #end if
1
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350
0
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351 #end for
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352
2
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353 rownames(QC_numbers) = c("min m/z", "max mz", "# features", "median \n# features", "median\nintensity")
1
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354 plot(0,type='n',axes=FALSE,ann=FALSE)
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355 grid.table(t(QC_numbers))
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356
0
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357 dev.off()
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358
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359 ## export imzML file
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360 if (length(maldi_data)>0){
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361 #if $infile.ext == 'rdata'
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362 MALDIquantForeign::exportImzMl(maldi_data, file="out.imzMl", processed=$export_processed, coordinates=cardinal_coordinates)
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363 #else
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364 MALDIquantForeign::exportImzMl(maldi_data, file="out.imzMl", processed=$export_processed)
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365 #end if
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366
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367 }else{"All spectra are empty, outputfiles will be empty,too."}
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368
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369 ]]>
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370 </configfile>
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371 </configfiles>
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372 <inputs>
2
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373 <param name="infile" type="data" format="imzml,rdata,analyze75" label="Inputfile as imzML or Cardinal MSImageSet saved as RData" help="This file is in imzML format or Cardinal MSImageSet saved as RData. The file must be in profile mode, not centroided"/>
0
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374 <conditional name="restriction_conditional">
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375 <param name="restriction" type="select" label="Read in only spectra of interest" help="This option only works for imzML files">
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376 <option value="no_restriction" selected="True">Calculate on entire file</option>
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377 <option value="restrict">Restrict to coordinates of interest</option>
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378 </param>
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379 <when value="restrict">
1
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380 <param name="coordinates_file" type="data" format="tabular" label="Tabular file with coordinates" help="x-values in first column, y-values in second column"/>
2
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381 <param name="coordinates_header" type="boolean" label="File contains a header line" truevalue="TRUE" falsevalue="FALSE"/>
0
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382 </when>
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383 <when value="no_restriction"/>
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384 </conditional>
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385 <conditional name="tabular_annotation">
1
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386 <param name="load_annotation" type="select" label="For Cardinal RData only: Use pixel annotation from tabular file to have updated annotation information in case empty spectra will be removed">
0
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387 <option value="no_annotation" selected="True">use no annotation</option>
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388 <option value="yes_annotation">use pixel annotation from a tabular file</option>
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389 </param>
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390 <when value="yes_annotation">
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391 <param name="annotation_file" type="data" format="tabular" label="Use annotations from tabular file"
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392 help="Tabular file with three columns: x values, y values and pixel annotations"/>
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393 <param name="column_x" data_ref="annotation_file" label="Column with x values" type="data_column"/>
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394 <param name="column_y" data_ref="annotation_file" label="Column with y values" type="data_column"/>
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395 <param name="column_names" data_ref="annotation_file" label="Column with pixel annotations" type="data_column"/>
2
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396 <param name="tabular_header" type="boolean" label="File contains a header line" truevalue="TRUE" falsevalue="FALSE"/>
0
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397 </when>
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398 <when value="no_annotation"/>
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399 </conditional>
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400 <repeat name="methods" title="Method" min="1">
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401 <conditional name="methods_conditional">
1
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402 <param name="method" type="select" label="Select a method">
0
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403 <option value="Transformation" selected="True">Transformation</option>
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404 <option value="Smoothing">Smoothing</option>
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405 <option value="Baseline">Baseline removal</option>
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406 <option value="Calibrate">Calibrate</option>
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407 <option value="Align">Align Spectra (warping/phase correction)</option>
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408 <validator type="empty_field" />
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409 </param>
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410 <when value="Transformation">
2
e754c2b545a9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
411 <param name="transform_method" type="select" label="Select a transfprormation method">
0
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
412 <option value="sqrt" selected="True">sqrt</option>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
413 <option value="log">log</option>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
414 <option value="log2">log2</option>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
415 <option value="log10">log10</option>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
416 <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
417 </param>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
418 </when>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
419 <when value="Smoothing">
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
420 <conditional name="methods_for_smoothing">
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
421 <param name="smooth_method" type="select" label="This method smoothes the intensity values of a MassSpectrum object">
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
422 <option value="SavitzkyGolay" selected="True">SavitzkyGolay</option>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
423 <option value="MovingAverage">MovingAverage</option>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
424 </param>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
425 <when value="SavitzkyGolay">
2
e754c2b545a9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
426 <param name="polynomial" value="3" type="text" label="PolynomialOrder argument to control the order of the filter"
e754c2b545a9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
427 help="should be smaller than the resulting window"/>
0
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
428 </when>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
429 <when value="MovingAverage">
2
e754c2b545a9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
430 <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"/>
0
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
431 </when>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
432 </conditional>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
433 <param name="halfWindowSize" type="integer" value="10"
2
e754c2b545a9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
434 label="Half window size (number of data points)"
0
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
435 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
436 mass[currentIndex-halfWindowSize] to mass[currentIndex+halfWindowSize]
2
e754c2b545a9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
437 (window size is 2*halfWindowSize+1)."/>
0
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
438 </when>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
439 <when value="Baseline">
1
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
440 <conditional name="methods_for_baseline">
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
441 <param name="baseline_method" type="select" label="Baseline removal method">
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
442 <option value="SNIP" selected="True">SNIP</option>
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
443 <option value="TopHat">TopHat</option>
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
444 <option value="ConvexHull">ConvexHull</option>
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
445 <option value="median">median</option>
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
446 <validator type="empty_field" />
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
447 </param>
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
448 <when value="SNIP">
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
449 <param name="iterations" type="integer" value="100"
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
450 label="Number of iterations" help="Corresponds to half window size: The resulting window reaches from mass[cur_index-iterations] to mass[cur_index+iterations]"/>
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
451 </when>
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
452 <when value="TopHat">
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
453 <param name="tophat_halfWindowSize" type="integer" value="10"
2
e754c2b545a9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
454 label="Half window size (number of data points)"
e754c2b545a9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
455 help="The resulting window reaches from
1
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
456 mass[currentIndex-halfWindowSize] to mass[currentIndex+halfWindowSize]"/>
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
457 </when>
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
458 <when value="ConvexHull"/>
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
459 <when value="median">
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
460 <param name="median_halfWindowSize" type="integer" value="10"
2
e754c2b545a9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
461 label="Half window size (number of data points)"
e754c2b545a9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
462 help="The resulting window reaches from
1
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
463 mass[currentIndex-halfWindowSize] to mass[currentIndex+halfWindowSize]"/>
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
464 </when>
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
465 </conditional>
0
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
466 </when>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
467 <when value="Calibrate">
2
e754c2b545a9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
468 <param name="calibrate_method" type="select" label="Intensity calibration (normalization) method">
0
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
469 <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
470 <option value="PQN">PQN</option>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
471 <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
472 <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
473 </param>
2
e754c2b545a9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
474 <conditional name="cond_calibration_range">
e754c2b545a9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
475 <param name="calibration_range" type="select" label="Instead of the whole m/z range, a specified m/z range can be used to calculate the scaling factor">
e754c2b545a9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
476 <option value="no" selected="True">complete m/z range</option>
e754c2b545a9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
477 <option value="yes">specify a m/z range</option>
e754c2b545a9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
478 </param>
e754c2b545a9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
479 <when value="no"/>
e754c2b545a9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
480 <when value="yes">
e754c2b545a9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
481 <param name="mass_start" type="integer" value="800"
e754c2b545a9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
482 label="Start of m/z range, has to be inside m/z range"
e754c2b545a9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
483 help="Scaling factor is calculated on the mass range and applied to the whole spectrum."/>
e754c2b545a9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
484 <param name="mass_end" type="integer" value="3000"
e754c2b545a9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
485 label="End of m/z range, has to be inside m/z range"/>
e754c2b545a9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
486 </when>
e754c2b545a9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
487 </conditional>
0
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
488 </when>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
489 <when value="Align">
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
490 <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
491 <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:
diff changeset
492 <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
493 <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
494 <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
495 </param>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
496
2
e754c2b545a9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
497 <param name="tolerance" type="float" value="0.00005"
e754c2b545a9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
498 label="Tolerance = abs(mz1 - mz2)/mz2"
e754c2b545a9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
499 help="Maximal relative deviation of a peak position (m/z) to be considered as identical. For 50ppm use 0.00005 or 50e-6" />
0
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
500
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
501 <param name="halfWindowSize" type="integer" value="20"
2
e754c2b545a9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
502 label="Half window size (number of data points)"
0
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
503 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
504 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
505 (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
506 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
507
1
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
508 <param name="snr" type="integer" value="2" label="Signal-to-noise-ratio"/>
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
509 <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"/>
2
e754c2b545a9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
510 <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"/>
1
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
511 <param name="remove_empty" type="boolean" label="Should empty spectra be removed" truevalue="TRUE" falsevalue="FALSE" help="For Cardinal RData files this step can only be performed if pixel annotations were provided"/>
0
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
512
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
513 <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
514 <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
515 <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
516 <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
517 </param>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
518 <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
519 <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
520 <param name="reference_file" type="data" format="tabular"
2
e754c2b545a9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
521 label="Tabular file with m/z (MassPeaks) which should be used for spectra alignment"
e754c2b545a9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
522 help="At least 2 reference m/z per spectrum are needed"/>
e754c2b545a9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
523 <param name="reference_header" type="boolean" label="File contains a header line" truevalue="TRUE" falsevalue="FALSE"/>
0
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
524 </when>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
525 </conditional>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
526 </when>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
527 </conditional>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
528 </repeat>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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diff changeset
529 <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
530 </inputs>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
531 <outputs>
2
e754c2b545a9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
532 <data format="imzml" name="outfile_imzml" label="${tool.name} on ${on_string}" />
e754c2b545a9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
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diff changeset
533 <data format="pdf" name="plots" from_work_dir="prepro_qc_plot.pdf" label="${tool.name} on ${on_string}: QC"/>
0
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
534 </outputs>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
535 <tests>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
536 <test>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
537 <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
538 <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
539 <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
540 </param>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
541 <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
542 <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
543 <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
544 </conditional>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
545 <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
546 <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
547 <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
548 <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
549 <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
550 <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
551 <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
552 </conditional>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
553 <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
554 <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
555 <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
556 </test>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
557 <test>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
558 <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
559 <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
560 <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
561 <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
562 </conditional>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
563 <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
564 <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
565 <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
566 </test>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
567 <test>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
568 <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
569 <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
570 <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
571 </param>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
572 <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
573 <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
574 <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
575 <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
576 <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
577 <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
578 <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
579 </conditional>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
580 <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
581 <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
582 <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
583 <param name="halfWindowSize" value="1"/>
2
e754c2b545a9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 1
diff changeset
584 <param name="tolerance" value="0.002"/>
1
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
585 <param name="allow_nomatch" value="TRUE"/>
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
586 <param name="remove_empty" value="TRUE"/>
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
587 <param name="empty_nomatch" value="TRUE"/>
0
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
588 <conditional name="reference_for_alignment">
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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diff changeset
589 <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
590 <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
591 </conditional>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
592 </conditional>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
593 <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
594 <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
595 <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
596 </test>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
597 </tests>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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diff changeset
598 <help><![CDATA[
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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parents:
diff changeset
599
1
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
600 @MADLI_QUANT_DESCRIPTION@
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
601
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
602 -----
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
603
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
604 **Input data**
0
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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diff changeset
605
1
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
606 - MSI data: 2 types of input data can be used:
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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parents: 0
diff changeset
607
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
608 - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/wp/imzml/>`_
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
609 - Cardinal "MSImageSet" data saved as .RData
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
610 - Only for Cardinal RData files and when remove empty spectra is chosen: Tabular file with coordinates annotations. Separate columns for x and y coordinates and a third column with pixel annotations. Tabular files with any header name or no header at all are supported
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
611 - Optional: Tabular file with pixel coordinates to restrict reading of imzML files to coordinates of interest. The file has to contain x values in the first column and y values in the second columns. Further columns are allowed. Tabular files with any header name or no header at all are supported.
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
612
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
613 ::
0
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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parents:
diff changeset
614
1
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
615 x_coord y_coord
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
616 1 1
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
617 2 1
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
618 3 1
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
619 ...
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
620 ...
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
621
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
622 - Optional: Tabular file with reference m/z for the spectra align function. At least 2 m/z values of the input list must be present in every spectrum to peform the alignment. First column must contain m/z values, without empty fields or letters. Tabular files with any header name or no header at all are supported.
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
623
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
624 ::
0
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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diff changeset
625
1
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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parents: 0
diff changeset
626
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
627 m/z
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
628 100.0
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
629 100.01
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
630 100.02
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
631 ...
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
632 ...
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
633
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
634
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
635
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
636 **Options**
0
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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diff changeset
637
2
e754c2b545a9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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diff changeset
638 - Transformation: Variance stabilization through intensity transformation:'log', 'log2', 'log10' and 'squareroot' (sqrt) are available
e754c2b545a9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
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diff changeset
639 - Smoothing: Smoothing of the peaks reduces noise and improves peak detection. Available smoothing methods are 'SavitzkyGolay' and 'Moving Average'
e754c2b545a9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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diff changeset
640
e754c2b545a9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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diff changeset
641 - For all smoothing methods: The larger the 'Half window size'f, the stronger the smoothing. The resulting window should be smaller than the FWHM (full width at half maximum) of the typical peaks. Moving average needs smaller window size than SavitzkyGolay.
e754c2b545a9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
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diff changeset
642 - Moving average: Recommended for broader peaks/high m/z range spectra. Weighted moving average: Points in the center get larger weight factors than points away from the center.
e754c2b545a9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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diff changeset
643 - SavitzkyGolay: Recommended for sharp peaks/low m/z range, preserves the shape of the local maxima. The PolynomialOrder should be smaller than the resulting window. Negative values will be replaced with 0.
e754c2b545a9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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diff changeset
644
1
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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parents: 0
diff changeset
645 - Baseline reduction: Baseline reduction removes background intensity generated by chemical noise (common in MALDI datasets).
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
646
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
647 - Available methods are SNIP, TopHat,ConvexHull and median:
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
648 - SNIP is the default baseline reduction method in MALDIquant.
2
e754c2b545a9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
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diff changeset
649 - ConvexHull is not appropriate for MALDI-TOF baseline removal.
1
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
650 - The moving median may generate negative intensities.
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
651 - Except for the ConvexHull all methods have a parameter for the 'Half window size' (in SNIP it is called 'iterations'). The smaller the window the more baseline will be removed but also parts of the peaks. Wider windows preserve the peak height better and produce a smoother baseline, but some local background variation will remain.
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
652
0
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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diff changeset
653 - Intensity calibration (normalization): Normalization of intensities to Total Ion Current (TIC), median spectrum, Probabilistic Quotient Normalization (PQN)
2
e754c2b545a9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
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diff changeset
654
e754c2b545a9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
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diff changeset
655 - TIC and median are local calibration methods: each spectrum is normalized on its own (each peak is divided by the TIC or median of the spectrum)
e754c2b545a9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
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656 - PQN is a global calibration method: In PQN all spectra are calibrated using the TIC calibration first. Subsequently, a median reference spectrum is created and the intensities in all spectra are standardized using the reference spectrum and a spectrum-specific median is calculated for each spectrum. Finally, each spectrum is rescaled by the median of the ratios of its intensity values and that of the reference spectrum
e754c2b545a9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit d2f311f7fff24e54c565127c40414de708e31b3c
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657
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658 - Spectra alignment (warping): alignment for (re)calibration of m/z values, 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 "logical, 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.
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659
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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660
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0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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661 **Output**
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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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662
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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663 - imzML file (imzML format can be continuous or processed)
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664 - PDF with average mass spectra after each preprocessing step
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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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665
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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666 .. _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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667
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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668 ]]>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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669 </help>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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670 <expand macro="citation"/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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671 </tool>