Mercurial > repos > galaxyp > maldi_quant_preprocessing

annotate maldi_quant_preprocessing.xml @ 1:0892a051eb17 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
author galaxyp
date Mon, 01 Oct 2018 01:09:28 -0400
parents e2aa05746a69
children e754c2b545a9
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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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1 <tool id="maldi_quant_preprocessing" name="MALDIquant preprocessing" version="@VERSION@.1">
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2 <description>
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3 Preprocessing of mass-spectrometry imaging data
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4 </description>
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5 <macros>
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6 <import>maldi_macros.xml</import>
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7 </macros>
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8 <expand macro="requirements"/>
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9 <command detect_errors="exit_code">
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10 <![CDATA[
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11 #if $infile.ext == 'imzml'
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12 cp '${infile.extra_files_path}/imzml' infile.imzML &&
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13 cp '${infile.extra_files_path}/ibd' infile.ibd &&
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14 #elif $infile.ext == 'analyze75'
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15 cp '${infile.extra_files_path}/hdr' infile.hdr &&
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16 cp '${infile.extra_files_path}/img' infile.img &&
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17 cp '${infile.extra_files_path}/t2m' infile.t2m &&
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18 du infile.hdr &&
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19 du infile.img &&
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20 du -s -B1 infile.hdr &&
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21 #else
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22 ln -s $infile infile.RData &&
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23 #end if
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24 Rscript "${maldi_quant_preprocessing}" &&
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25 mkdir $outfile_imzml.files_path &&
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26 mv ./out.imzMl "${os.path.join($outfile_imzml.files_path, 'imzml')}" | true &&
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27 mv ./out.ibd "${os.path.join($outfile_imzml.files_path, 'ibd')}" | true &&
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28 echo "imzML file:" > $outfile_imzml &&
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29 ls -l "$outfile_imzml.files_path" >> $outfile_imzml
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30 ]]>
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31 </command>
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32 <configfiles>
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33 <configfile name="maldi_quant_preprocessing"><![CDATA[
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34
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35 @R_IMPORTS@
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37 #if $restriction_conditional.restriction == 'restrict':
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38
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39 print('Reading mask region')
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40 ## Import imzML file
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41
1
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42 coordinate_matrix = as.matrix(read.delim("$restriction_conditional.coordinates_file", header = $restriction_conditional.coordinates_header, stringsAsFactors = FALSE))[,1:2]
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43
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44 maldi_data = importImzMl('infile.imzML',
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45 coordinates = coordinate_matrix)
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46 pixelnames = paste0("x = ", coordinates(maldi_data)[,1],", y = ", coordinates(maldi_data)[,2])
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47
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48 #else:
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49
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50 print('Reading entire file')
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51 #if $infile.ext == 'imzml'
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52 ## Import imzML file
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53 maldi_data = import( 'infile.imzML', type="imzML" )
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54 coordinates_info = cbind(coordinates(maldi_data)[,1:2], c(1:length(maldi_data)))
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55 #elif $infile.ext == 'analyze75'
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56 ## Import analyze7.5 file
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57 maldi_data = import( 'infile.hdr' )
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58 coordinates_info = cbind(coordinates(maldi_data)[,1:2], c(1:length(maldi_data)))
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59 #else
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60 loadRData <- function(fileName){
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61 #loads an RData file, and returns it
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62 load(fileName)
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63 get(ls()[ls() != "fileName"])
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64 }
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65 msidata = loadRData('infile.RData')
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66 ## save coordinates
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67 cardinal_coordinates = as.matrix(Cardinal::coord(msidata)[,1:2])
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68 ## save mz values
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69 cardinal_mzs = Cardinal::mz(msidata)
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70 ## create MALDIquant MassSpectrum object
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71 maldi_data = list()
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72 for(number_spectra in 1:ncol(msidata)){
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73 maldi_data[[number_spectra]] = createMassSpectrum(mass = cardinal_mzs, intensity = iData(msidata)[,number_spectra])
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74 coordinates_info = cbind(cardinal_coordinates, c(1:length(maldi_data)))
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75 }
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76
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77 #end if
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78
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79 #end if
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80
1
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81 ## Quality control plots during preprocessing
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82
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83 pdf("prepro_qc_plot.pdf", fonts = "Times", pointsize = 12)
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84 plot(0,type='n',axes=FALSE,ann=FALSE)
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85
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86 ## if no filename is given, name of file in Galaxy history is used
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87 #set $filename = $infile.display_name
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88 title(main=paste("$filename"))
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89
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90 #if str($tabular_annotation.load_annotation) == 'yes_annotation':
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91 print("use annotation file")
1
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92
0
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93 ## read and extract x,y,annotation information
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94 input_tabular = read.delim("$tabular_annotation.annotation_file", header = $tabular_annotation.tabular_header, stringsAsFactors = FALSE)
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95 annotation_input = input_tabular[,c($tabular_annotation.column_x, $tabular_annotation.column_y, $tabular_annotation.column_names)]
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96 colnames(annotation_input) = c("x", "y", "annotation") ## rename annotations header to default name "annotation"
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97
1
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98 ## merge with coordinate information (from above) of MSI data
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99 colnames(coordinates_info)[3] = "pixel_index"
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100 merged_annotation = merge(coordinates_info, annotation_input, by=c("x", "y"), all.x=TRUE)
0
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101 merged_annotation[is.na(merged_annotation)] = "NA"
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102 merged_annotation = merged_annotation[order(merged_annotation\$pixel_index),]
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103 samples = as.factor(merged_annotation\$annotation)
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104
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105 ## print annotation overview into PDF output
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106
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107 ## the more annotation groups a file has the smaller will be the legend
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108 number_combined = length(levels(as.factor(merged_annotation\$annotation)))
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109 if (number_combined<20){
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110 legend_size = 10
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111 }else if (number_combined>20 && number_combined<40){
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112 legend_size = 9
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113 }else if (number_combined>40 && number_combined<60){
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114 legend_size = 8
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115 }else if (number_combined>60 && number_combined<100){
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116 legend_size = 7
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117 }else{
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118 legend_size = 6
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119 }
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120
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121 combine_plot = ggplot(merged_annotation, aes(x=x, y=y, fill=annotation))+
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122 geom_tile() +
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123 coord_fixed()+
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124 ggtitle("Spatial orientation of annotated data")+
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125 theme_bw()+
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126 theme(plot.title = element_text(hjust = 0.5))+
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127 theme(text=element_text(family="ArialMT", face="bold", size=12))+
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128 theme(legend.position="bottom",legend.direction="vertical")+
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129 theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = legend_size))+
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130 guides(fill=guide_legend(ncol=5,byrow=TRUE))
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131
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132 print(combine_plot)
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133
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134 #end if
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135
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136 #################### Preprocessing methods #####################################
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137
1
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138 ## QC plot on input file
0
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139 avgSpectra = averageMassSpectra(maldi_data,method="mean")
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140 plot(avgSpectra, main="Average spectrum for input file")
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141
1
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142 pixel_number = length(maldi_data)
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143 minmz = round(min(unlist(lapply(maldi_data,mass))), digits=4)
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144 maxmz = round(max(unlist(lapply(maldi_data,mass))), digits=4)
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145 maxfeatures = round(length(unlist(lapply(maldi_data,mass)))/length(maldi_data), digits=2)
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146 medint = round(median(unlist(lapply(maldi_data,intensity))), digits=2)
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147 inputdata = c(minmz, maxmz,maxfeatures, medint)
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148 QC_numbers= data.frame(inputdata = c(minmz, maxmz,maxfeatures, medint))
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149 vectorofactions = "inputdata"
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150
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151
0
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152 #for $method in $methods:
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153
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154 #if str( $method.methods_conditional.method ) == 'Transformation':
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155
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156 print('transforming')
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157 ##transformation
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158 maldi_data = transformIntensity(maldi_data, method="$method.methods_conditional.transform_method")
1
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159 ## QC plot and numbers
0
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160 avgSpectra = averageMassSpectra(maldi_data,method="mean")
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161 plot(avgSpectra, main="Average spectrum after transformation")
1
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162 pixel_number = length(maldi_data)
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163 minmz = round(min(unlist(lapply(maldi_data,mass))), digits=4)
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164 maxmz = round(max(unlist(lapply(maldi_data,mass))), digits=4)
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165 maxfeatures = round(length(unlist(lapply(maldi_data,mass)))/length(maldi_data), digits=2)
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166 medint = round(median(unlist(lapply(maldi_data,intensity))), digits=2)
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167 transformed = c(minmz, maxmz,maxfeatures, medint)
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168 QC_numbers= cbind(QC_numbers, transformed)
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169 vectorofactions = append(vectorofactions, "transformed")
0
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170
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171
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172 #elif str( $method.methods_conditional.method ) == 'Smoothing':
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173
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174 print('smoothing')
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175 ##smoothing
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176
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177 #if str($method.methods_conditional.methods_for_smoothing.smooth_method ) == 'SavitzkyGolay':
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178 print('SavitzkyGolay')
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179
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180 maldi_data = smoothIntensity(maldi_data,
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181 method="SavitzkyGolay", polynomialOrder=$method.methods_conditional.methods_for_smoothing.polynomial,
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182 halfWindowSize=$method.methods_conditional.halfWindowSize)
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183
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184 #elif str($method.methods_conditional.methods_for_smoothing.smooth_method ) == 'MovingAverage':
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185 print('MovingAverage')
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186
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187 maldi_data = smoothIntensity(maldi_data,
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188 method="MovingAverage", weighted=$method.methods_conditional.methods_for_smoothing.weighted,
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189 halfWindowSize=$method.methods_conditional.halfWindowSize)
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190
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191 #end if
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192
1
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193 ## QC plot and numbers
0
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194 avgSpectra = averageMassSpectra(maldi_data,method="mean")
1
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195 plot(avgSpectra, main="Average spectrum after smoothing", sub="")
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196 pixel_number = length(maldi_data)
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197 minmz = round(min(unlist(lapply(maldi_data,mass))), digits=4)
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198 maxmz = round(max(unlist(lapply(maldi_data,mass))), digits=4)
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199 maxfeatures = round(length(unlist(lapply(maldi_data,mass)))/length(maldi_data), digits=2)
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200 medint = round(median(unlist(lapply(maldi_data,intensity))), digits=2)
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201 smoothed = c(minmz, maxmz,maxfeatures, medint)
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202 QC_numbers= cbind(QC_numbers, smoothed)
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203 vectorofactions = append(vectorofactions, "smoothed")
0
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204
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205
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206 #elif str( $method.methods_conditional.method ) == 'Baseline':
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207
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208 print('baseline removing')
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209 ## Remove baseline
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210
1
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211 #if str($method.methods_conditional.methods_for_baseline.baseline_method ) == 'SNIP':
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212 print('SNIP')
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213 random_spectra = sample(1:length(maldi_data), 4, replace=FALSE)
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214 par(mfrow = c(2,2))
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215 for (random_sample in random_spectra){
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216 maldi_data_baseline = estimateBaseline(maldi_data[[random_sample]],
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217 method="SNIP", iterations=$method.methods_conditional.methods_for_baseline.iterations)
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218 plot(maldi_data[[random_sample]], sub="", main=paste0("Estimated baseline for spectrum ", random_sample))
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219 lines(maldi_data_baseline, col="blue", lwd=2)}
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220
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221 maldi_data = removeBaseline(maldi_data,
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222 method="SNIP",
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223 iterations=$method.methods_conditional.methods_for_baseline.iterations)
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224
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225 #elif str($method.methods_conditional.methods_for_baseline.baseline_method ) == 'TopHat':
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226 print('TopHat')
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227
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228 maldi_data = removeBaseline(maldi_data,
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229 method="TopHat",
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230 halfWindowSize=$method.methods_conditional.methods_for_baseline.tophat_halfWindowSize)
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231
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232 #elif str($method.methods_conditional.methods_for_baseline.baseline_method ) == 'ConvexHull':
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233 print('ConvexHull')
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234
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235 maldi_data = removeBaseline(maldi_data,
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236 method="ConvecHull")
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237
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238 #elif str($method.methods_conditional.methods_for_baseline.baseline_method ) == 'median':
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239 print('median')
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240
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241 maldi_data = removeBaseline(maldi_data,
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242 method="TopHat",
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243 halfWindowSize=$method.methods_conditional.methods_for_baseline.median_halfWindowSize)
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244
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245 #end if
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246
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247 ## QC plot and numbers
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248 par(mfrow = c(1,1))
0
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249 avgSpectra = averageMassSpectra(maldi_data,method="mean")
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250 plot(avgSpectra, main="Average spectrum after baseline removal")
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251 pixel_number = length(maldi_data)
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252 minmz = round(min(unlist(lapply(maldi_data,mass))), digits=4)
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253 maxmz = round(max(unlist(lapply(maldi_data,mass))), digits=4)
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254 maxfeatures = round(length(unlist(lapply(maldi_data,mass)))/length(maldi_data), digits=2)
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255 medint = round(median(unlist(lapply(maldi_data,intensity))), digits=2)
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256 baseline_removed = c(minmz, maxmz,maxfeatures, medint)
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257 QC_numbers= cbind(QC_numbers, baseline_removed)
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258 vectorofactions = append(vectorofactions, "baseline_removed")
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259
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260
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261 #elif str( $method.methods_conditional.method ) == 'Calibrate':
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262
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263 print('calibrate')
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264 ##calibrate
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265
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266 #if $method.methods_conditional.mass_start != 0 and $method.methods_conditional.mass_end != 0:
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267 ## calibrate only given m/z range
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268 maldi_data = calibrateIntensity(maldi_data,
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269 method="$method.methods_conditional.calibrate_method",
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270 range=c($method.methods_conditional.mass_start, $method.methods_conditional.mass_end))
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271 #else:
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272 maldi_data = calibrateIntensity(maldi_data,
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273 method="$method.methods_conditional.calibrate_method")
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274 #end if
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275 ## QC plot and numbers
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276 avgSpectra = averageMassSpectra(maldi_data,method="mean")
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277 plot(avgSpectra, main="Average spectrum after normalization")
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278 pixel_number = length(maldi_data)
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279 minmz = round(min(unlist(lapply(maldi_data,mass))), digits=4)
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280 maxmz = round(max(unlist(lapply(maldi_data,mass))), digits=4)
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281 maxfeatures = round(length(unlist(lapply(maldi_data,mass)))/length(maldi_data), digits=2)
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282 medint = round(median(unlist(lapply(maldi_data,intensity))), digits=2)
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283 intensity_calibrated = c(minmz, maxmz,maxfeatures, medint)
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284 QC_numbers= cbind(QC_numbers, intensity_calibrated )
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285 vectorofactions = append(vectorofactions, "intensity_calibrated ")
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286
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287
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288 #elif str( $method.methods_conditional.method ) == 'Align':
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289
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290 print('align')
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291 ##align spectra
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292
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293 #if str($method.methods_conditional.reference_for_alignment.align_ref) == 'no_reference':
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294 maldi_data = alignSpectra(maldi_data, halfWindowSize=$method.methods_conditional.halfWindowSize,
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295 SNR=$method.methods_conditional.snr, tolerance=$method.methods_conditional.tolerance,
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296 allowNoMatches =$method.methods_conditional.allow_nomatch, emptyNoMatches = $method.methods_conditional.empty_nomatch,
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297 warpingMethod="$method.methods_conditional.warping_method")
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298
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299 #elif str($method.methods_conditional.reference_for_alignment.align_ref) == 'yes_reference':
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300 ## create reference mass_vector from tabular file
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301 mass_vector = read.delim("$method.methods_conditional.reference_for_alignment.reference_file", header = $method.methods_conditional.reference_for_alignment.reference_header, stringsAsFactors = FALSE)[,1]
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302 int_vector = rep(1,length(mass_vector))
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303 mass_list = createMassPeaks(mass_vector, int_vector)
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304
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305 maldi_data = alignSpectra(maldi_data, halfWindowSize=$method.methods_conditional.halfWindowSize,
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306 SNR=$method.methods_conditional.snr,
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307 tolerance=$method.methods_conditional.tolerance,
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308 warpingMethod="$method.methods_conditional.warping_method",
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309 reference = mass_list, allowNoMatches =$method.methods_conditional.allow_nomatch, emptyNoMatches = $method.methods_conditional.empty_nomatch)
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310
1
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311 #end if
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312
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313 #if $method.methods_conditional.remove_empty:
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314 print("remove empty spectra")
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315
1
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316 #if $infile.ext == 'rdata'
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317 cardinal_coordinates = cardinal_coordinates[-findEmptyMassObjects(maldi_data),] ## remove coordinates of empty spectra for Cardinal RData input
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318 #end if
1
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319 #if str($tabular_annotation.load_annotation) == 'yes_annotation':
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320 merged_annotation = merged_annotation[-findEmptyMassObjects(maldi_data),] ## remove coordinate annotations for empty spectra
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321 #end if
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322 maldi_data = removeEmptyMassObjects(maldi_data)
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323 #end if
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324
1
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325
0
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326 ## QC plot
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327
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328 if (length(maldi_data)>0){
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329 avgSpectra = averageMassSpectra(maldi_data,method="mean")
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330 plot(avgSpectra, main="Average spectrum after alignment")
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331 }else{"All spectra are empty"}
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332
1
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333 pixel_number = length(maldi_data)
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334 minmz = round(min(unlist(lapply(maldi_data,mass))), digits=4)
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335 maxmz = round(max(unlist(lapply(maldi_data,mass))), digits=4)
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336 maxfeatures = round(length(unlist(lapply(maldi_data,mass)))/length(maldi_data), digits=2)
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337 medint = round(median(unlist(lapply(maldi_data,intensity))), digits=2)
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338 spectra_aligned = c(minmz, maxmz,maxfeatures, medint)
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339 QC_numbers= cbind(QC_numbers, spectra_aligned )
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340 vectorofactions = append(vectorofactions, "spectra_aligned")
0
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341 #end if
1
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342
0
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343 #end for
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344
1
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345 rownames(QC_numbers) = c("min m/z", "max mz", "# features", "median\nintensity")
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346 plot(0,type='n',axes=FALSE,ann=FALSE)
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347 grid.table(t(QC_numbers))
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348
0
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349 dev.off()
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350
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351 ## export imzML file
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352 if (length(maldi_data)>0){
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353 #if $infile.ext == 'rdata'
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354 MALDIquantForeign::exportImzMl(maldi_data, file="out.imzMl", processed=$export_processed, coordinates=cardinal_coordinates)
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355 #else
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356 MALDIquantForeign::exportImzMl(maldi_data, file="out.imzMl", processed=$export_processed)
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357 #end if
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358
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359 ## export annotation tabular file
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360 #if str($tabular_annotation.load_annotation) == 'yes_annotation':
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361 write.table(merged_annotation, file="$annotation_output", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
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362 #end if
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363 }else{"All spectra are empty, outputfiles will be empty,too."}
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364
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365 ]]>
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366 </configfile>
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367 </configfiles>
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368 <inputs>
1
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369 <param name="infile" type="data" format="imzml,rdata" 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
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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370 <conditional name="restriction_conditional">
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371 <param name="restriction" type="select" label="Read in only spectra of interest" help="This option only works for imzML files">
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372 <option value="no_restriction" selected="True">Calculate on entire file</option>
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373 <option value="restrict">Restrict to coordinates of interest</option>
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374 </param>
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375 <when value="restrict">
1
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376 <param name="coordinates_file" type="data" format="tabular" label="Tabular file with coordinates" help="x-values in first column, y-values in second column"/>
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377 <param name="coordinates_header" type="boolean" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/>
0
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378 </when>
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379 <when value="no_restriction"/>
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380 </conditional>
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381 <conditional name="tabular_annotation">
1
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382 <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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383 <option value="no_annotation" selected="True">use no annotation</option>
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384 <option value="yes_annotation">use pixel annotation from a tabular file</option>
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385 </param>
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386 <when value="yes_annotation">
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387 <param name="annotation_file" type="data" format="tabular" label="Use annotations from tabular file"
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388 help="Tabular file with three columns: x values, y values and pixel annotations"/>
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389 <param name="column_x" data_ref="annotation_file" label="Column with x values" type="data_column"/>
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390 <param name="column_y" data_ref="annotation_file" label="Column with y values" type="data_column"/>
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391 <param name="column_names" data_ref="annotation_file" label="Column with pixel annotations" type="data_column"/>
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392 <param name="tabular_header" type="boolean" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/>
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393 </when>
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394 <when value="no_annotation"/>
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395 </conditional>
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396 <repeat name="methods" title="Method" min="1">
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397 <conditional name="methods_conditional">
1
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398 <param name="method" type="select" label="Select a method">
0
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399 <option value="Transformation" selected="True">Transformation</option>
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400 <option value="Smoothing">Smoothing</option>
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401 <option value="Baseline">Baseline removal</option>
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402 <option value="Calibrate">Calibrate</option>
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403 <option value="Align">Align Spectra (warping/phase correction)</option>
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404 <validator type="empty_field" />
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405 </param>
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406 <when value="Transformation">
1
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407 <param name="transform_method" type="select" label="Select the transfprormation method">
0
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408 <option value="sqrt" selected="True">sqrt</option>
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409 <option value="log">log</option>
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410 <option value="log2">log2</option>
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411 <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
412 <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
413 </param>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
414 </when>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
415 <when value="Smoothing">
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
416 <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
417 <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
418 <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
419 <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
420 </param>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
421 <when value="SavitzkyGolay">
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
422 <param name="polynomial" value="3" type="text" label="PolynomialOrder argument to control the order of the filter"/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
423 </when>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
424 <when value="MovingAverage">
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
425 <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"/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
426 </when>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
427 </conditional>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
428 <param name="halfWindowSize" type="integer" value="10"
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
429 label="Half window size"
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
430 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
431 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
432 (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
433 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
434 </when>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
435 <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
436 <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
437 <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
438 <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
439 <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
440 <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
441 <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
442 <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
443 </param>
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
444 <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
445 <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
446 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
447 </when>
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="TopHat">
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="tophat_halfWindowSize" type="integer" value="10"
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
450 label="Half window size" help="The resulting window reaches from
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
451 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
452 </when>
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
453 <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
454 <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
455 <param name="median_halfWindowSize" type="integer" value="10"
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
456 label="Half window size" help="The resulting window reaches from
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
457 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
458 </when>
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
459 </conditional>
0
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
460 </when>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
461 <when value="Calibrate">
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
462 <param name="calibrate_method" type="select" label="Calibration method">
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
463 <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
464 <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
465 <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
466 <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
467 </param>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
468 <param name="mass_start" type="integer" value="0"
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
469 label="Start of m/z range, has to be inside m/z range"
1
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
470 help="Scaling factor is calculated on the mass range and applied to the whole spectrum. Start and end are not allowed to be 0"/>
0
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
471 <param name="mass_end" type="integer" value="0"
1
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
472 label="End of m/z range, has to be inside m/z range"/>
0
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
473 </when>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
474 <when value="Align">
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
475 <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
476 <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
477 <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
478 <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
479 <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
480 </param>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
481
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
482 <param name="tolerance" type="float" value="0.002"
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
483 label="Tolerance"
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
484 help="Double, maximal relative deviation of a peak position (m/z) to be considered as identical" />
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
485
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
486 <param name="halfWindowSize" type="integer" value="20"
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
487 label="Half window size"
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
488 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
489 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
490 (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
491 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
492
1
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
493 <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
494 <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"/>
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
495 <param name="empty_nomatch" type="boolean" label="logical, if TRUE the intensity values of MassSpectrum or MassPeaks objects with missing (NA) warping functions are set to zero" truevalue="TRUE" falsevalue="FALSE"/>
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
496 <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
497
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
498 <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
499 <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
500 <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
501 <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
502 </param>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
503 <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
504 <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
505 <param name="reference_file" type="data" format="tabular"
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
506 label="Tabular file with m/z of internal calibrants (MassPeaks) which should be used for spectra alignment"
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
507 help="calibration of m/z values to internal calibrants, at least 2 m/z per spectrum are needed"/>
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="reference_header" type="boolean" label="Tabular 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
509 </when>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
510 </conditional>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
511 </when>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
512 </conditional>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
513 </repeat>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
514 <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
515 </inputs>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
516 <outputs>
1
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
517 <data format="imzml" name="outfile_imzml" label="$infile.display_name preprocessed" />
0
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
518 <data format="pdf" name="plots" from_work_dir="prepro_qc_plot.pdf" label="$infile.display_name preprocessed QC"/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
519 <data format="tabular" name="annotation_output" label="$infile.display_name annotations">
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
520 <filter>tabular_annotation["load_annotation"] == 'yes_annotation'</filter>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
521 </data>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
522 </outputs>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
523 <tests>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
524 <test>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
525 <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
526 <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
527 <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
528 </param>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
529 <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
530 <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
531 <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
532 </conditional>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
533 <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
534 <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
535 <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
536 <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
537 <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
538 <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
539 <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
540 </conditional>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
541 <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
542 <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
543 <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
544 </test>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
545 <test>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
546 <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
547 <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
548 <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
549 <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
550 </conditional>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
551 <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
552 <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
553 <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
554 </test>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
555 <test>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
556 <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
557 <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
558 <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
559 </param>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
560 <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
561 <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
562 <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
563 <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
564 <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
565 <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
566 <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
567 </conditional>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
568 <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
569 <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
570 <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
571 <param name="halfWindowSize" value="1"/>
1
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
572 <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
573 <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
574 <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
575 <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
576 <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
577 <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
578 </conditional>
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
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diff changeset
580 <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
581 <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
582 <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
583 <output name="annotation_output" file="annotations_output3.tabular"/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
584 </test>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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diff changeset
585 </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
586 <help><![CDATA[
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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diff changeset
587
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
588 @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
589
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
590 -----
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
591
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
592 **Input data**
0
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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diff changeset
593
1
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
594 - 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
galaxyp
parents: 0
diff changeset
595
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
596 - 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
597 - 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
598 - 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
parents: 0
diff changeset
599 - 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
600
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
601 ::
0
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents:
diff changeset
602
1
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
603 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
604 1 1
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
605 2 1
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
606 3 1
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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 ...
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
609
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
610 - 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
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diff changeset
611
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
612 ::
0
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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diff changeset
613
1
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
614
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents: 0
diff changeset
615 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
616 100.0
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
617 100.01
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
618 100.02
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
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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
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diff changeset
622
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
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diff changeset
624 **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
625
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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diff changeset
626 - Transformation: transformation of intensities with log, log2, log10 and squareroot
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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627 - Smoothing: Smoothing of the peaks reduces noise and improves peak detection. Available smoothing methods are SavitzkyGolay and Moving Average
1
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
628 - 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
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diff changeset
629
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
630 - 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
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diff changeset
631 - SNIP is the default baseline reduction method in MALDIquant.
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
632 - ConvexHull cannot be used for MALDI-TOF baseline removal.
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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633 - The moving median may generate negative intensities.
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
634 - 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
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diff changeset
635
0
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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diff changeset
636 - Intensity calibration (normalization): Normalization of intensities to Total Ion Current (TIC), median spectrum, Probabilistic Quotient Normalization (PQN)
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
637 - 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.
0
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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diff changeset
638
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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diff changeset
639
1
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
640 **Output**
0
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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641
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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diff changeset
642 - imzML file (imzML format can be continuous or processed)
1
0892a051eb17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
643 - PDF with average mass spectra after each preprocessing step
0
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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diff changeset
644
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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diff changeset
645 .. _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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646
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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647 ]]>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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648 </help>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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diff changeset
649 <expand macro="citation"/>
e2aa05746a69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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650 </tool>