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annotate msi_preprocessing.xml @ 7:1a3d477bc54a draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
author galaxyp
date Fri, 06 Jul 2018 14:13:48 -0400
parents d3fd539f477e
children d77c5228fd1a
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1a3d477bc54a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
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1 <tool id="mass_spectrometry_imaging_preprocessing" name="MSI preprocessing" version="1.10.0.4">
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2 <description>
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3 mass spectrometry imaging preprocessing
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4 </description>
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5 <requirements>
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6 <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement>
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7 <requirement type="package" version="2.2.1">r-gridextra</requirement>
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8 <requirement type="package" version="0.20-35">r-lattice</requirement>
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9 </requirements>
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10 <command detect_errors="exit_code">
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11 <![CDATA[
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13 #if $infile.ext == 'imzml'
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14 ln -s '${infile.extra_files_path}/imzml' infile.imzML &&
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15 ln -s '${infile.extra_files_path}/ibd' infile.ibd &&
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16 #elif $infile.ext == 'analyze75'
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17 ln -s '${infile.extra_files_path}/hdr' infile.hdr &&
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18 ln -s '${infile.extra_files_path}/img' infile.img &&
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19 ln -s '${infile.extra_files_path}/t2m' infile.t2m &&
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20 #else
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21 ln -s '$infile' infile.RData &&
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22 #end if
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23 cat '${cardinal_preprocessing}' &&
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24 Rscript '${cardinal_preprocessing}'
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25
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26 ]]>
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27 </command>
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28 <configfiles>
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29 <configfile name="cardinal_preprocessing"><![CDATA[
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31 ################################# load libraries and read file #################
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32
0
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33 library(Cardinal)
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34 library(gridExtra)
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35 library(lattice)
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36
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37 #if $infile.ext == 'imzml'
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38 #if str($processed_cond.processed_file) == "processed":
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39 msidata <- readImzML('infile', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units")
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40 #else
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41 msidata <- readImzML('infile', attach.only=TRUE)
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42 #end if
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43 #elif $infile.ext == 'analyze75'
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44 msidata = readAnalyze('infile', attach.only=TRUE)
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45 #else
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46 load('infile.RData')
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47 #end if
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48
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49 print(paste0("Number of NA in input file: ",sum(is.na(spectra(msidata)[]))))
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50
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51 ## function to later read RData reference files in
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52
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53 loadRData <- function(fileName){
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54 #loads an RData file, and returns it
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55 load(fileName)
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56 get(ls()[ls() != "fileName"])
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57 }
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58
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59 if (sum(spectra(msidata)[]>0, na.rm=TRUE)> 0){
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60 ######################### preparations for QC report #################
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61
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62 maxfeatures = length(features(msidata))
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63 medianpeaks = median(colSums(spectra(msidata)[]>0, na.rm=TRUE))
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64 medint = round(median(spectra(msidata)[],na.rm=TRUE), digits=2)
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65 TICs = round(mean(colSums(spectra(msidata)[], na.rm=TRUE)), digits=1)
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66 QC_numbers= data.frame(inputdata = c(maxfeatures, medianpeaks, medint, TICs))
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67 vectorofactions = "inputdata"
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68
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69 ############################### Preprocessing steps ###########################
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70 ###############################################################################
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71
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72 #for $method in $methods:
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74 ############################### Normalization ###########################
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75
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76 #if str( $method.methods_conditional.preprocessing_method ) == 'Normalization':
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77 print('Normalization')
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78 ##normalization
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79
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80 msidata = normalize(msidata, method="tic")
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82 ############################### QC ###########################
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83
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84 maxfeatures = length(features(msidata))
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85 medianpeaks = median(colSums(spectra(msidata)[]>0, na.rm=TRUE),)
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86 medint = round(median(spectra(msidata)[], na.rm=TRUE), digits=2)
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87 TICs = round(mean(colSums(spectra(msidata)[], na.rm=TRUE)), digits=1)
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88 normalized = c(maxfeatures, medianpeaks, medint, TICs)
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89 QC_numbers= cbind(QC_numbers, normalized)
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90 vectorofactions = append(vectorofactions, "normalized")
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91
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92 ############################### Baseline reduction ###########################
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93
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94 #elif str( $method.methods_conditional.preprocessing_method ) == 'Baseline_reduction':
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95 print('Baseline_reduction')
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96 ##baseline reduction
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97
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98 msidata = reduceBaseline(msidata, method="median", blocks=$method.methods_conditional.blocks_baseline)
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99
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100 ############################### QC ###########################
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101
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102 maxfeatures = length(features(msidata))
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103 medianpeaks = median(colSums(spectra(msidata)[]>0, na.rm=TRUE))
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104 medint = round(median(spectra(msidata)[], na.rm=TRUE), digits=2)
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105 TICs = round(mean(colSums(spectra(msidata)[], na.rm=TRUE)), digits=1)
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106 baseline= c(maxfeatures, medianpeaks, medint, TICs)
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107 QC_numbers= cbind(QC_numbers, baseline)
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108 vectorofactions = append(vectorofactions, "baseline red.")
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109
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110 ############################### Smoothing ###########################
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111
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112 #elif str( $method.methods_conditional.preprocessing_method ) == 'Smoothing':
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113 print('Smoothing')
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114 ## Smoothing
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115
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116 #if str( $method.methods_conditional.methods_for_smoothing.smoothing_method) == 'gaussian':
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117 print('gaussian smoothing')
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118
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119 msidata = smoothSignal(msidata, method="$method.methods_conditional.methods_for_smoothing.smoothing_method", window=$method.methods_conditional.window_smoothing, sd = $method.methods_conditional.methods_for_smoothing.sd_gaussian)
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120
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121 #elif str( $method.methods_conditional.methods_for_smoothing.smoothing_method) == 'sgolay':
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122 print('sgolay smoothing')
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123
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124 msidata = smoothSignal(msidata, method="$method.methods_conditional.methods_for_smoothing.smoothing_method", window=$method.methods_conditional.window_smoothing, order = $method.methods_conditional.methods_for_smoothing.order_of_filters)
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125 #elif str($method.methods_conditional.methods_for_smoothing.smoothing_method) == 'ma':
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126 print('sgolay smoothing')
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127
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128 msidata = smoothSignal(msidata, method="$method.methods_conditional.methods_for_smoothing.smoothing_method", window=$method.methods_conditional.window_smoothing, coef = $method.methods_conditional.methods_for_smoothing.coefficients_ma_filter)
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129
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130 #end if
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131
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132 ############################### QC ###########################
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133
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134 maxfeatures = length(features(msidata))
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135 medianpeaks = median(colSums(spectra(msidata)[]>0, na.rm=TRUE))
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136 medint = round(median(spectra(msidata)[], na.rm=TRUE), digits=2)
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137 TICs = round(mean(colSums(spectra(msidata)[], na.rm=TRUE)), digits=1)
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138 smoothed= c(maxfeatures, medianpeaks, medint, TICs)
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139 QC_numbers= cbind(QC_numbers, smoothed)
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140 vectorofactions = append(vectorofactions, "smoothed")
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141
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142 ############################### Peak picking ###########################
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143
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144 #elif str( $method.methods_conditional.preprocessing_method) == 'Peak_picking':
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145 print('Peak_picking')
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146 ## Peakpicking
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147
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148
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149 ## remove duplicated coordinates, otherwise peak picking will fail
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150 print(paste0(sum(duplicated(coord(msidata))), " coordinates were removed"))
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151 msidata <- msidata[,!duplicated(coord(msidata))]
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152
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153 #if str( $method.methods_conditional.methods_for_picking.picking_method) == 'adaptive':
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154 print('adaptive peakpicking')
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155
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156 msidata = peakPick(msidata, window = $method.methods_conditional.window_picking, blocks = $method.methods_conditional.blocks_picking, method='$method.methods_conditional.methods_for_picking.picking_method', SNR=$method.methods_conditional.SNR_picking_method, spar=$method.methods_conditional.methods_for_picking.spar_picking)
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157
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158 #elif str( $method.methods_conditional.methods_for_picking.picking_method) == 'limpic':
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159 print('limpic peakpicking')
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160
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161 msidata = peakPick(msidata, window = $method.methods_conditional.window_picking, blocks = $method.methods_conditional.blocks_picking, method='$method.methods_conditional.methods_for_picking.picking_method', SNR=$method.methods_conditional.SNR_picking_method, thresh=$method.methods_conditional.methods_for_picking.tresh_picking)
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162
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163 #elif str( $method.methods_conditional.methods_for_picking.picking_method) == 'simple':
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164 print('simple peakpicking')
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165
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166 msidata = peakPick(msidata, window = $method.methods_conditional.window_picking, blocks = $method.methods_conditional.blocks_picking, method='$method.methods_conditional.methods_for_picking.picking_method', SNR=$method.methods_conditional.SNR_picking_method)
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167
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168 #end if
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169
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170 ############################### QC ###########################
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171
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172 maxfeatures = length(features(msidata))
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173 medianpeaks = median(colSums(spectra(msidata)[]>0, na.rm=TRUE))
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174 medint = round(median(spectra(msidata)[], na.rm=TRUE), digits=2)
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175 TICs = round(mean(colSums(spectra(msidata)[], na.rm=TRUE)), digits=1)
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176 picked= c(maxfeatures, medianpeaks, medint, TICs)
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177 QC_numbers= cbind(QC_numbers, picked)
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178 vectorofactions = append(vectorofactions, "picked")
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179
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180 ############################### Peak alignment ###########################
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181
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182 #elif str( $method.methods_conditional.preprocessing_method ) == 'Peak_alignment':
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183 print('Peak_alignment')
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184 ## Peakalignment
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185
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186 #if str( $method.methods_conditional.align_ref_type.align_reference_datatype) == 'align_noref':
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187
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188 align_peak_reference = msidata
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189
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190 #elif str( $method.methods_conditional.align_ref_type.align_reference_datatype) == 'align_table':
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191
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192 align_reference_table = read.delim("$method.methods_conditional.align_ref_type.align_peaks_table", header = FALSE, stringsAsFactors = FALSE)
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193 align_reference_column = align_reference_table[,$method.methods_conditional.align_ref_type.align_mass_column]
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194 align_peak_reference = align_reference_column[align_reference_column>=min(mz(msidata)) & align_reference_column<=max(mz(msidata))]
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195 if (length(align_peak_reference) == 0)
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196 {align_peak_reference = 0}
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197
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198 #elif str( $method.methods_conditional.align_ref_type.align_reference_datatype) == 'align_msidata_ref':
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199
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200 align_peak_reference = loadRData('$method.methods_conditional.align_ref_type.align_peaks_msidata')
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201
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202 #end if
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203
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204 #if str( $method.methods_conditional.methods_for_alignment.alignment_method) == 'diff':
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205 print('diff peakalignment')
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206
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207 msidata = peakAlign(msidata, method='$method.methods_conditional.methods_for_alignment.alignment_method',diff.max =$method.methods_conditional.methods_for_alignment.value_diffalignment, units = "$method.methods_conditional.methods_for_alignment.units_diffalignment", ref=align_peak_reference)
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208
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209 #elif str( $method.methods_conditional.methods_for_alignment.alignment_method) == 'DP':
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210 print('DPpeakalignment')
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211
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212 msidata = peakAlign(msidata, method='$method.methods_conditional.methods_for_alignment.alignment_method',gap = $method.methods_conditional.methods_for_alignment.gap_DPalignment, ref=align_peak_reference)
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213
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214 #end if
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215
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216 ############################### QC ###########################
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217
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218 maxfeatures = length(features(msidata))
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219 medianpeaks = median(colSums(spectra(msidata)[]>0, na.rm=TRUE))
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220 medint = round(median(spectra(msidata)[], na.rm=TRUE), digits=2)
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221 TICs = round(mean(colSums(spectra(msidata)[], na.rm=TRUE)), digits=1)
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222 aligned= c(maxfeatures, medianpeaks, medint, TICs)
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223 QC_numbers= cbind(QC_numbers, aligned)
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224 vectorofactions = append(vectorofactions, "aligned")
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225
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226 ############################### Peak filtering ###########################
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227
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228 #elif str( $method.methods_conditional.preprocessing_method) == 'Peak_filtering':
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229 print('Peak_filtering')
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230
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231 msidata = peakFilter(msidata, method='freq', freq.min = $method.methods_conditional.frequ_filtering)
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232
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233 ############################### QC ###########################
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234
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235 maxfeatures = length(features(msidata))
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236 medianpeaks = median(colSums(spectra(msidata)[]>0, na.rm=TRUE))
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237 medint = round(median(spectra(msidata)[], na.rm=TRUE), digits=2)
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238 TICs = round(mean(colSums(spectra(msidata)[], na.rm=TRUE)), digits=1)
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239 filtered= c(maxfeatures, medianpeaks, medint, TICs)
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240 QC_numbers= cbind(QC_numbers, filtered)
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241 vectorofactions = append(vectorofactions, "filtered")
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242
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243 ############################### Data reduction ###########################
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244
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245 #elif str( $method.methods_conditional.preprocessing_method) == 'Data_reduction':
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246 print('Data_reduction')
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247
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248 #if str( $method.methods_conditional.methods_for_reduction.reduction_method) == 'bin':
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249 print('bin reduction')
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250
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251 msidata = reduceDimension(msidata, method="bin", width=$method.methods_conditional.methods_for_reduction.bin_width, units="$method.methods_conditional.methods_for_reduction.bin_units", fun=$method.methods_conditional.methods_for_reduction.bin_fun)
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252
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253 #elif str( $method.methods_conditional.methods_for_reduction.reduction_method) == 'resample':
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254 print('resample reduction')
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255
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256 msidata = reduceDimension(msidata, method="resample", step=$method.methods_conditional.methods_for_reduction.resample_step)
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257
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258 #elif str( $method.methods_conditional.methods_for_reduction.reduction_method) == 'peaks':
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259 print('peaks reduction')
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260
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261 #if str( $method.methods_conditional.methods_for_reduction.ref_type.reference_datatype) == 'table':
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262
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263 reference_table = read.delim("$method.methods_conditional.methods_for_reduction.ref_type.peaks_table", header = FALSE, stringsAsFactors = FALSE)
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264 reference_column = reference_table[,$method.methods_conditional.methods_for_reduction.ref_type.mass_column]
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265 peak_reference = reference_column[reference_column>min(mz(msidata)) & reference_column<max(mz(msidata))]
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266
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267 #elif str( $method.methods_conditional.methods_for_reduction.ref_type.reference_datatype) == 'msidata_ref':
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268
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269 peak_reference = loadRData('$method.methods_conditional.methods_for_reduction.ref_type.peaks_msidata')
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270
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271 #end if
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272
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273 msidata = reduceDimension(msidata, method="peaks", ref=peak_reference, type="$method.methods_conditional.methods_for_reduction.peaks_type")
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274 #end if
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275 ############################### QC ###########################
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276
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277 maxfeatures = length(features(msidata))
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278 medianpeaks = median(colSums(spectra(msidata)[]>0, na.rm=TRUE))
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279 medint = round(median(spectra(msidata)[], na.rm=TRUE), digits=2)
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280 TICs = round(mean(colSums(spectra(msidata)[], na.rm=TRUE)), digits=1)
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281 reduced= c(maxfeatures, medianpeaks, medint, TICs)
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282 QC_numbers= cbind(QC_numbers, reduced)
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283 vectorofactions = append(vectorofactions, "reduced")
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284
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285 ############################### Transformation ###########################
0
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286
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287 #elif str( $method.methods_conditional.preprocessing_method) == 'Transformation':
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288 print('Transformation')
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289
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290 #if str( $method.methods_conditional.transf_conditional.trans_type) == 'log2':
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291 print('log2 transformation')
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292
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293 spectra(msidata)[][spectra(msidata)[] ==0] = NA
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294 print(paste0("Number of 0 which were converted into NA:",sum(is.na(spectra(msidata)[]))))
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295 spectra(msidata)[] = log2(spectra(msidata)[])
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296
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297 #elif str( $method.methods_conditional.transf_conditional.trans_type) == 'sqrt':
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298 print('squareroot transformation')
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299
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300 spectra(msidata)[] = sqrt(spectra(msidata)[])
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301
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302 #end if
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303
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304 ############################### QC ###########################
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305
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306 maxfeatures = length(features(msidata))
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307 medianpeaks = median(colSums(spectra(msidata)[]>0, na.rm=TRUE))
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308 medint = round(median(spectra(msidata)[], na.rm=TRUE), digits=2)
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309 TICs = round(mean(colSums(spectra(msidata)[], na.rm=TRUE)), digits=1)
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310 transformed= c(maxfeatures, medianpeaks, medint, TICs)
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311 QC_numbers= cbind(QC_numbers, transformed)
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312 vectorofactions = append(vectorofactions, "transformed")
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313
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314 #end if
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315 #end for
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316
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317 ############# Outputs: summar matrix, RData, tabular and QC report #############
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318 ################################################################################
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319 ## optional summarized matrix
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320 print('Summarized matrix')
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321
7
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322 #if "mean" in str($summary_type).split(","):
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323 print("mean matrix")
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324 if (!is.null(levels(msidata\$combined_sample))){
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325
7
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326 sample_matrix = matrix(,ncol=0, nrow=nrow(msidata))
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327 count = 1
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328 for (subsample in levels(msidata\$combined_sample)){
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329 subsample_pixels = msidata[,msidata\$combined_sample == subsample]
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330 subsample_calc = apply(spectra(subsample_pixels)[],1,mean, na.rm=TRUE)
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331 sample_matrix = cbind(sample_matrix, subsample_calc)
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332 count = count+1
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333 }
1a3d477bc54a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
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334 rownames(sample_matrix) = mz(msidata)
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335 colnames(sample_matrix) = levels(msidata\$combined_sample)
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336 write.table(sample_matrix, file="$summarized_output_mean", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t")
1a3d477bc54a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
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diff changeset
337 }else{
1a3d477bc54a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
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338 full_sample_calc = as.data.frame(apply(spectra(msidata)[],1,mean, na.rm=TRUE))
1a3d477bc54a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
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339 rownames(full_sample_calc) = mz(msidata)
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340 colnames(full_sample_calc) = "$infile.display_name"
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341 write.table(full_sample_calc, file="$summarized_output_mean", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t")
5
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342 }
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343
7
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344 #end if
5
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345
7
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346 #if "median" in str($summary_type).split(","):
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347 print("median matrix")
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348 if (!is.null(levels(msidata\$combined_sample))){
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349 sample_matrix = matrix(,ncol=0, nrow=nrow(msidata))
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350 count = 1
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351 for (subsample in levels(msidata\$combined_sample)){
1a3d477bc54a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
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352 subsample_pixels = msidata[,msidata\$combined_sample == subsample]
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353 subsample_calc = apply(spectra(subsample_pixels)[],1,median, na.rm=TRUE)
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354 sample_matrix = cbind(sample_matrix, subsample_calc)
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355 count = count+1
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356 }
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357
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358 rownames(sample_matrix) = mz(msidata)
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359 colnames(sample_matrix) = levels(msidata\$combined_sample)
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360 write.table(sample_matrix, file="$summarized_output_median", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t")
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diff changeset
361 }else{
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362 full_sample_calc = as.data.frame(apply(spectra(msidata)[],1,median, na.rm=TRUE))
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363 rownames(full_sample_calc) = mz(msidata)
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364 colnames(full_sample_calc) = "$infile.display_name"
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365 write.table(full_sample_calc, file="$summarized_output_median", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t")
5
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366 }
7
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367 #end if
5
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368
7
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369 #if "sd" in str($summary_type).split(","):
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370 print("sd matrix")
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371 if (!is.null(levels(msidata\$combined_sample))){
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372 sample_matrix = matrix(,ncol=0, nrow=nrow(msidata))
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373 count = 1
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374 for (subsample in levels(msidata\$combined_sample)){
1a3d477bc54a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
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375 subsample_pixels = msidata[,msidata\$combined_sample == subsample]
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376 subsample_calc = apply(spectra(subsample_pixels)[],1,sd, na.rm=TRUE)
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377 sample_matrix = cbind(sample_matrix, subsample_calc)
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diff changeset
378 count = count+1
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379 }
2
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380
7
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381 rownames(sample_matrix) = mz(msidata)
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382 colnames(sample_matrix) = levels(msidata\$combined_sample)
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383 write.table(sample_matrix, file="$summarized_output_sd", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t")
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diff changeset
384 }else{
2
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385
7
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386 full_sample_calc = as.data.frame(apply(spectra(msidata)[],1,sd, na.rm=TRUE))
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387 rownames(full_sample_calc) = mz(msidata)
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diff changeset
388 colnames(full_sample_calc) = "$infile.display_name"
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389 write.table(full_sample_calc, file="$summarized_output_sd", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t")
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390 }
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diff changeset
391 #end if
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392 print(paste0("Number of NA in output file: ",sum(is.na(spectra(msidata)[]))))
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393
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394 ## save as (.RData)
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395 save(msidata, file="$msidata_preprocessed")
2
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396
7
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397 ## save output matrix
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398 #if $output_matrix:
2
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399
7
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diff changeset
400 if (length(features(msidata))> 0 & length(pixels(msidata)) > 0){
1a3d477bc54a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
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diff changeset
401 spectramatrix = spectra(msidata)[]
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diff changeset
402 spectramatrix = cbind(mz(msidata),spectramatrix)
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diff changeset
403 newmatrix = rbind(c("mz | spectra", names(pixels(msidata))), spectramatrix)
1a3d477bc54a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
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404 write.table(newmatrix, file="$matrixasoutput", quote = FALSE, row.names = FALSE, col.names=FALSE, sep = "\t")
4
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diff changeset
405 }else{
7
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406 print("file has no features or pixels left")
4
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diff changeset
407 }
7
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diff changeset
408 #end if
2
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409
7
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410 ## save QC report
2
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411
5
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diff changeset
412 pdf("Preprocessing.pdf", fonts = "Times", pointsize = 12)
2fccfd11360d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 4
diff changeset
413 plot(0,type='n',axes=FALSE,ann=FALSE)
2fccfd11360d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 4
diff changeset
414 title(main=paste("Quality control during preprocessing \n", "Filename:", "$infile.display_name"))
2
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
415 rownames(QC_numbers) = c("# features", "median # peaks", "median intensity", "median TIC")
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
416 grid.table(t(QC_numbers))
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
417 dev.off()
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
418
7
1a3d477bc54a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 6
diff changeset
419 }else{
1a3d477bc54a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 6
diff changeset
420 print("inputfile has no intensities > 0")
1a3d477bc54a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 6
diff changeset
421 }
1a3d477bc54a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 6
diff changeset
422
0
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
423 ]]></configfile>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
424 </configfiles>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
425 <inputs>
7
1a3d477bc54a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 6
diff changeset
426 <param name="infile" type="data" format="imzml,rdata,analyze75"
5
2fccfd11360d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 4
diff changeset
427 label="MSI data as imzml, analyze7.5 or Cardinal MSImageSet saved as RData"
1
c4abf42419c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 0
diff changeset
428 help="load imzml and ibd file by uploading composite datatype imzml"/>
6
d3fd539f477e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 5
diff changeset
429 <conditional name="processed_cond">
d3fd539f477e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 5
diff changeset
430 <param name="processed_file" type="select" label="Is the input file a processed imzML file ">
d3fd539f477e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 5
diff changeset
431 <option value="no_processed" selected="True">not a processed imzML</option>
d3fd539f477e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 5
diff changeset
432 <option value="processed">processed imzML</option>
d3fd539f477e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 5
diff changeset
433 </param>
d3fd539f477e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 5
diff changeset
434 <when value="no_processed"/>
d3fd539f477e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 5
diff changeset
435 <when value="processed">
d3fd539f477e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 5
diff changeset
436 <param name="accuracy" type="float" value="50" label="Mass accuracy to which the m/z values will be binned" help="This should be set to the native accuracy of the mass spectrometer, if known"/>
d3fd539f477e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 5
diff changeset
437 <param name="units" display="radio" type="select" label="Unit of the mass accuracy" help="either m/z or ppm">
d3fd539f477e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 5
diff changeset
438 <option value="mz" >mz</option>
d3fd539f477e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 5
diff changeset
439 <option value="ppm" selected="True" >ppm</option>
d3fd539f477e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 5
diff changeset
440 </param>
d3fd539f477e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 5
diff changeset
441 </when>
d3fd539f477e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 5
diff changeset
442 </conditional>
0
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
443 <repeat name="methods" title="Preprocessing" min="1" max="50">
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
444 <conditional name="methods_conditional">
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
445 <param name="preprocessing_method" type="select" label="Select the preprocessing methods you want to apply">
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
446 <option value="Normalization" selected="True">Normalization to TIC</option>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
447 <option value="Baseline_reduction">Baseline Reduction</option>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
448 <option value="Smoothing">Peak smoothing</option>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
449 <option value="Peak_picking">Peak picking</option>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
450 <option value="Peak_alignment">Peak alignment</option>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
451 <option value="Peak_filtering">Peak filtering</option>
2
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
452 <option value="Data_reduction">Data reduction</option>
5
2fccfd11360d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 4
diff changeset
453 <option value="Transformation">Transformation</option>
0
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
454 </param>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
455 <when value="Normalization"/>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
456 <when value="Baseline_reduction">
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
457 <param name="blocks_baseline" type="integer" value="50"
2
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
458 label="Blocks"/>
0
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
459 </when>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
460 <when value="Smoothing">
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
461 <conditional name="methods_for_smoothing">
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
462 <param name="smoothing_method" type="select" label="Smoothing method">
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
463 <option value="gaussian" selected="True">gaussian</option>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
464 <option value="sgolay">Savitsky-Golay</option>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
465 <option value="ma">moving average</option>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
466 </param>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
467 <when value="gaussian">
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
468 <param name="sd_gaussian" type="float" value="4"
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
469 label="The standard deviation for the Gaussian kernel (window/sd)"/>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
470 </when>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
471 <when value="sgolay">
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
472 <param name="order_of_filters" type="integer" value="3"
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
473 label="The order of the smoothing filter"/>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
474 </when>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
475 <when value="ma">
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
476 <param name="coefficients_ma_filter" type="integer" value="1"
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
477 label="The coefficients for the moving average filter"/>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
478 </when>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
479 </conditional>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
480 <param name="window_smoothing" type="integer" value="9"
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
481 label="Window size"/>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
482 </when>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
483 <when value="Peak_picking">
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
484 <param name="SNR_picking_method" type="integer" value="3"
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
485 label="Signal to noise ratio"
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
486 help="The minimal signal to noise ratio for peaks to be considered as a valid peak."/>
2
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
487 <param name="blocks_picking" type="integer" value="100" label = "Number of blocks"
0
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
488 help="Number of blocks in which to divide mass spectrum to calculate noise"/>
2
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
489 <param name="window_picking" type="integer" value="5" label= "Window size" help="Window width for seeking local maxima"/>
0
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
490 <conditional name="methods_for_picking">
2
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
491 <param name="picking_method" type="select" label="Peak picking method" help="only simple works for processed imzML files">
0
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
492 <option value="adaptive" selected="True">adaptive</option>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
493 <option value="limpic">limpic</option>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
494 <option value="simple">simple</option>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
495 </param>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
496 <when value="adaptive">
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
497 <param name="spar_picking" type="float" value="1.0"
2
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
498 label="Spar value"
0
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
499 help = "Smoothing parameter for the spline smoothing
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
500 applied to the spectrum in order to decide the cutoffs
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
501 for throwing away false noise spikes that might occur inside peaks"/>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
502 </when>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
503 <when value="limpic">
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
504 <param name="tresh_picking" type="float" value="0.75"
2
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
505 label="thresh value" help="The thresholding quantile to use when comparing slopes in order to throw away peaks that are too flat"/>
0
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
506 </when>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
507 <when value="simple"/>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
508 </conditional>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
509 </when>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
510 <when value="Peak_alignment">
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
511 <conditional name="methods_for_alignment">
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
512 <param name="alignment_method" type="select" label="Alignment method">
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
513 <option value="diff" selected="True">diff</option>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
514 <option value="DP">DP</option>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
515 </param>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
516 <when value="diff">
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
517 <param name="value_diffalignment" type="integer" value="200"
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
518 label="diff.max" help="Peaks that differ less than this value will be aligned together"/>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
519 <param name="units_diffalignment" type="select" display = "radio" optional = "False"
4
42580292d381 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 3
diff changeset
520 label="units">
0
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
521 <option value="ppm" selected="True">ppm</option>
6
d3fd539f477e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 5
diff changeset
522 <option value="Da">m/z</option>
0
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
523 </param>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
524 </when>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
525 <when value="DP">
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
526 <param name="gap_DPalignment" type="integer" value="0"
2
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
527 label="Gap" help="The gap penalty for the dynamic programming sequence alignment"/>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
528 </when>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
529 </conditional>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
530 <conditional name="align_ref_type">
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
531 <param name="align_reference_datatype" type="select" label="Choose reference">
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
532 <option value="align_noref" selected="True">no reference</option>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
533 <option value="align_table" >tabular file as reference</option>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
534 <option value="align_msidata_ref">msidata file as reference</option>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
535 </param>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
536 <when value="align_noref"/>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
537 <when value="align_table">
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
538 <param name="align_peaks_table" type="data" format="tabular"
4
42580292d381 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 3
diff changeset
539 label="Reference m/z values to use for alignment - only these will be kept" help="One column with m/z values (without empty cells or letters)"/>
42580292d381 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 3
diff changeset
540 <param name="align_mass_column" data_ref="align_peaks_table" label="Column with reference m/z" type="data_column"/>
2
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
541 </when>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
542 <when value="align_msidata_ref">
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
543 <param name="align_peaks_msidata" type="data" format="rdata," label="Picked and aligned Cardinal MSImageSet saved as RData"/>
0
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
544 </when>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
545 </conditional>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
546 </when>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
547 <when value="Peak_filtering">
2
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
548 <param name="frequ_filtering" type="integer" value="1000"
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
549 label="Freq.min" help="Peaks that occur in the dataset fewer times than this will be removed. Number should be between 1 (no filtering) and number of spectra (pixel)"/>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
550 </when>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
551 <when value="Data_reduction">
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
552 <conditional name="methods_for_reduction">
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
553 <param name="reduction_method" type="select" label="Reduction method">
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
554 <option value="bin" selected="True">bin</option>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
555 <option value="resample">resample</option>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
556 <option value="peaks">peaks</option>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
557 </param>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
558 <when value="bin">
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
559 <param name="bin_width" type="float" value="1"
4
42580292d381 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 3
diff changeset
560 label="The width of a bin in m/z or ppm" help="Width must be greater than range of m/z values divided by number of m/z features"/>
2
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
561 <param name="bin_units" type="select" display="radio"
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
562 label="Unit for bin">
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
563 <option value="mz" selected="True">mz</option>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
564 <option value="ppm">ppm</option>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
565 </param>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
566 <param name="bin_fun" type="select" display="radio"
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
567 label="Calculate sum or mean intensity for ions of the same bin">
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
568 <option value="mean" selected="True">mean</option>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
569 <option value="sum">sum</option>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
570 </param>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
571 </when>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
572 <when value="resample">
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
573 <param name="resample_step" type="float" value="1"
4
42580292d381 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 3
diff changeset
574 label="The step size in m/z" help="Step size must be greater than range of m/z values divided by number of m/z features"/>
2
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
575 </when>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
576 <when value="peaks">
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
577 <param name="peaks_type" type="select" display="radio"
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
578 label="Should the peak height or area under the curve be taken as the intensity value?">
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
579 <option value="height" selected="True">height</option>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
580 <option value="area">area</option>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
581 </param>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
582 <conditional name="ref_type">
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
583 <param name="reference_datatype" type="select" label="Choose reference datatype">
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
584 <option value="table" selected="True">tabular file</option>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
585 <option value="msidata_ref">msidata file</option>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
586 </param>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
587 <when value="table">
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
588 <param name="peaks_table" type="data" format="tabular"
4
42580292d381 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 3
diff changeset
589 label="Reference m/z values to use to reduce the dimension" help="One column with m/z values (without empty cells or letters, m/z outside m/z range are not used for filtering)"/>
42580292d381 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 3
diff changeset
590 <param name="mass_column" data_ref="peaks_table" label="Column with reference m/z" type="data_column"/>
2
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
591 </when>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
592 <when value="msidata_ref">
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
593 <param name="peaks_msidata" type="data" format="rdata," label="Picked and aligned Cardinal MSImageSet saved as RData"/>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
594 </when>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
595 </conditional>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
596 </when>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
597 </conditional>
0
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
598 </when>
5
2fccfd11360d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 4
diff changeset
599 <when value="Transformation">
3
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
600 <conditional name="transf_conditional">
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
601 <param name="trans_type" type="select" label="Choose which intensity transformation you want to apply" help="logarithm base 2 (log2) or squareroot (sqrt)">
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
602 <option value="log2" selected="True">log2</option>
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
603 <option value="sqrt">sqrt</option>
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
604 </param>
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
605 <when value="log2"/>
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
606 <when value="sqrt"/>
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
607 </conditional>
5
2fccfd11360d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 4
diff changeset
608 </when>
0
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
609 </conditional>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
610 </repeat>
5
2fccfd11360d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 4
diff changeset
611 <param name="summary_type" type="select" display="checkboxes" multiple="true" label="Summarize all pixels of a sample and calculate the mean, median or standard deviation">
2fccfd11360d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 4
diff changeset
612 <option value="mean">mean</option>
2fccfd11360d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 4
diff changeset
613 <option value="median">median</option>
2fccfd11360d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 4
diff changeset
614 <option value="sd">standard deviation</option>
2fccfd11360d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 4
diff changeset
615 </param>
2fccfd11360d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 4
diff changeset
616 <param name="output_matrix" type="boolean" label="Intensity matrix output"/>
0
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
617 </inputs>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
618 <outputs>
4
42580292d381 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 3
diff changeset
619 <data format="rdata" name="msidata_preprocessed" label="$infile.display_name preprocessed"/>
7
1a3d477bc54a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 6
diff changeset
620 <data format="pdf" name="QC_overview" from_work_dir="Preprocessing.pdf" label = "$infile.display_name preprocessed_QC"/>
5
2fccfd11360d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 4
diff changeset
621 <data format="tabular" name="summarized_output_mean" label="$infile.display_name mean_matrix">
2fccfd11360d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 4
diff changeset
622 <filter>summary_type and "mean" in summary_type</filter>
2fccfd11360d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 4
diff changeset
623 </data>
2fccfd11360d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 4
diff changeset
624 <data format="tabular" name="summarized_output_median" label="$infile.display_name median_matrix">
2fccfd11360d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 4
diff changeset
625 <filter>summary_type and "median" in summary_type</filter>
2fccfd11360d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 4
diff changeset
626 </data>
2fccfd11360d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 4
diff changeset
627 <data format="tabular" name="summarized_output_sd" label="$infile.display_name sd_matrix">
2fccfd11360d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 4
diff changeset
628 <filter>summary_type and "sd" in summary_type</filter>
2
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
629 </data>
4
42580292d381 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 3
diff changeset
630 <data format="tabular" name="matrixasoutput" label="$infile.display_name preprocessed_matrix">
2
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
631 <filter>output_matrix</filter>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
632 </data>
0
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
633 </outputs>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
634 <tests>
5
2fccfd11360d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 4
diff changeset
635 <test expect_num_outputs="3">
0
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
636 <param name="infile" value="" ftype="imzml">
1
c4abf42419c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 0
diff changeset
637 <composite_data value="Example_Continuous.imzML"/>
c4abf42419c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 0
diff changeset
638 <composite_data value="Example_Continuous.ibd"/>
0
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
639 </param>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
640 <repeat name="methods">
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
641 <conditional name="methods_conditional">
3
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
642 <param name="preprocessing_method" value="Normalization"/>
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
643 </conditional>
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
644 </repeat>
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
645 <repeat name="methods">
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
646 <conditional name="methods_conditional">
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
647 <param name="preprocessing_method" value="Smoothing"/>
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
648 <conditional name="methods_for_smoothing">
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
649 <param name="smoothing_method" value="gaussian"/>
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
650 </conditional>
0
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
651 </conditional>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
652 </repeat>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
653 <repeat name="methods">
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
654 <conditional name="methods_conditional">
3
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
655 <param name="preprocessing_method" value="Peak_picking"/>
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
656 <conditional name="methods_for_picking">
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
657 <param name="picking_method" value="adaptive"/>
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
658 </conditional>
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
659 <param name="blocks_picking" value="3"/>
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
660 <param name="window_picking" value="3"/>
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
661 </conditional>
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
662 </repeat>
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
663 <repeat name="methods">
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
664 <conditional name="methods_conditional">
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
665 <param name="preprocessing_method" value="Peak_alignment"/>
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
666 <conditional name="methods_for_alignment">
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
667 <param name="alignment_method" value="diff"/>
0
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
668 </conditional>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
669 </conditional>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
670 </repeat>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
671 <repeat name="methods">
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
672 <conditional name="methods_conditional">
3
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
673 <param name="preprocessing_method" value="Peak_filtering"/>
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
674 <param name="frequ_filtering" value="2"/>
0
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
675 </conditional>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
676 </repeat>
5
2fccfd11360d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 4
diff changeset
677 <repeat name="methods">
0
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
678 <conditional name="methods_conditional">
3
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
679 <param name="preprocessing_method" value="Transformation"/>
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
680 <conditional name="transf_conditional">
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
681 <param name="trans_type" value="sqrt"/>
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
682 </conditional>
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
683 </conditional>
5
2fccfd11360d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 4
diff changeset
684 </repeat>
3
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
685 <param name="output_matrix" value="True"/>
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
686 <output name="msidata_preprocessed" file="preprocessing_results1.RData" compare="sim_size"/>
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
687 <output name="matrixasoutput" file="preprocessing_results1.txt"/>
7
1a3d477bc54a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 6
diff changeset
688 <output name="QC_overview" file="preprocessing_results1.pdf" compare="sim_size"/>
3
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
689 </test>
5
2fccfd11360d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 4
diff changeset
690 <test expect_num_outputs="4">
2fccfd11360d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 4
diff changeset
691 <param name="infile" value="123_combined.RData" ftype="rdata"/>
3
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
692 <repeat name="methods">
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
693 <conditional name="methods_conditional">
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
694 <param name="preprocessing_method" value="Peak_picking"/>
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
695 <param name="blocks_picking" value="3"/>
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
696 <param name="window_picking" value="5"/>
4
42580292d381 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 3
diff changeset
697 <param name="SNR_picking_method" value="2"/>
3
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
698 <conditional name="methods_for_picking">
4
42580292d381 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 3
diff changeset
699 <param name="picking_method" value="adaptive"/>
0
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
700 </conditional>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
701 </conditional>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
702 </repeat>
2
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
703 <repeat name="methods">
0
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
704 <conditional name="methods_conditional">
3
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
705 <param name="preprocessing_method" value="Peak_alignment"/>
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
706 <conditional name="methods_for_alignment">
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
707 <param name="alignment_method" value="DP"/>
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
708 </conditional>
0
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
709 </conditional>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
710 </repeat>
5
2fccfd11360d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 4
diff changeset
711 <param name="summary_type" value="median,sd"/>
3
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
712 <output name="msidata_preprocessed" file="preprocessing_results2.RData" compare="sim_size"/>
5
2fccfd11360d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 4
diff changeset
713 <output name="summarized_output_median" file="preprocessing_median2.txt" lines_diff="2"/>
2fccfd11360d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 4
diff changeset
714 <output name="summarized_output_sd" file="preprocessing_sd2.txt" lines_diff="2"/>
7
1a3d477bc54a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 6
diff changeset
715 <output name="QC_overview" file="preprocessing_results2.pdf" compare="sim_size"/>
0
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
716 </test>
5
2fccfd11360d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 4
diff changeset
717 <test expect_num_outputs="3">
0
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
718 <param name="infile" value="" ftype="analyze75">
1
c4abf42419c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 0
diff changeset
719 <composite_data value="Analyze75.hdr"/>
c4abf42419c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 0
diff changeset
720 <composite_data value="Analyze75.img"/>
c4abf42419c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 0
diff changeset
721 <composite_data value="Analyze75.t2m"/>
0
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
722 </param>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
723 <repeat name="methods">
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
724 <conditional name="methods_conditional">
3
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
725 <param name="preprocessing_method" value="Normalization"/>
0
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
726 </conditional>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
727 </repeat>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
728 <repeat name="methods">
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
729 <conditional name="methods_conditional">
3
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
730 <param name="preprocessing_method" value="Peak_picking"/>
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
731 <param name="blocks_picking" value="100"/>
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
732 <param name="window_picking" value="5"/>
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
733 <param name="picking_method" value="limpic"/>
0
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
734 </conditional>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
735 </repeat>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
736 <repeat name="methods">
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
737 <conditional name="methods_conditional">
3
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
738 <param name="preprocessing_method" value="Peak_alignment"/>
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
739 <conditional name="methods_for_alignment">
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
740 <param name="alignment_method" value="diff"/>
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
741 </conditional>
0
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
742 </conditional>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
743 </repeat>
5
2fccfd11360d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 4
diff changeset
744 <param name="summary_type" value="mean"/>
3
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
745 <output name="msidata_preprocessed" file="preprocessing_results3.RData" compare="sim_size"/>
7
1a3d477bc54a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 6
diff changeset
746 <output name="QC_overview" file="preprocessing_results3.pdf" compare="sim_size"/>
5
2fccfd11360d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 4
diff changeset
747 <output name="summarized_output_mean" file="preprocessing_mean3.txt" lines_diff="2"/>
0
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
748 </test>
5
2fccfd11360d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 4
diff changeset
749 <test expect_num_outputs="3">
2
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
750 <param name="infile" value="" ftype="analyze75">
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
751 <composite_data value="Analyze75.hdr"/>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
752 <composite_data value="Analyze75.img"/>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
753 <composite_data value="Analyze75.t2m"/>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
754 </param>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
755 <repeat name="methods">
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
756 <conditional name="methods_conditional">
3
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
757 <param name="preprocessing_method" value="Normalization"/>
2
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
758 </conditional>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
759 </repeat>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
760 <repeat name="methods">
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
761 <conditional name="methods_conditional">
3
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
762 <param name="preprocessing_method" value="Data_reduction"/>
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
763 <param name="bin_width" value="0.1"/>
2
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
764 </conditional>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
765 </repeat>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
766 <param name="output_matrix" value="True"/>
3
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
767 <output name="msidata_preprocessed" file="preprocessing_results4.RData" compare="sim_size"/>
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
768 <output name="matrixasoutput" file="preprocessing_results4.txt"/>
7
1a3d477bc54a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 6
diff changeset
769 <output name="QC_overview" file="preprocessing_results4.pdf" compare="sim_size"/>
2
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
770 </test>
5
2fccfd11360d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 4
diff changeset
771 <test expect_num_outputs="2">
2
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
772 <param name="infile" value="" ftype="imzml">
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
773 <composite_data value="Example_Continuous.imzML"/>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
774 <composite_data value="Example_Continuous.ibd"/>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
775 </param>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
776 <repeat name="methods">
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
777 <conditional name="methods_conditional">
3
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
778 <param name="preprocessing_method" value="Data_reduction"/>
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
779 <conditional name="methods_for_reduction">
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
780 <param name="reduction_method" value="resample"/>
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
781 <param name="step_width" value="0.1"/>
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
782 </conditional>
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
783 </conditional>
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
784 </repeat>
5
2fccfd11360d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 4
diff changeset
785 <output name="msidata_preprocessed" file="preprocessing_results5.RData" compare="sim_size"/>
7
1a3d477bc54a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 6
diff changeset
786 <output name="QC_overview" file="preprocessing_results5.pdf" compare="sim_size"/>
2
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
787 </test>
0
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
788 </tests>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
789 <help>
1
c4abf42419c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 0
diff changeset
790 <![CDATA[
3
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
791
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
792 Cardinal is an R package that implements statistical & computational tools for analyzing mass spectrometry imaging datasets. `More information on Cardinal <http://cardinalmsi.org//>`_
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
793
4
42580292d381 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 3
diff changeset
794 This tool provides provides multiple Cardinal functions to preprocess mass spectrometry imaging data.
3
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
795
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
796 Input data: 3 types of input data can be used:
0
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
797
3
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
798 - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/wp/imzml/>`_
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
799 - Analyze7.5 (upload hdr, img and t2m file via the "composite" function)
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
800 - Cardinal "MSImageSet" data (with variable name "msidata", saved as .RData)
0
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
801
3
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
802 Options:
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
803
0
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
804 - Normalization: Normalization of intensities to total ion current (TIC)
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
805 - Baseline reduction: Baseline reduction removes backgroundintensity generated by chemical noise (common in MALDI datasets)
4
42580292d381 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 3
diff changeset
806 - Smoothening: Smoothing of the peaks reduces noise and improves peak detection
3
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
807 - Peak picking: relevant peaks are picked while noise-peaks are removed (needs peak alignment afterwards)
4
42580292d381 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 3
diff changeset
808 - Peak alignment: only possible after peak picking, m/z inaccuracies are removed by alignment of same peaks to a common m/z value
3
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
809 - Peak filtering: works only on centroided data (after peak picking and alignment or data reduction with peak filtering), removes peaks that occur only in a small proportion of pixels. If not sure which cutoff to chose run qualitycontrol first and decide according to the zero value plot.
2
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
810 - Data reduction: binning, resampling or peak filtering to reduce data
6
d3fd539f477e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 5
diff changeset
811 - Transformation: log2 or squareroot transformation of all intensities; when using log2 transformation zero intensities will become NA, this can lead to compatibility problems.
4
42580292d381 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 3
diff changeset
812
3
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
813
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
814 Output:
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
815
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
816 - imzML file, preprocessed
5
2fccfd11360d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 4
diff changeset
817 - pdf with key values after each processing step
4
42580292d381 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 3
diff changeset
818 - optional: intensity matrix as tabular file (intensities for m/z in rows and pixel in columns)
3
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
819
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
820 Tip:
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
821
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
822 - Peak alignment works only after peak picking
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
823 - Peak filtering works only on centroided data (peak picking and alignment or Data reduction peaks)
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
824
0
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
825 ]]>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
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826 </help>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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827 <citations>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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828 <citation type="doi">10.1093/bioinformatics/btv146</citation>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
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829 </citations>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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830 </tool>