Mercurial > repos > galaxyp > msi_preprocessing

annotate msi_preprocessing.xml @ 9:4d5578b57a77 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
author galaxyp
date Wed, 22 Aug 2018 13:43:04 -0400
parents d77c5228fd1a
children df8d7f6f210b
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1 <tool id="mass_spectrometry_imaging_preprocessing" name="MSI preprocessing" version="1.10.0.6">
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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 <requirement type="package" version="2.2.1">r-ggplot2</requirement>
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10 </requirements>
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11 <command detect_errors="exit_code">
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12 <![CDATA[
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14 #if $infile.ext == 'imzml'
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15 ln -s '${infile.extra_files_path}/imzml' infile.imzML &&
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16 ln -s '${infile.extra_files_path}/ibd' infile.ibd &&
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17 #elif $infile.ext == 'analyze75'
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18 ln -s '${infile.extra_files_path}/hdr' infile.hdr &&
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19 ln -s '${infile.extra_files_path}/img' infile.img &&
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20 ln -s '${infile.extra_files_path}/t2m' infile.t2m &&
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21 #else
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22 ln -s '$infile' infile.RData &&
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23 #end if
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24 cat '${cardinal_preprocessing}' &&
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25 Rscript '${cardinal_preprocessing}'
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27 ]]>
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28 </command>
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29 <configfiles>
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30 <configfile name="cardinal_preprocessing"><![CDATA[
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32 ################################# load libraries and read file #################
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33
0
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34 library(Cardinal)
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35 library(gridExtra)
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36 library(lattice)
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37 library(ggplot2)
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39 #if $infile.ext == 'imzml'
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40 #if str($processed_cond.processed_file) == "processed":
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41 msidata <- readImzML('infile', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units")
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42 #else
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43 msidata <- readImzML('infile', attach.only=TRUE)
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44 #end if
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45 #elif $infile.ext == 'analyze75'
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46 msidata = readAnalyze('infile', attach.only=TRUE)
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47 #else
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48 loadRData <- function(fileName){
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49 load(fileName)
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50 get(ls()[ls() != "fileName"])
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51 }
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52 msidata = loadRData('infile.RData')
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53 #end if
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54
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55 print(paste0("Number of NA in input file: ",sum(is.na(spectra(msidata)[]))))
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56
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57 ## function to later read RData reference files in
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58
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59 loadRData <- function(fileName){
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60 #loads an RData file, and returns it
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61 load(fileName)
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62 get(ls()[ls() != "fileName"])
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63 }
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64
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65 if (sum(spectra(msidata)[]>0, na.rm=TRUE)> 0){
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66 ######################### preparations for QC report #################
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67
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68 maxfeatures = length(features(msidata))
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69 medianpeaks = median(colSums(spectra(msidata)[]>0, na.rm=TRUE))
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70 medint = round(median(spectra(msidata)[],na.rm=TRUE), digits=2)
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71 minmz = round(min(mz(msidata)), digits=2)
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72 maxmz = round(max(mz(msidata)), digits=2)
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73 QC_numbers= data.frame(inputdata = c(minmz, maxmz,maxfeatures, medianpeaks, medint))
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74 vectorofactions = "inputdata"
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75
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76 ############################### Preprocessing steps ###########################
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77 ###############################################################################
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78
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79 #for $method in $methods:
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80
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81 ############################### Normalization ###########################
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82
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83 #if str( $method.methods_conditional.preprocessing_method ) == 'Normalization':
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84 print('Normalization')
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85 ##normalization
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86
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87 msidata = normalize(msidata, method="tic")
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88
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89 ############################### QC ###########################
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90
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91 maxfeatures = length(features(msidata))
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92 medianpeaks = median(colSums(spectra(msidata)[]>0, na.rm=TRUE),)
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93 medint = round(median(spectra(msidata)[], na.rm=TRUE), digits=2)
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94 minmz = round(min(mz(msidata)), digits=2)
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95 maxmz = round(max(mz(msidata)), digits=2)
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96 normalized = c(minmz, maxmz,maxfeatures, medianpeaks, medint)
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97 QC_numbers= cbind(QC_numbers, normalized)
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98 vectorofactions = append(vectorofactions, "normalized")
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99
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100 ############################### Baseline reduction ###########################
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101
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102 #elif str( $method.methods_conditional.preprocessing_method ) == 'Baseline_reduction':
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103 print('Baseline_reduction')
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104 ##baseline reduction
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105
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106 msidata = reduceBaseline(msidata, method="median", blocks=$method.methods_conditional.blocks_baseline)
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107
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108 ############################### QC ###########################
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109
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110 maxfeatures = length(features(msidata))
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111 medianpeaks = median(colSums(spectra(msidata)[]>0, na.rm=TRUE))
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112 medint = round(median(spectra(msidata)[], na.rm=TRUE), digits=2)
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113 minmz = round(min(mz(msidata)), digits=2)
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114 maxmz = round(max(mz(msidata)), digits=2)
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115 baseline = c(minmz, maxmz,maxfeatures, medianpeaks, medint)
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116 QC_numbers= cbind(QC_numbers, baseline)
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117 vectorofactions = append(vectorofactions, "baseline red.")
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118
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119 ############################### Smoothing ###########################
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120
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121 #elif str( $method.methods_conditional.preprocessing_method ) == 'Smoothing':
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122 print('Smoothing')
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123 ## Smoothing
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124
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125 #if str( $method.methods_conditional.methods_for_smoothing.smoothing_method) == 'gaussian':
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126 print('gaussian smoothing')
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127
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128 msidata = smoothSignal(msidata, method="$method.methods_conditional.methods_for_smoothing.smoothing_method", window=$method.methods_conditional.window_smoothing, sd = $method.methods_conditional.methods_for_smoothing.sd_gaussian)
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129
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130 #elif str( $method.methods_conditional.methods_for_smoothing.smoothing_method) == 'sgolay':
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131 print('sgolay smoothing')
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132
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133 msidata = smoothSignal(msidata, method="$method.methods_conditional.methods_for_smoothing.smoothing_method", window=$method.methods_conditional.window_smoothing, order = $method.methods_conditional.methods_for_smoothing.order_of_filters)
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134 #elif str($method.methods_conditional.methods_for_smoothing.smoothing_method) == 'ma':
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135 print('sgolay smoothing')
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136
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137 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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138
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139 #end if
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140
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141 ############################### QC ###########################
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142
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143 maxfeatures = length(features(msidata))
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144 medianpeaks = median(colSums(spectra(msidata)[]>0, na.rm=TRUE))
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145 medint = round(median(spectra(msidata)[], na.rm=TRUE), digits=2)
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146 minmz = round(min(mz(msidata)), digits=2)
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147 maxmz = round(max(mz(msidata)), digits=2)
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148 smoothed = c(minmz, maxmz,maxfeatures, medianpeaks, medint)
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149 QC_numbers= cbind(QC_numbers, smoothed)
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150 vectorofactions = append(vectorofactions, "smoothed")
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151
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152 ############################### Peak picking ###########################
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153
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154 #elif str( $method.methods_conditional.preprocessing_method) == 'Peak_picking':
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155 print('Peak_picking')
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156 ## Peakpicking
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157
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158 ## remove duplicated coordinates, otherwise peak picking will fail
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159 print(paste0(sum(duplicated(coord(msidata))), " coordinates were removed"))
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160 msidata <- msidata[,!duplicated(coord(msidata))]
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161
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162 #if str( $method.methods_conditional.methods_for_picking.picking_method) == 'adaptive':
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163 print('adaptive peakpicking')
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164
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165 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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166
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167 #elif str( $method.methods_conditional.methods_for_picking.picking_method) == 'limpic':
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168 print('limpic peakpicking')
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169
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170 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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171
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172 #elif str( $method.methods_conditional.methods_for_picking.picking_method) == 'simple':
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173 print('simple peakpicking')
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174
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175 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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176
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177 #end if
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178
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179 ############################### QC ###########################
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180
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181 maxfeatures = length(features(msidata))
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182 medianpeaks = median(colSums(spectra(msidata)[]>0, na.rm=TRUE))
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183 medint = round(median(spectra(msidata)[], na.rm=TRUE), digits=2)
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184 minmz = round(min(mz(msidata)), digits=2)
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185 maxmz = round(max(mz(msidata)), digits=2)
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186 picked = c(minmz, maxmz,maxfeatures, medianpeaks, medint)
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187 QC_numbers= cbind(QC_numbers, picked)
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188 vectorofactions = append(vectorofactions, "picked")
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189
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190 ############################### Peak alignment ###########################
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191
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192 #elif str( $method.methods_conditional.preprocessing_method ) == 'Peak_alignment':
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193 print('Peak_alignment')
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194 ## Peakalignment
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195
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196 #if str( $method.methods_conditional.align_ref_type.align_reference_datatype) == 'align_noref':
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197
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198 align_peak_reference = msidata
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199
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200 #elif str( $method.methods_conditional.align_ref_type.align_reference_datatype) == 'align_table':
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201
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202 align_reference_table = read.delim("$method.methods_conditional.align_ref_type.align_peaks_table", header = FALSE, stringsAsFactors = FALSE)
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203 align_reference_column = align_reference_table[,$method.methods_conditional.align_ref_type.align_mass_column]
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204 align_peak_reference = align_reference_column[align_reference_column>=min(mz(msidata)) & align_reference_column<=max(mz(msidata))]
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205 if (length(align_peak_reference) == 0)
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206 {align_peak_reference = 0}
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207
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208 #elif str( $method.methods_conditional.align_ref_type.align_reference_datatype) == 'align_msidata_ref':
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209
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210 align_peak_reference = loadRData('$method.methods_conditional.align_ref_type.align_peaks_msidata')
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211
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212 #end if
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213
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214 #if str( $method.methods_conditional.methods_for_alignment.alignment_method) == 'diff':
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215 print('diff peakalignment')
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216
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217 msidata = peakAlign(msidata, method='$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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218
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219 #elif str( $method.methods_conditional.methods_for_alignment.alignment_method) == 'DP':
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220 print('DPpeakalignment')
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221
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222 msidata = peakAlign(msidata, method='$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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223
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224 #end if
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225
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226 ############################### QC ###########################
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227
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228 maxfeatures = length(features(msidata))
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229 medianpeaks = median(colSums(spectra(msidata)[]>0, na.rm=TRUE))
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230 medint = round(median(spectra(msidata)[], na.rm=TRUE), digits=2)
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231 minmz = round(min(mz(msidata)), digits=2)
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232 maxmz = round(max(mz(msidata)), digits=2)
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233 aligned = c(minmz, maxmz,maxfeatures, medianpeaks, medint)
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234 QC_numbers= cbind(QC_numbers, aligned)
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235 vectorofactions = append(vectorofactions, "aligned")
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236
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237 ############################### Peak filtering ###########################
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238
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239 #elif str( $method.methods_conditional.preprocessing_method) == 'Peak_filtering':
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240 print('Peak_filtering')
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241
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242 msidata = peakFilter(msidata, method='freq', freq.min = $method.methods_conditional.frequ_filtering)
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243
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244 ############################### QC ###########################
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245
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246 maxfeatures = length(features(msidata))
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247 medianpeaks = median(colSums(spectra(msidata)[]>0, na.rm=TRUE))
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248 medint = round(median(spectra(msidata)[], na.rm=TRUE), digits=2)
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249 minmz = round(min(mz(msidata)), digits=2)
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250 maxmz = round(max(mz(msidata)), digits=2)
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251 filtered = c(minmz, maxmz,maxfeatures, medianpeaks, medint)
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252 QC_numbers= cbind(QC_numbers, filtered)
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253 vectorofactions = append(vectorofactions, "filtered")
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254
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255 ############################### Data reduction ###########################
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256
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257 #elif str( $method.methods_conditional.preprocessing_method) == 'Data_reduction':
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258 print('Data_reduction')
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259
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260 #if str( $method.methods_conditional.methods_for_reduction.reduction_method) == 'bin':
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261 print('bin reduction')
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262
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263 msidata = reduceDimension(msidata, method="bin", width=$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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264
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265 #elif str( $method.methods_conditional.methods_for_reduction.reduction_method) == 'resample':
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266 print('resample reduction')
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267
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268 msidata = reduceDimension(msidata, method="resample", step=$method.methods_conditional.methods_for_reduction.resample_step)
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269
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270 #elif str( $method.methods_conditional.methods_for_reduction.reduction_method) == 'peaks':
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271 print('peaks reduction')
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272
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273 #if str( $method.methods_conditional.methods_for_reduction.ref_type.reference_datatype) == 'table':
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274
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275 reference_table = read.delim("$method.methods_conditional.methods_for_reduction.ref_type.peaks_table", header = FALSE, stringsAsFactors = FALSE)
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276 reference_column = reference_table[,$method.methods_conditional.methods_for_reduction.ref_type.mass_column]
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277 peak_reference = reference_column[reference_column>min(mz(msidata)) & reference_column<max(mz(msidata))]
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278
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279 #elif str( $method.methods_conditional.methods_for_reduction.ref_type.reference_datatype) == 'msidata_ref':
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280
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281 peak_reference = loadRData('$method.methods_conditional.methods_for_reduction.ref_type.peaks_msidata')
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282
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283 #end if
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284
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285 msidata = reduceDimension(msidata, method="peaks", ref=peak_reference, type="$method.methods_conditional.methods_for_reduction.peaks_type")
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286 #end if
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287 ############################### QC ###########################
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288
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289 maxfeatures = length(features(msidata))
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290 medianpeaks = median(colSums(spectra(msidata)[]>0, na.rm=TRUE))
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291 medint = round(median(spectra(msidata)[], na.rm=TRUE), digits=2)
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292 minmz = round(min(mz(msidata)), digits=2)
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293 maxmz = round(max(mz(msidata)), digits=2)
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294 reduced = c(minmz, maxmz,maxfeatures, medianpeaks, medint)
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295 QC_numbers= cbind(QC_numbers, reduced)
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296 vectorofactions = append(vectorofactions, "reduced")
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297
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298 ############################### Transformation ###########################
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299
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300 #elif str( $method.methods_conditional.preprocessing_method) == 'Transformation':
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301 print('Transformation')
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302
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303 #if str( $method.methods_conditional.transf_conditional.trans_type) == 'log2':
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304 print('log2 transformation')
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305
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306 spectra(msidata)[][spectra(msidata)[] ==0] = NA
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307 print(paste0("Number of 0 which were converted into NA:",sum(is.na(spectra(msidata)[]))))
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308 spectra(msidata)[] = log2(spectra(msidata)[])
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309
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310 #elif str( $method.methods_conditional.transf_conditional.trans_type) == 'sqrt':
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311 print('squareroot transformation')
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312
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313 spectra(msidata)[] = sqrt(spectra(msidata)[])
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314
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315 #end if
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316
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317 ############################### QC ###########################
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318
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319 maxfeatures = length(features(msidata))
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320 medianpeaks = median(colSums(spectra(msidata)[]>0, na.rm=TRUE))
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321 medint = round(median(spectra(msidata)[], na.rm=TRUE), digits=2)
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322 minmz = round(min(mz(msidata)), digits=2)
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323 maxmz = round(max(mz(msidata)), digits=2)
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324 transformed = c(minmz, maxmz,maxfeatures, medianpeaks, medint)
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325 QC_numbers= cbind(QC_numbers, transformed)
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326 vectorofactions = append(vectorofactions, "transformed")
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327
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328 #end if
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329 #end for
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330
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331 ############# Outputs: summar matrix, RData, tabular and QC report #############
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332 ################################################################################
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333 ## optional summarized matrix
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334 print('Summarized matrix')
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335
8
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336 ## optional annotation from tabular file to obtain groups over which to apply mean, median or sd (otherwise all pixels are considered to be sample)
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337
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338 #if str($tabular_annotation.load_annotation) == 'yes_annotation':
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339
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340 ## read and extract x,y,annotation information
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341 input_tabular = read.delim("$tabular_annotation.annotation_file", header = $tabular_annotation.tabular_header, stringsAsFactors = FALSE)
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342 annotation_input = input_tabular[,c($tabular_annotation.column_x, $tabular_annotation.column_y, $tabular_annotation.column_names)]
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343 colnames(annotation_input) = c("x", "y", "annotation")
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344
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345 ## merge with coordinate information of msidata
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346 msidata_coordinates = cbind(coord(msidata)[,1:2], c(1:ncol(msidata)))
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347 colnames(msidata_coordinates)[3] = "pixel_index"
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348 merged_annotation = merge(msidata_coordinates, annotation_input, by=c("x", "y"), all.x=TRUE)
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349 merged_annotation[is.na(merged_annotation)] = "NA"
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350 merged_annotation = merged_annotation[order(merged_annotation\$pixel_index),]
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351 msidata\$annotation = as.factor(merged_annotation[,4])
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352
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353 #end if
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354
7
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355 #if "mean" in str($summary_type).split(","):
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356 print("mean matrix")
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357 if (!is.null(levels(msidata\$annotation))){
5
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358
7
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359 sample_matrix = matrix(,ncol=0, nrow=nrow(msidata))
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360 count = 1
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361 for (subsample in levels(msidata\$annotation)){
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362 subsample_pixels = msidata[,msidata\$annotation == subsample]
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363 subsample_calc = apply(spectra(subsample_pixels)[],1,mean, na.rm=TRUE)
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364 sample_matrix = cbind(sample_matrix, subsample_calc)
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365 count = count+1
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366 }
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367 rownames(sample_matrix) = mz(msidata)
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368 colnames(sample_matrix) = levels(msidata\$annotation)
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369 write.table(sample_matrix, file="$summarized_output_mean", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t")
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diff changeset
370 }else{
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371 full_sample_calc = as.data.frame(apply(spectra(msidata)[],1,mean, na.rm=TRUE))
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372 rownames(full_sample_calc) = mz(msidata)
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373 colnames(full_sample_calc) = "$infile.display_name"
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374 write.table(full_sample_calc, file="$summarized_output_mean", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t")
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375 }
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376
7
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377 #end if
5
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378
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379 #if "median" in str($summary_type).split(","):
1a3d477bc54a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
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380 print("median matrix")
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381 if (!is.null(levels(msidata\$annotation))){
7
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382 sample_matrix = matrix(,ncol=0, nrow=nrow(msidata))
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diff changeset
383 count = 1
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diff changeset
384 for (subsample in levels(msidata\$annotation)){
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diff changeset
385
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386 subsample_pixels = msidata[,msidata\$annotation == subsample] ## no idea why it does not work??? NA problem?!
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diff changeset
387
7
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388 subsample_calc = apply(spectra(subsample_pixels)[],1,median, na.rm=TRUE)
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diff changeset
389
7
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diff changeset
390 sample_matrix = cbind(sample_matrix, subsample_calc)
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diff changeset
391 count = count+1
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diff changeset
392 }
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393
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394 rownames(sample_matrix) = mz(msidata)
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diff changeset
395 colnames(sample_matrix) = levels(msidata\$annotation)
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396 write.table(sample_matrix, file="$summarized_output_median", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t")
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diff changeset
397 }else{
1a3d477bc54a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
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398 full_sample_calc = as.data.frame(apply(spectra(msidata)[],1,median, na.rm=TRUE))
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399 rownames(full_sample_calc) = mz(msidata)
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400 colnames(full_sample_calc) = "$infile.display_name"
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401 write.table(full_sample_calc, file="$summarized_output_median", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t")
5
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402 }
7
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diff changeset
403 #end if
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diff changeset
404
7
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405 #if "sd" in str($summary_type).split(","):
1a3d477bc54a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
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406 print("sd matrix")
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407 if (!is.null(levels(msidata\$annotation))){
7
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408 sample_matrix = matrix(,ncol=0, nrow=nrow(msidata))
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diff changeset
409 count = 1
8
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
410 for (subsample in levels(msidata\$annotation)){
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
411 subsample_pixels = msidata[,msidata\$annotation == subsample]
7
1a3d477bc54a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 6
diff changeset
412 subsample_calc = apply(spectra(subsample_pixels)[],1,sd, na.rm=TRUE)
1a3d477bc54a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 6
diff changeset
413 sample_matrix = cbind(sample_matrix, subsample_calc)
1a3d477bc54a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 6
diff changeset
414 count = count+1
1a3d477bc54a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 6
diff changeset
415 }
2
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
416
7
1a3d477bc54a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 6
diff changeset
417 rownames(sample_matrix) = mz(msidata)
8
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
418 colnames(sample_matrix) = levels(msidata\$annotation)
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 write.table(sample_matrix, file="$summarized_output_sd", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t")
1a3d477bc54a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 6
diff changeset
420 }else{
2
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
421
7
1a3d477bc54a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 6
diff changeset
422 full_sample_calc = as.data.frame(apply(spectra(msidata)[],1,sd, na.rm=TRUE))
1a3d477bc54a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 6
diff changeset
423 rownames(full_sample_calc) = mz(msidata)
1a3d477bc54a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 6
diff changeset
424 colnames(full_sample_calc) = "$infile.display_name"
1a3d477bc54a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 6
diff changeset
425 write.table(full_sample_calc, file="$summarized_output_sd", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t")
1a3d477bc54a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 6
diff changeset
426 }
1a3d477bc54a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 6
diff changeset
427 #end if
1a3d477bc54a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 6
diff changeset
428 print(paste0("Number of NA in output file: ",sum(is.na(spectra(msidata)[]))))
1a3d477bc54a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 6
diff changeset
429
1a3d477bc54a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 6
diff changeset
430 ## save as (.RData)
1a3d477bc54a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 6
diff changeset
431 save(msidata, file="$msidata_preprocessed")
2
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
432
7
1a3d477bc54a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 6
diff changeset
433 ## save output matrix
1a3d477bc54a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 6
diff changeset
434 #if $output_matrix:
2
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
435
7
1a3d477bc54a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 6
diff changeset
436 if (length(features(msidata))> 0 & length(pixels(msidata)) > 0){
1a3d477bc54a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 6
diff changeset
437 spectramatrix = spectra(msidata)[]
1a3d477bc54a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 6
diff changeset
438 spectramatrix = cbind(mz(msidata),spectramatrix)
1a3d477bc54a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 6
diff changeset
439 newmatrix = rbind(c("mz | spectra", names(pixels(msidata))), spectramatrix)
1a3d477bc54a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 6
diff changeset
440 write.table(newmatrix, file="$matrixasoutput", quote = FALSE, row.names = FALSE, col.names=FALSE, sep = "\t")
4
42580292d381 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 3
diff changeset
441 }else{
7
1a3d477bc54a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
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diff changeset
442 print("file has no features or pixels left")
4
42580292d381 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 3
diff changeset
443 }
7
1a3d477bc54a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 6
diff changeset
444 #end if
2
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
445
7
1a3d477bc54a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 6
diff changeset
446 ## save QC report
2
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
447
5
2fccfd11360d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 4
diff changeset
448 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
449 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
450 title(main=paste("Quality control during preprocessing \n", "Filename:", "$infile.display_name"))
9
4d5578b57a77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents: 8
diff changeset
451 rownames(QC_numbers) = c("min m/z", "max mz", "# features", "median\n# peaks", "median\nintensity")
2
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
452 grid.table(t(QC_numbers))
8
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
453
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
454 #if str($tabular_annotation.load_annotation) == 'yes_annotation':
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
455
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
456 ## the more annotation groups a file has the smaller will be the legend
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
457 number_combined = length(levels(msidata\$annotation))
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
458 if (number_combined<20){
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
459 legend_size = 10
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
460 }else if (number_combined>20 && number_combined<40){
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
461 legend_size = 9
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
462 }else if (number_combined>40 && number_combined<60){
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
463 legend_size = 8
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
464 }else if (number_combined>60 && number_combined<100){
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
465 legend_size = 7
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
466 }else{
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
467 legend_size = 6
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
468 }
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
469
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
470 position_df = cbind(coord(msidata)[,1:2], msidata\$annotation)
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
471 colnames(position_df)[3] = "sample_name"
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
472
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
473 combine_plot = ggplot(position_df, aes(x=x, y=y, fill=sample_name))+
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
474 geom_tile() +
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
475 coord_fixed()+
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
476 ggtitle("Spatial orientation of annotated data")+
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
477 theme_bw()+
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
478 theme(plot.title = element_text(hjust = 0.5))+
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
479 theme(text=element_text(family="ArialMT", face="bold", size=12))+
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
480 theme(legend.position="bottom",legend.direction="vertical")+
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
481 theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = legend_size))+
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
482 guides(fill=guide_legend(ncol=5,byrow=TRUE))
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
483 coord_labels = aggregate(cbind(x,y)~sample_name, data=position_df, mean)
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
484 coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$sample_name)
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
485 for(file_count in 1:nrow(coord_labels))
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
486 {combine_plot = combine_plot + annotate("text",x=coord_labels[file_count,"x"],
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
487 y=coord_labels[file_count,"y"],label=toString(coord_labels[file_count,4]))}
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
488
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
489 print(combine_plot)
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
490 #end if
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
491
2
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
492 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
493
7
1a3d477bc54a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 6
diff changeset
494 }else{
1a3d477bc54a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 6
diff changeset
495 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
496 }
1a3d477bc54a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 6
diff changeset
497
0
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
498 ]]></configfile>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
499 </configfiles>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
500 <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
501 <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
502 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
503 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
504 <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
505 <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
506 <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
507 <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
508 </param>
d3fd539f477e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 5
diff changeset
509 <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
510 <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
511 <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
512 <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
513 <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
514 <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
515 </param>
d3fd539f477e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 5
diff changeset
516 </when>
d3fd539f477e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 5
diff changeset
517 </conditional>
0
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
518 <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
519 <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
520 <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
521 <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
522 <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
523 <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
524 <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
525 <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
526 <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
527 <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
528 <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
529 </param>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
530 <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
531 <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
532 <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
533 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
534 </when>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
535 <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
536 <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
537 <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
538 <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
539 <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
540 <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
541 </param>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
542 <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
543 <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
544 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
545 </when>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
546 <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
547 <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
548 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
549 </when>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
550 <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
551 <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
552 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
553 </when>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
554 </conditional>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
555 <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
556 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
557 </when>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
558 <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
559 <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
560 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
561 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
562 <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
563 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
564 <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
565 <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
566 <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
567 <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
568 <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
569 <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
570 </param>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
571 <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
572 <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
573 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
574 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
575 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
576 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
577 </when>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
578 <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
579 <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
580 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
581 </when>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
582 <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
583 </conditional>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
584 </when>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
585 <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
586 <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
587 <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
588 <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
589 <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
590 </param>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
591 <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
592 <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
593 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
594 <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
595 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
596 <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
597 <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
598 </param>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
599 </when>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
600 <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
601 <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
602 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
603 </when>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
604 </conditional>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
605 <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
606 <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
607 <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
608 <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
609 <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
610 </param>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
611 <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
612 <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
613 <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
614 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
615 <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
616 </when>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
617 <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
618 <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
619 </when>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
620 </conditional>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
621 </when>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
622 <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
623 <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
624 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
625 </when>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
626 <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
627 <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
628 <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
629 <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
630 <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
631 <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
632 </param>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
633 <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
634 <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
635 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
636 <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
637 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
638 <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
639 <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
640 </param>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
641 <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
642 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
643 <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
644 <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
645 </param>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
646 </when>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
647 <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
648 <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
649 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
650 </when>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
651 <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
652 <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
653 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
654 <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
655 <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
656 </param>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
657 <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
658 <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
659 <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
660 <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
661 </param>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
662 <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
663 <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
664 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
665 <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
666 </when>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
667 <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
668 <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
669 </when>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
670 </conditional>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
671 </when>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
672 </conditional>
0
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
673 </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
674 <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
675 <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
676 <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
677 <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
678 <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
679 </param>
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
680 <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
681 <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
682 </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
683 </when>
0
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
684 </conditional>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
685 </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
686 <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
687 <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
688 <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
689 <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
690 </param>
8
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
691 <conditional name="tabular_annotation">
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
692 <param name="load_annotation" type="select" label="Use pixel annotations from tabular file to summarize pixel">
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
693 <option value="no_annotation" selected="True">summarize over all pixels</option>
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
694 <option value="yes_annotation">summarize over categories from annotation file</option>
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
695 </param>
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
696 <when value="yes_annotation">
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
697 <param name="annotation_file" type="data" format="tabular" label="Use annotations from tabular file to summarize pixel"
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
698 help="Tabular file with three columns: x values, y values and pixel annotations"/>
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
699 <param name="column_x" data_ref="annotation_file" label="Column with x values" type="data_column"/>
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
700 <param name="column_y" data_ref="annotation_file" label="Column with y values" type="data_column"/>
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
701 <param name="column_names" data_ref="annotation_file" label="Column with pixel annotations" type="data_column"/>
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
702 <param name="tabular_header" type="boolean" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/>
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
703 </when>
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
704 <when value="no_annotation"/>
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
705 </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
706 <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
707 </inputs>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
708 <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
709 <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
710 <data format="pdf" name="QC_overview" from_work_dir="Preprocessing.pdf" label = "$infile.display_name preprocessed_QC"/>
5
2fccfd11360d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 4
diff changeset
711 <data format="tabular" name="summarized_output_mean" label="$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
712 <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
713 </data>
2fccfd11360d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 4
diff changeset
714 <data format="tabular" name="summarized_output_median" label="$infile.display_name median_matrix">
2fccfd11360d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 4
diff changeset
715 <filter>summary_type and "median" in summary_type</filter>
2fccfd11360d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 4
diff changeset
716 </data>
2fccfd11360d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 4
diff changeset
717 <data format="tabular" name="summarized_output_sd" label="$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
718 <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
719 </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
720 <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
721 <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
722 </data>
0
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
723 </outputs>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
724 <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
725 <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
726 <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
727 <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
728 <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
729 </param>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
730 <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
731 <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
732 <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
733 </conditional>
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
734 </repeat>
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
735 <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
736 <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
737 <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
738 <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
739 <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
740 </conditional>
0
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
741 </conditional>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
742 </repeat>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
743 <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
744 <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
745 <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
746 <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
747 <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
748 </conditional>
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
749 <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
750 <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
751 </conditional>
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
752 </repeat>
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
753 <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
754 <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
755 <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
756 <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
757 <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
758 </conditional>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
759 </conditional>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
760 </repeat>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
761 <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
762 <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
763 <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
764 <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
765 </conditional>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
766 </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
767 <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
768 <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
769 <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
770 <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
771 <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
772 </conditional>
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
773 </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
774 </repeat>
8
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
775 <conditional name="tabular_annotation">
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
776 <param name="load_annotation" value="no_annotation"/>
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
777 </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="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
779 <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
780 <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
781 <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
782 </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
783 <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
784 <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
785 <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
786 <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
787 <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
788 <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
789 <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
790 <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
791 <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
792 <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
793 </conditional>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
794 </conditional>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
795 </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
796 <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
797 <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
798 <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
799 <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
800 <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
801 </conditional>
0
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
802 </conditional>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
803 </repeat>
8
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
804 <conditional name="tabular_annotation">
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
805 <param name="load_annotation" value="yes_annotation"/>
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
806 <param name="annotation_file" value="pixel_annotations.tabular"/>
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
807 <param name="column_x" value="1"/>
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
808 <param name="column_y" value="2"/>
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
809 <param name="column_names" value="3"/>
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
810 <param name="tabular_header" value="FALSE"/>
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
811 </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
812 <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
813 <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
814 <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
815 <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
816 <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
817 </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
818 <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
819 <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
820 <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
821 <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
822 <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
823 </param>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
824 <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
825 <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
826 <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
827 </conditional>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
828 </repeat>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
829 <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
830 <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
831 <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
832 <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
833 <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
834 <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
835 </conditional>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
836 </repeat>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
837 <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
838 <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
839 <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
840 <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
841 <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
842 </conditional>
0
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
843 </conditional>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
844 </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
845 <param name="summary_type" value="mean"/>
8
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
846 <conditional name="tabular_annotation">
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
847 <param name="load_annotation" value="no_annotation"/>
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
848 </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
849 <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
850 <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
851 <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
852 </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
853 <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
854 <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
855 <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
856 <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
857 <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
858 </param>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
859 <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
860 <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
861 <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
862 </conditional>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
863 </repeat>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
864 <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
865 <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
866 <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
867 <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
868 </conditional>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
869 </repeat>
8
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
870 <conditional name="tabular_annotation">
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
871 <param name="load_annotation" value="no_annotation"/>
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
872 </conditional>
2
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
873 <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
874 <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
875 <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
876 <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
877 </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
878 <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
879 <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
880 <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
881 <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
882 </param>
50ba097d03e0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
883 <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
884 <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
885 <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
886 <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
887 <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
888 <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
889 </conditional>
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
890 </conditional>
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
891 </repeat>
8
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
892 <conditional name="tabular_annotation">
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
893 <param name="load_annotation" value="no_annotation"/>
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
894 </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
895 <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
896 <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
897 </test>
0
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
898 </tests>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
899 <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
900 <![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
901
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
902 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
903
4
42580292d381 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 3
diff changeset
904 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
905
9
4d5578b57a77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents: 8
diff changeset
906 Input data: 3 types of MSI 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
907
3
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
908 - 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
909 - 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
910 - Cardinal "MSImageSet" data (with variable name "msidata", saved as .RData)
9
4d5578b57a77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents: 8
diff changeset
911 - Coordinates stored as decimals rather than integers will be rounded to obtain a regular pixel grid. This might lead to duplicated coordinates which will be automatically removed before peak picking.
8
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
912 - optional: tabular file with pixel annotations: x and y values in separate columns and the corresponding annotation in a third column
0
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
913
3
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
914 Options:
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
915
0
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
916 - Normalization: Normalization of intensities to total ion current (TIC)
9
4d5578b57a77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents: 8
diff changeset
917 - Baseline reduction: Baseline reduction removes background intensity generated by chemical noise (common in MALDI datasets)
4d5578b57a77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents: 8
diff changeset
918 - Smoothing: 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
919 - 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
920 - 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
921 - 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
922 - 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
923 - 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
924
3
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
925
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
926 Output:
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
927
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
928 - imzML file, preprocessed
8
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
929 - pdf with key values after each processing step, in case of loaded annotations file overview plot of pixel annotations
9
4d5578b57a77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents: 8
diff changeset
930 - optional: intensity matrix as tabular file (m/z in rows and pixel in columns, filled with intensity values)
8
d77c5228fd1a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 7
diff changeset
931 - optional: summarized intensity matrix: mean, median or standard deviation for each m/z feature; in case pixel annotations are provided the intensity values are summarized for each pixel group
3
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
932
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
933 Tip:
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
934
b9523950e79d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
935 - 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
936 - 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
937
0
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
938 ]]>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
939 </help>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
940 <citations>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
941 <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:
diff changeset
942 </citations>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
943 </tool>