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annotate msi_preprocessing.xml @ 3:c17eb2cc0048 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
author galaxyp
date Mon, 28 May 2018 12:34:27 -0400
parents 55e081b9f6ac
children ada9dee67b5d
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c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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1 <tool id="mass_spectrometry_imaging_preprocessing" name="MSI preprocessing" version="1.10.0.0">
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2 <description>
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3 mass spectrometry imaging preprocessing
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4 </description>
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5 <requirements>
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6 <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement>
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7 <requirement type="package" version="2.2.1">r-gridextra</requirement>
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8 <requirement type="package" version="0.20-35">r-lattice</requirement>
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9 </requirements>
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10 <command detect_errors="exit_code">
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11 <![CDATA[
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13 #if $infile.ext == 'imzml'
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14 ln -s '${infile.extra_files_path}/imzml' infile.imzML &&
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15 ln -s '${infile.extra_files_path}/ibd' infile.ibd &&
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16 #elif $infile.ext == 'analyze75'
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17 ln -s '${infile.extra_files_path}/hdr' infile.hdr &&
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18 ln -s '${infile.extra_files_path}/img' infile.img &&
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19 ln -s '${infile.extra_files_path}/t2m' infile.t2m &&
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20 #else
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21 ln -s '$infile' infile.RData &&
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22 #end if
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23 cat '${cardinal_preprocessing}' &&
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24 Rscript '${cardinal_preprocessing}'
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26 ]]>
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27 </command>
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28 <configfiles>
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29 <configfile name="cardinal_preprocessing"><![CDATA[
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30 library(Cardinal)
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31 library(gridExtra)
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32 library(lattice)
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34 #if $infile.ext == 'imzml'
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35 msidata = readImzML('infile')
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36 #elif $infile.ext == 'analyze75'
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37 msidata = readAnalyze('infile')
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38 #else
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39 load('infile.RData')
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40 #end if
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43 ##################################### Preparations for QC report ###############
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45 #if $outputs.outputs_select == "quality_control":
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47 ### values for QC table:
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48 maxfeatures = length(features(msidata))
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49 medianpeaks = median(colSums(spectra(msidata)[]>0))
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50 medint = round(median(spectra(msidata)[]), digits=2)
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51 TICs = round(mean(colSums(spectra(msidata)[])), digits=1)
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52 QC_numbers= data.frame(rawdata = c(maxfeatures, medianpeaks, medint, TICs))
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53 vectorofactions = "rawdata"
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56 ### Read tabular file with calibrant masses:
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57 calibrant_list = read.delim("$outputs.calibrant_file", header = FALSE, stringsAsFactors = FALSE)
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59 ### calculate how many input calibrant masses are valid:
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60 inputcalibrants = calibrant_list[calibrant_list[,$outputs.calibrants_column]>min(mz(msidata)) & calibrant_list[,$outputs.calibrants_column]<max(mz(msidata)),$outputs.calibrants_column]
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61 number_calibrants_in = length(calibrant_list[,$outputs.calibrants_column])
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62 number_calibrants_valid = length(inputcalibrants)
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67 ### Quality control report
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68
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70 pdf("Preprocessing.pdf", fonts = "Times", pointsize = 12)
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71 plot(0,type='n',axes=FALSE,ann=FALSE)
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72 title(main=paste("Quality control during preprocessing \n", "Filename:", "$infile.display_name"))
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73 title(main=paste0("\n\n\n\n Number valid masses in ", "$outputs.calibrant_file.display_name",": ", number_calibrants_valid, "/", number_calibrants_in))
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77 for (calibrant in inputcalibrants)
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78 {
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80 currentimage = image(msidata , mz=calibrant, strip = strip.custom(bg="lightgrey",
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81 par.strip.text=list(col="black", cex=.9)),lattice=TRUE,
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82 scales = list(draw = FALSE), plusminus = $outputs.plusminus_dalton, main="raw")
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83
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84 assign(paste("rawdata",calibrant, sep="_"), currentimage)
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85 }
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86
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87
3
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88 current_plot_raw = vector(length(inputcalibrants), mode='list')
2
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89
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90
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91 #end if
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92
3
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93 ############################### Preprocessing steps ###########################
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94 #for $method in $methods:
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95
0
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96 #if str( $method.methods_conditional.preprocessing_method ) == 'Normalization':
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97 print('Normalization')
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98 ##normalization
2
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99
3
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100 msidata = normalize(msidata, method="tic")
2
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101
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102 #if $outputs.outputs_select == "quality_control":
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103 ### values for QC table:
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104 maxfeatures = length(features(msidata))
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105 medianpeaks = median(colSums(spectra(msidata)[]>0))
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106 medint = round(median(spectra(msidata)[]), digits=2)
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107 TICs = round(mean(colSums(spectra(msidata)[])), digits=1)
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108 normalized = c(maxfeatures, medianpeaks, medint, TICs)
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109 QC_numbers= cbind(QC_numbers, normalized)
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110 ### preparation for QC plots
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111 vectorofactions = append(vectorofactions, "normalized")
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112
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113 for (calibrant in inputcalibrants)
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114 {
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115 currentimage = image(msidata , mz=calibrant, strip = strip.custom(bg="lightgrey",
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116 par.strip.text=list(col="black", cex=.9)),lattice=TRUE,
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117 scales = list(draw = FALSE), plusminus = $outputs.plusminus_dalton, main="normalized")
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118
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119 assign(paste("normalized",calibrant, sep="_"), currentimage)
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120 }
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121
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122
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123 #end if
0
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124
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125 #elif str( $method.methods_conditional.preprocessing_method ) == 'Baseline_reduction':
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126 print('Baseline_reduction')
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127 ##baseline reduction
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128 msidata = reduceBaseline(msidata, method="median", blocks=$method.methods_conditional.blocks_baseline)
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129
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130 #if $outputs.outputs_select == "quality_control":
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131 maxfeatures = length(features(msidata))
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132 medianpeaks = median(colSums(spectra(msidata)[]>0))
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133 medint = round(median(spectra(msidata)[]), digits=2)
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134 TICs = round(mean(colSums(spectra(msidata)[])), digits=1)
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135 baseline= c(maxfeatures, medianpeaks, medint, TICs)
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136 QC_numbers= cbind(QC_numbers, baseline)
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137 ### preparation for QC plots
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138 vectorofactions = append(vectorofactions, "baseline_rem")
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139
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140 for (calibrant in inputcalibrants)
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141 {
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142 currentimage = image(msidata , mz=calibrant, strip = strip.custom(bg="lightgrey",
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143 par.strip.text=list(col="black", cex=.9)),lattice=TRUE,
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144 scales = list(draw = FALSE), plusminus = $outputs.plusminus_dalton, main="baseline removed")
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145
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146 assign(paste("baseline_rem",calibrant, sep="_"), currentimage)
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147 }
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148 #end if
0
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149
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150 #elif str( $method.methods_conditional.preprocessing_method ) == 'Smoothing':
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151 print('Smoothing')
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152 ## Smoothing
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153
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154 #if str( $method.methods_conditional.methods_for_smoothing.smoothing_method) == 'gaussian':
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155 print('gaussian smoothing')
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156 msidata = smoothSignal(msidata, method="$method.methods_conditional.methods_for_smoothing.smoothing_method", window=$method.methods_conditional.window_smoothing, sd = $method.methods_conditional.methods_for_smoothing.sd_gaussian)
0
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157 #elif str( $method.methods_conditional.methods_for_smoothing.smoothing_method) == 'sgolay':
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158 print('sgolay smoothing')
3
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159 msidata = smoothSignal(msidata, method="$method.methods_conditional.methods_for_smoothing.smoothing_method", window=$method.methods_conditional.window_smoothing, order = $method.methods_conditional.methods_for_smoothing.order_of_filters)
0
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160 #elif str($method.methods_conditional.methods_for_smoothing.smoothing_method) == 'ma':
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161 print('sgolay smoothing')
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162 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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163 #end if
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164
2
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165 #if $outputs.outputs_select == "quality_control":
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166 maxfeatures = length(features(msidata))
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167 medianpeaks = median(colSums(spectra(msidata)[]>0))
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168 medint = round(median(spectra(msidata)[]), digits=2)
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169 TICs = round(mean(colSums(spectra(msidata)[])), digits=1)
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170 smoothed= c(maxfeatures, medianpeaks, medint, TICs)
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171 QC_numbers= cbind(QC_numbers, smoothed)
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172 ### preparation for QC plots
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173 vectorofactions = append(vectorofactions, "smoothed")
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174
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175 for (calibrant in inputcalibrants)
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176 {
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177 currentimage = image(msidata , mz=calibrant, strip = strip.custom(bg="lightgrey",
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178 par.strip.text=list(col="black", cex=.9)),lattice=TRUE,
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179 scales = list(draw = FALSE), plusminus = $outputs.plusminus_dalton, main="smoothed")
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180
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181 assign(paste("smoothed",calibrant, sep="_"), currentimage)
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182 }
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183 #end if
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184
0
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185 #elif str( $method.methods_conditional.preprocessing_method) == 'Peak_picking':
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186 print('Peak_picking')
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187 ## Peakpicking
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188
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189 #if str( $method.methods_conditional.methods_for_picking.picking_method) == 'adaptive':
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190 print('adaptive peakpicking')
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191 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)
0
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192
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193 #elif str( $method.methods_conditional.methods_for_picking.picking_method) == 'limpic':
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194 print('limpic peakpicking')
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195 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)
0
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196
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197 #elif str( $method.methods_conditional.methods_for_picking.picking_method) == 'simple':
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198 print('simple peakpicking')
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199 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)
0
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200 #end if
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201
2
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202 #if $outputs.outputs_select == "quality_control":
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203 maxfeatures = length(features(msidata))
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204 medianpeaks = median(colSums(spectra(msidata)[]>0))
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205 medint = round(median(spectra(msidata)[]), digits=2)
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206 TICs = round(mean(colSums(spectra(msidata)[])), digits=1)
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207 picked= c(maxfeatures, medianpeaks, medint, TICs)
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208 QC_numbers= cbind(QC_numbers, picked)
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209 ### preparation for QC plots
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210 vectorofactions = append(vectorofactions, "picked")
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211
2
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212 for (calibrant in inputcalibrants)
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213 {
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214 currentimage = image(msidata , mz=calibrant, strip = strip.custom(bg="lightgrey",
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215 par.strip.text=list(col="black", cex=.9)),lattice=TRUE,
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216 scales = list(draw = FALSE), plusminus = $outputs.plusminus_dalton, main="picked")
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217
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218 assign(paste("picked",calibrant, sep="_"), currentimage)
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219 }
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220 #end if
1
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221
0
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222 #elif str( $method.methods_conditional.preprocessing_method ) == 'Peak_alignment':
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223 print('Peak_alignment')
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224 ## Peakalignment
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225
2
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226 #if str( $method.methods_conditional.align_ref_type.align_reference_datatype) == 'align_noref':
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227 align_peak_reference = msidata
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228
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229 #elif str( $method.methods_conditional.align_ref_type.align_reference_datatype) == 'align_table':
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230 align_reference_table = read.delim("$method.methods_conditional.align_ref_type.align_peaks_table", header = FALSE, stringsAsFactors = FALSE)
2
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231
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232 align_reference_column = align_reference_table[,$method.methods_conditional.align_ref_type.align_mass_column]
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233
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234 align_peak_reference = align_reference_column[align_reference_column>=min(mz(msidata)) & align_reference_column<=max(mz(msidata))]
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235 if (length(align_peak_reference) == 0)
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236 {align_peak_reference = 0
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237 }
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238
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239
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240
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241 #### if length <0: align_peak_reference = 0
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242
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243
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244 #elif str( $method.methods_conditional.align_ref_type.align_reference_datatype) == 'align_msidata_ref':
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245 loadRData <- function(fileName){
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246 #loads an RData file, and returns it
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247 load(fileName)
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248 get(ls()[ls() != "fileName"])
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249 }
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250 align_peak_reference = loadRData('$method.methods_conditional.align_ref_type.align_peaks_msidata')
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251 #end if
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252
0
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253 #if str( $method.methods_conditional.methods_for_alignment.alignment_method) == 'diff':
2
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254 print('diff peakalignment')
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255 msidata = peakAlign(msidata, method='$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)
0
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256
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257 #elif str( $method.methods_conditional.methods_for_alignment.alignment_method) == 'DP':
2
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258 print('DPpeakalignment')
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259 msidata = peakAlign(msidata, method='$method.methods_conditional.methods_for_alignment.alignment_method',gap = $method.methods_conditional.methods_for_alignment.gap_DPalignment, ref=align_peak_reference)
0
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260 #end if
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261
2
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262 #if $outputs.outputs_select == "quality_control":
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263 maxfeatures = length(features(msidata))
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264 medianpeaks = median(colSums(spectra(msidata)[]>0))
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265 medint = round(median(spectra(msidata)[]), digits=2)
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266 TICs = round(mean(colSums(spectra(msidata)[])), digits=1)
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267 aligned= c(maxfeatures, medianpeaks, medint, TICs)
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268 QC_numbers= cbind(QC_numbers, aligned)
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269 ### preparation for QC plots
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270 vectorofactions = append(vectorofactions, "aligned")
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271
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272 for (calibrant in inputcalibrants)
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273 {
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274 currentimage = image(msidata , mz=calibrant, strip = strip.custom(bg="lightgrey",
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275 par.strip.text=list(col="black", cex=.9)),lattice=TRUE,
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276 scales = list(draw = FALSE), plusminus = $outputs.plusminus_dalton, main="aligned")
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277
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278 assign(paste("aligned",calibrant, sep="_"), currentimage)
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279 }
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280 #end if
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281
0
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282 #elif str( $method.methods_conditional.preprocessing_method) == 'Peak_filtering':
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283 print('Peak_filtering')
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284 msidata = peakFilter(msidata, method='freq', freq.min = $method.methods_conditional.frequ_filtering)
2
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285
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286 #if $outputs.outputs_select == "quality_control":
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287 maxfeatures = length(features(msidata))
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288 medianpeaks = median(colSums(spectra(msidata)[]>0))
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289 medint = round(median(spectra(msidata)[]), digits=2)
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290 TICs = round(mean(colSums(spectra(msidata)[])), digits=1)
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291 filtered= c(maxfeatures, medianpeaks, medint, TICs)
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292 QC_numbers= cbind(QC_numbers, filtered)
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293 ### preparation for QC plots
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294 vectorofactions = append(vectorofactions, "filtered")
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295
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296 for (calibrant in inputcalibrants)
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297 {
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298 currentimage = image(msidata , mz=calibrant, strip = strip.custom(bg="lightgrey",
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299 par.strip.text=list(col="black", cex=.9)),lattice=TRUE,
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300 scales = list(draw = FALSE), plusminus = $outputs.plusminus_dalton, main="filtered")
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301
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302 assign(paste("filtered",calibrant, sep="_"), currentimage)
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303 }
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304 #end if
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305
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306 #elif str( $method.methods_conditional.preprocessing_method) == 'Data_reduction':
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307 print('Data_reduction')
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308
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309 #if str( $method.methods_conditional.methods_for_reduction.reduction_method) == 'bin':
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310 print('bin reduction')
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311 msidata = reduceDimension(msidata, method="bin", width=$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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312
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313 #elif str( $method.methods_conditional.methods_for_reduction.reduction_method) == 'resample':
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314 print('resample reduction')
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315 msidata = reduceDimension(msidata, method="resample", step=$method.methods_conditional.methods_for_reduction.resample_step)
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316
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317 #elif str( $method.methods_conditional.methods_for_reduction.reduction_method) == 'peaks':
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318 print('peaks reduction')
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319
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320 #if str( $method.methods_conditional.methods_for_reduction.ref_type.reference_datatype) == 'table':
3
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321 reference_table = read.delim("$method.methods_conditional.methods_for_reduction.ref_type.peaks_table", header = FALSE, stringsAsFactors = FALSE)
2
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322 reference_column = reference_table[,$method.methods_conditional.methods_for_reduction.ref_type.mass_column]
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323 peak_reference = reference_column[reference_column>min(mz(msidata)) & reference_column<max(mz(msidata))]
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324
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325 #elif str( $method.methods_conditional.methods_for_reduction.ref_type.reference_datatype) == 'msidata_ref':
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326 loadRData <- function(fileName){
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327 #loads an RData file, and returns it
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328 load(fileName)
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329 get(ls()[ls() != "fileName"])
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330 }
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331 peak_reference = loadRData('$method.methods_conditional.methods_for_reduction.ref_type.peaks_msidata')
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332 #end if
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333 msidata = reduceDimension(msidata, method="peaks", ref=peak_reference, type="$method.methods_conditional.methods_for_reduction.peaks_type")
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334 #end if
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335
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336 #if $outputs.outputs_select == "quality_control":
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337 maxfeatures = length(features(msidata))
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338 medianpeaks = median(colSums(spectra(msidata)[]>0))
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339 medint = round(median(spectra(msidata)[]), digits=2)
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340 TICs = round(mean(colSums(spectra(msidata)[])), digits=1)
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341 reduced= c(maxfeatures, medianpeaks, medint, TICs)
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342 QC_numbers= cbind(QC_numbers, reduced)
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343 ### preparation for QC plots
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344 vectorofactions = append(vectorofactions, "reduced")
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345
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346 for (calibrant in inputcalibrants)
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347 {
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348 currentimage = image(msidata , mz=calibrant, strip = strip.custom(bg="lightgrey",
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349 par.strip.text=list(col="black", cex=.9)),lattice=TRUE,
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350 scales = list(draw = FALSE), plusminus = $outputs.plusminus_dalton, main="reduced")
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351
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352 assign(paste("reduced",calibrant, sep="_"), currentimage)
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353 }
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354 #end if
3
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355
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356 #elif str( $method.methods_conditional.preprocessing_method) == 'Transformation':
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357 print('Transformation')
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358
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359 #if str( $method.methods_conditional.transf_conditional.trans_type) == 'log2':
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360 print('log2 transformation')
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361 spectra(msidata)[spectra(msidata) ==0] = NA
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362 print(paste0("Number of 0 which were converted into NA:",sum(is.na(spectra(msidata)))))
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363 spectra(msidata) = log2(spectra(msidata))
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364
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365 #elif str( $method.methods_conditional.transf_conditional.trans_type) == 'sqrt':
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366 print('squareroot transformation')
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367 spectra(msidata) = sqrt(spectra(msidata))
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368
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369 #end if
0
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370 #end if
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371 #end for
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372
3
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373 ###################### Outputs: RData, tabular and QC report ###################
1
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374
2
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375
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376 ## save as (.RData)
0
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377 save(msidata, file="$msidata_preprocessed")
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378
2
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379
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380 #if $output_matrix:
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381
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382
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383 if (length(features(msidata))> 0)
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384 {
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385
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386 ## save as intensity matrix
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387
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388 spectramatrix = spectra(msidata)
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389 rownames(spectramatrix) = mz(msidata)
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390 newmatrix = rbind(pixels(msidata), spectramatrix)
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391 write.table(newmatrix[2:nrow(newmatrix),], file="$matrixasoutput", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t")
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392
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393 }else{
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394 print("file has no features left")
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395 write.table(matrix(rownames(coord(msidata)), ncol=ncol(msidata), nrow=1), file="$matrixasoutput", quote = FALSE, row.names = FALSE, col.names=FALSE, sep = "\t")
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396 }
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397
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398 #end if
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399
1
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parents: 0
diff changeset
400
2
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
401 #if $outputs.outputs_select == "quality_control":
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
402
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
403 rownames(QC_numbers) = c("# features", "median # peaks", "median intensity", "median TIC")
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
404 grid.table(t(QC_numbers))
1
641316f29395 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 0
diff changeset
405
2
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
406 for (calibrant in inputcalibrants)
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
407 {
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
408 imagelist = list()
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
409
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
410 for (numberprepro in 1:length(vectorofactions)){
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
411
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
412 imagelist[[numberprepro]] = get(paste(vectorofactions[numberprepro],calibrant, sep="_"))
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
413
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
414
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
415 }
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
416
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
417 do.call(grid.arrange,imagelist)
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
418 }
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
419
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
420
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
421 dev.off()
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
422
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
423 #end if
1
641316f29395 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 0
diff changeset
424
0
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
425
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
426 ]]></configfile>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
427 </configfiles>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
428 <inputs>
3
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
429 <param name="infile" type="data" format="imzml,rdata,danalyze75"
2
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
430 label="MSI rawdata as imzml, analyze7.5 or Cardinal MSImageSet saved as RData"
1
641316f29395 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 0
diff changeset
431 help="load imzml and ibd file by uploading composite datatype imzml"/>
0
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
432 <repeat name="methods" title="Preprocessing" min="1" max="50">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
433 <conditional name="methods_conditional">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
434 <param name="preprocessing_method" type="select" label="Select the preprocessing methods you want to apply">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
435 <option value="Normalization" selected="True">Normalization to TIC</option>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
436 <option value="Baseline_reduction">Baseline Reduction</option>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
437 <option value="Smoothing">Peak smoothing</option>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
438 <option value="Peak_picking">Peak picking</option>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
439 <option value="Peak_alignment">Peak alignment</option>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
440 <option value="Peak_filtering">Peak filtering</option>
2
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
441 <option value="Data_reduction">Data reduction</option>
3
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
442 <option value="Transformation">Transformation</option>
0
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
443 </param>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
444 <when value="Normalization"/>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
445 <when value="Baseline_reduction">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
446 <param name="blocks_baseline" type="integer" value="50"
2
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
447 label="Blocks"/>
0
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
448 </when>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
449 <when value="Smoothing">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
450 <conditional name="methods_for_smoothing">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
451 <param name="smoothing_method" type="select" label="Smoothing method">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
452 <option value="gaussian" selected="True">gaussian</option>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
453 <option value="sgolay">Savitsky-Golay</option>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
454 <option value="ma">moving average</option>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
455 </param>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
456 <when value="gaussian">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
457 <param name="sd_gaussian" type="float" value="4"
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
458 label="The standard deviation for the Gaussian kernel (window/sd)"/>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
459 </when>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
460 <when value="sgolay">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
461 <param name="order_of_filters" type="integer" value="3"
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
462 label="The order of the smoothing filter"/>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
463 </when>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
464 <when value="ma">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
465 <param name="coefficients_ma_filter" type="integer" value="1"
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
466 label="The coefficients for the moving average filter"/>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
467 </when>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
468 </conditional>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
469 <param name="window_smoothing" type="integer" value="9"
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
470 label="Window size"/>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
471 </when>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
472 <when value="Peak_picking">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
473 <param name="SNR_picking_method" type="integer" value="3"
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
474 label="Signal to noise ratio"
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
475 help="The minimal signal to noise ratio for peaks to be considered as a valid peak."/>
2
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
476 <param name="blocks_picking" type="integer" value="100" label = "Number of blocks"
0
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
477 help="Number of blocks in which to divide mass spectrum to calculate noise"/>
2
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
478 <param name="window_picking" type="integer" value="5" label= "Window size" help="Window width for seeking local maxima"/>
0
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
479 <conditional name="methods_for_picking">
2
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
480 <param name="picking_method" type="select" label="Peak picking method" help="only simple works for processed imzML files">
0
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
481 <option value="adaptive" selected="True">adaptive</option>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
482 <option value="limpic">limpic</option>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
483 <option value="simple">simple</option>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
484 </param>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
485 <when value="adaptive">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
486 <param name="spar_picking" type="float" value="1.0"
2
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
487 label="Spar value"
0
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
488 help = "Smoothing parameter for the spline smoothing
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
489 applied to the spectrum in order to decide the cutoffs
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
490 for throwing away false noise spikes that might occur inside peaks"/>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
491 </when>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
492 <when value="limpic">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
493 <param name="tresh_picking" type="float" value="0.75"
2
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
494 label="thresh value" help="The thresholding quantile to use when comparing slopes in order to throw away peaks that are too flat"/>
0
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
495 </when>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
496 <when value="simple"/>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
497 </conditional>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
498 </when>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
499 <when value="Peak_alignment">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
500 <conditional name="methods_for_alignment">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
501 <param name="alignment_method" type="select" label="Alignment method">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
502 <option value="diff" selected="True">diff</option>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
503 <option value="DP">DP</option>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
504 </param>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
505 <when value="diff">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
506 <param name="value_diffalignment" type="integer" value="200"
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
507 label="diff.max" help="Peaks that differ less than this value will be aligned together"/>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
508 <param name="units_diffalignment" type="select" display = "radio" optional = "False"
2
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
509 label="units" help="The coefficients for the moving average filter">
0
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
510 <option value="ppm" selected="True">ppm</option>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
511 <option value="Da">Da</option>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
512 </param>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
513 </when>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
514 <when value="DP">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
515 <param name="gap_DPalignment" type="integer" value="0"
2
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
516 label="Gap" help="The gap penalty for the dynamic programming sequence alignment"/>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
517 </when>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
518 </conditional>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
519 <conditional name="align_ref_type">
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
520 <param name="align_reference_datatype" type="select" label="Choose reference">
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
521 <option value="align_noref" selected="True">no reference</option>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
522 <option value="align_table" >tabular file as reference</option>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
523 <option value="align_msidata_ref">msidata file as reference</option>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
524 </param>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
525 <when value="align_noref"/>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
526 <when value="align_table">
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
527 <param name="align_peaks_table" type="data" format="tabular"
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
528 label="Reference mz values to use for alignment - only these will be kept" help="One column with mz values (without empty cells or letters)"/>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
529 <param name="align_mass_column" data_ref="align_peaks_table" label="Column with reference mz" type="data_column"/>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
530 </when>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
531 <when value="align_msidata_ref">
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
532 <param name="align_peaks_msidata" type="data" format="rdata," label="Picked and aligned Cardinal MSImageSet saved as RData"/>
0
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
533 </when>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
534 </conditional>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
535 </when>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
536 <when value="Peak_filtering">
2
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
537 <param name="frequ_filtering" type="integer" value="1000"
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
538 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)"/>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
539 </when>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
540 <when value="Data_reduction">
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
541 <conditional name="methods_for_reduction">
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
542 <param name="reduction_method" type="select" label="Reduction method">
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
543 <option value="bin" selected="True">bin</option>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
544 <option value="resample">resample</option>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
545 <option value="peaks">peaks</option>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
546 </param>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
547 <when value="bin">
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
548 <param name="bin_width" type="float" value="1"
3
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
549 label="The width of a bin in mz or ppm" help="Width must be greater than range of mz values divided by number of mz features"/>
2
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
550 <param name="bin_units" type="select" display="radio"
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
551 label="Unit for bin">
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
552 <option value="mz" selected="True">mz</option>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
553 <option value="ppm">ppm</option>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
554 </param>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
555 <param name="bin_fun" type="select" display="radio"
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
556 label="Calculate sum or mean intensity for ions of the same bin">
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
557 <option value="mean" selected="True">mean</option>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
558 <option value="sum">sum</option>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
559 </param>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
560 </when>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
561 <when value="resample">
55e081b9f6ac 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="resample_step" type="float" value="1"
3
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
563 label="The step size in mz" help="Step size must be greater than range of mz values divided by number of mz features"/>
2
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
564 </when>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
565 <when value="peaks">
55e081b9f6ac 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="peaks_type" type="select" display="radio"
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
567 label="Should the peak height or area under the curve be taken as the intensity value?">
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
568 <option value="height" selected="True">height</option>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
569 <option value="area">area</option>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
570 </param>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
571 <conditional name="ref_type">
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
572 <param name="reference_datatype" type="select" label="Choose reference datatype">
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
573 <option value="table" selected="True">tabular file</option>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
574 <option value="msidata_ref">msidata file</option>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
575 </param>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
576 <when value="table">
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
577 <param name="peaks_table" type="data" format="tabular"
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
578 label="Reference mz values to use to reduce the dimension" help="One column with mz values (without empty cells or letters, mz outside mz range are not used for filtering)"/>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
579 <param name="mass_column" data_ref="peaks_table" label="Column with reference mz" type="data_column"/>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
580 </when>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
581 <when value="msidata_ref">
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
582 <param name="peaks_msidata" type="data" format="rdata," label="Picked and aligned Cardinal MSImageSet saved as RData"/>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
583 </when>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
584 </conditional>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
585 </when>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
586 </conditional>
0
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
587 </when>
3
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
588 <when value="Transformation">
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
589 <conditional name="transf_conditional">
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
590 <param name="trans_type" type="select" label="Choose which intensity transformation you want to apply" help="logarithm base 2 (log2) or squareroot (sqrt)">
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
591 <option value="log2" selected="True">log2</option>
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
592 <option value="sqrt">sqrt</option>
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
593 </param>
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
594 <when value="log2"/>
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
595 <when value="sqrt"/>
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
596 </conditional>
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
597 </when>
0
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
598 </conditional>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
599 </repeat>
2
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
600 <conditional name="outputs">
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
601 <param name="outputs_select" type="select" label="Quality control output">
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
602 <option value="quality_control" selected="True">yes</option>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
603 <option value="no_quality_control">no</option>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
604 </param>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
605 <when value="quality_control">
55e081b9f6ac 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="calibrant_file" type="data" format="tabular"
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
607 label="Provide a list of masses which will be plotted in the quality control report"
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
608 help="Use internal calibrant masses"/>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
609 <param name="calibrants_column" data_ref="calibrant_file" label="Column with masses" type="data_column"/>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
610 <param name="plusminus_dalton" value="0.25" type="text" label="Mass range" help="Plusminus mass window in Dalton"/>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
611 </when>
55e081b9f6ac 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="no_quality_control"/>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
613 </conditional>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
614 <param name="output_matrix" type="boolean" display="radio" label="Intensity matrix output"/>
0
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
615 </inputs>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
616 <outputs>
2
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
617 <data format="rdata" name="msidata_preprocessed" label="Preprocessed ${on_string}"/>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
618 <data format="pdf" name="QC_plots" from_work_dir="Preprocessing.pdf" label = "QC preprocessing report on ${on_string}">
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
619 <filter>outputs["outputs_select"] == "quality_control"</filter>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
620 </data>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
621 <data format="tabular" name="matrixasoutput" label="Intensity matrix ${on_string}">
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
622 <filter>output_matrix</filter>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
623 </data>
0
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
624 </outputs>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
625 <tests>
3
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
626 <test expect_num_outputs="2">
0
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
627 <param name="infile" value="" ftype="imzml">
1
641316f29395 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 0
diff changeset
628 <composite_data value="Example_Continuous.imzML"/>
641316f29395 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 0
diff changeset
629 <composite_data value="Example_Continuous.ibd"/>
0
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
630 </param>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
631 <repeat name="methods">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
632 <conditional name="methods_conditional">
3
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
633 <param name="preprocessing_method" value="Normalization"/>
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
634 </conditional>
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
635 </repeat>
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
636 <repeat name="methods">
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
637 <conditional name="methods_conditional">
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
638 <param name="preprocessing_method" value="Smoothing"/>
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
639 <conditional name="methods_for_smoothing">
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
640 <param name="smoothing_method" value="gaussian"/>
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
641 </conditional>
0
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
642 </conditional>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
643 </repeat>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
644 <repeat name="methods">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
645 <conditional name="methods_conditional">
3
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
646 <param name="preprocessing_method" value="Peak_picking"/>
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
647 <conditional name="methods_for_picking">
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
648 <param name="picking_method" value="adaptive"/>
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
649 </conditional>
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
650 <param name="blocks_picking" value="3"/>
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
651 <param name="window_picking" value="3"/>
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
652 </conditional>
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
653 </repeat>
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
654 <repeat name="methods">
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
655 <conditional name="methods_conditional">
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
656 <param name="preprocessing_method" value="Peak_alignment"/>
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
657 <conditional name="methods_for_alignment">
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
658 <param name="alignment_method" value="diff"/>
0
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
659 </conditional>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
660 </conditional>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
661 </repeat>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
662 <repeat name="methods">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
663 <conditional name="methods_conditional">
3
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
664 <param name="preprocessing_method" value="Peak_filtering"/>
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
665 <param name="frequ_filtering" value="2"/>
0
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
666 </conditional>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
667 </repeat>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
668 <repeat name="methods">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
669 <conditional name="methods_conditional">
3
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
670 <param name="preprocessing_method" value="Transformation"/>
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
671 <conditional name="transf_conditional">
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
672 <param name="trans_type" value="sqrt"/>
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
673 </conditional>
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
674 </conditional>
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
675 </repeat>
c17eb2cc0048 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="outputs_select" value="no_quality_control"/>
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
677 <param name="output_matrix" value="True"/>
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
678 <output name="msidata_preprocessed" file="preprocessing_results1.RData" compare="sim_size"/>
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
679 <output name="matrixasoutput" file="preprocessing_results1.txt"/>
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
680 </test>
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
681 <test expect_num_outputs="3">
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
682 <param name="infile" value="example_continous.RData" ftype="rdata"/>
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
683 <repeat name="methods">
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
684 <conditional name="methods_conditional">
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
685 <param name="preprocessing_method" value="Peak_picking"/>
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
686 <param name="blocks_picking" value="3"/>
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
687 <param name="window_picking" value="5"/>
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
688 <conditional name="methods_for_picking">
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
689 <param name="picking_method" value="simple"/>
0
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
690 </conditional>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
691 </conditional>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
692 </repeat>
2
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
693 <repeat name="methods">
0
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
694 <conditional name="methods_conditional">
3
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
695 <param name="preprocessing_method" value="Peak_alignment"/>
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
696 <conditional name="methods_for_alignment">
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
697 <param name="alignment_method" value="DP"/>
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
698 </conditional>
0
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
699 </conditional>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
700 </repeat>
2
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
701 <param name="outputs_select" value="quality_control"/>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
702 <param name="calibrant_file" ftype="tabular" value="inputcalibrantfile2.tabular"/>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
703 <param name="calibrants_column" value="1"/>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
704 <param name="plusminus_dalton" value="0.25"/>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
705 <param name="output_matrix" value="True"/>
3
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
706 <output name="msidata_preprocessed" file="preprocessing_results2.RData" compare="sim_size"/>
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
707 <output name="matrixasoutput" file="preprocessing_results2.txt" lines_diff="2"/>
2
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
708 <output name="QC_plots" file="preprocessing_results2.pdf" compare="sim_size"/>
0
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
709 </test>
3
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
710 <test expect_num_outputs="2">
0
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
711 <param name="infile" value="" ftype="analyze75">
1
641316f29395 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 0
diff changeset
712 <composite_data value="Analyze75.hdr"/>
641316f29395 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 0
diff changeset
713 <composite_data value="Analyze75.img"/>
641316f29395 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 0
diff changeset
714 <composite_data value="Analyze75.t2m"/>
0
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
715 </param>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
716 <repeat name="methods">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
717 <conditional name="methods_conditional">
3
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
718 <param name="preprocessing_method" value="Normalization"/>
0
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
719 </conditional>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
720 </repeat>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
721 <repeat name="methods">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
722 <conditional name="methods_conditional">
3
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
723 <param name="preprocessing_method" value="Peak_picking"/>
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
724 <param name="blocks_picking" value="100"/>
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
725 <param name="window_picking" value="5"/>
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
726 <conditional name="methods_for_picking">
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
727 <param name="picking_method" value="limpic"/>
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
728 </conditional>
0
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
729 </conditional>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
730 </repeat>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
731 <repeat name="methods">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
732 <conditional name="methods_conditional">
3
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
733 <param name="preprocessing_method" value="Peak_alignment"/>
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
734 <conditional name="methods_for_alignment">
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
735 <param name="alignment_method" value="diff"/>
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
736 </conditional>
0
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
737 </conditional>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
738 </repeat>
2
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
739 <param name="outputs_select" value="quality_control"/>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
740 <param name="calibrant_file" ftype="tabular" value="inputcalibrantfile2.tabular"/>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
741 <param name="calibrants_column" value="1"/>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
742 <param name="plusminus_dalton" value="0.25"/>
3
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
743 <output name="msidata_preprocessed" file="preprocessing_results3.RData" compare="sim_size"/>
2
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
744 <output name="QC_plots" file="preprocessing_results3.pdf" compare="sim_size"/>
0
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
745 </test>
3
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
746 <test expect_num_outputs="2">
2
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
747 <param name="infile" value="" ftype="analyze75">
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
748 <composite_data value="Analyze75.hdr"/>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
749 <composite_data value="Analyze75.img"/>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
750 <composite_data value="Analyze75.t2m"/>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
751 </param>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
752 <repeat name="methods">
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
753 <conditional name="methods_conditional">
3
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
754 <param name="preprocessing_method" value="Normalization"/>
2
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
755 </conditional>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
756 </repeat>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
757 <repeat name="methods">
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
758 <conditional name="methods_conditional">
3
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
759 <param name="preprocessing_method" value="Data_reduction"/>
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
760 <param name="bin_width" value="0.1"/>
2
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
761 </conditional>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
762 </repeat>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
763 <param name="outputs_select" value="no_quality_control"/>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
764 <param name="output_matrix" value="True"/>
3
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
765 <output name="msidata_preprocessed" file="preprocessing_results4.RData" compare="sim_size"/>
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
766 <output name="matrixasoutput" file="preprocessing_results4.txt"/>
2
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
767 </test>
3
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
768 <test expect_num_outputs="3">
2
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
769 <param name="infile" value="" ftype="imzml">
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
770 <composite_data value="Example_Continuous.imzML"/>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
771 <composite_data value="Example_Continuous.ibd"/>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
772 </param>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
773 <repeat name="methods">
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
774 <conditional name="methods_conditional">
3
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
775 <param name="preprocessing_method" value="Data_reduction"/>
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
776 <conditional name="methods_for_reduction">
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
777 <param name="reduction_method" value="resample"/>
c17eb2cc0048 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="step_width" value="0.1"/>
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
779 </conditional>
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
780 </conditional>
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
781 </repeat>
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
782 <repeat name="methods">
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
783 <conditional name="methods_conditional">
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
784 <param name="preprocessing_method" value="Transformation"/>
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
785 <conditional name="transf_conditional">
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
786 <param name="trans_type" value="log2"/>
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
787 </conditional>
2
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
788 </conditional>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
789 </repeat>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
790 <param name="outputs_select" value="quality_control"/>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
791 <param name="calibrant_file" ftype="tabular" value="inputcalibrantfile1.tabular"/>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
792 <param name="calibrants_column" value="1"/>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
793 <param name="plusminus_dalton" value="0.25"/>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
794 <param name="output_matrix" value="True"/>
3
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
795 <output name="msidata_preprocessed" file="preprocessing_results5.RData" compare="sim_size"/>
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
796 <output name="matrixasoutput" file="preprocessing_results5.txt"/>
2
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
797 <output name="QC_plots" file="preprocessing_results5.pdf" compare="sim_size"/>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
798 </test>
0
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
799 </tests>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
800 <help>
1
641316f29395 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 0
diff changeset
801 <![CDATA[
3
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
802
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
803 Cardinal is an R package that implements statistical & computational tools for analyzing mass spectrometry imaging datasets. `More information on Cardinal <http://cardinalmsi.org//>`_
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
804
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
805 This tool provides provides multiple Cardinal functions to preprocess mass-spectrometry imaging data.
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
806
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
807 Input data: 3 types of input data can be used:
0
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
808
3
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
809 - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/wp/imzml/>`_
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
810 - Analyze7.5 (upload hdr, img and t2m file via the "composite" function)
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
811 - Cardinal "MSImageSet" data (with variable name "msidata", saved as .RData)
0
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
812
3
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
813 Options:
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
814
0
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
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815 - Normalization: Normalization of intensities to total ion current (TIC)
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
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816 - Baseline reduction: Baseline reduction removes backgroundintensity generated by chemical noise (common in MALDI datasets)
3
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
817 - Smoothening: Smoothing of the mass peaks reduces noise and improves peak detection
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
818 - Peak picking: relevant peaks are picked while noise-peaks are removed (needs peak alignment afterwards)
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
819 - Peak alignment: only possible after peak picking, mz inaccuracies are removed by alignment of same peaks to a common mz value
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
820 - 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
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
821 - Data reduction: binning, resampling or peak filtering to reduce data
3
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
822 - Transformation: log2 or squareroot transformation of all intensities
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
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823
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
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824 Output:
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
825
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
826 - imzML file, preprocessed
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
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827 - optional: pdf with heatmap of masses of interest after each preprocessing step
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
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828 - optional: intensity matrix as tabular file (intensities for masses in rows and pixel in columns)
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
829
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
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830 Tip:
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
831
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
832 - Peak alignment works only after peak picking
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
diff changeset
833 - Peak filtering works only on centroided data (peak picking and alignment or Data reduction peaks)
c17eb2cc0048 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 2
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834
0
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
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835 ]]>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
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836 </help>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
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837 <citations>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
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838 <citation type="doi">10.1093/bioinformatics/btv146</citation>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
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839 </citations>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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840 </tool>