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annotate msi_preprocessing.xml @ 2:55e081b9f6ac draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
author galaxyp
date Mon, 23 Apr 2018 17:17:08 -0400
parents 641316f29395
children c17eb2cc0048
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55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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1 <tool id="mass_spectrometry_imaging_preprocessing" name="MSI preprocessing" version="1.7.0.2">
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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="1.7.0">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>
0
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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 $infile.ext == 'imzml'
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14 cp '${infile.extra_files_path}/imzml' infile.imzML &&
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15 cp '${infile.extra_files_path}/ibd' infile.ibd &&
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16 #elif $infile.ext == 'analyze75'
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17 cp '${infile.extra_files_path}/hdr' infile.hdr &&
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18 cp '${infile.extra_files_path}/img' infile.img &&
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19 cp '${infile.extra_files_path}/t2m' infile.t2m &&
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20 #else
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21 ln -s '$infile' infile.RData &&
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22 #end if
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23 cat '${cardinal_preprocessing}' &&
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24 Rscript '${cardinal_preprocessing}'
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25
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26 ]]>
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27 </command>
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28 <configfiles>
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29 <configfile name="cardinal_preprocessing"><![CDATA[
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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 <- readMSIData('infile.imzML')
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36 #elif $infile.ext == 'analyze75'
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37 msidata <- readMSIData('infile.hdr')
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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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41
1
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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, na.strings=c("","NA"), 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
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88 current_plot_raw <- vector(length(inputcalibrants), mode='list')
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89
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90
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91 #end if
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92
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93 ################################################### Preprocessing steps #######################################################################################
0
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94 #for $method in $methods:
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95 #if str( $method.methods_conditional.preprocessing_method ) == 'Normalization':
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96 print('Normalization')
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97 ##normalization
2
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98
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99 msidata <- normalize(msidata, method="tic")
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100
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101 #if $outputs.outputs_select == "quality_control":
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102 ### values for QC table:
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103 maxfeatures = length(features(msidata))
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104 medianpeaks = median(colSums(spectra(msidata)[]>0))
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105 medint = round(median(spectra(msidata)[]), digits=2)
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106 TICs = round(mean(colSums(spectra(msidata)[])), digits=1)
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107 normalized = c(maxfeatures, medianpeaks, medint, TICs)
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108 QC_numbers= cbind(QC_numbers, normalized)
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109 ### preparation for QC plots
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110 vectorofactions = append(vectorofactions, "normalized")
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111
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112 for (calibrant in inputcalibrants)
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113 {
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114 currentimage = image(msidata , mz=calibrant, strip = strip.custom(bg="lightgrey",
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115 par.strip.text=list(col="black", cex=.9)),lattice=TRUE,
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116 scales = list(draw = FALSE), plusminus = $outputs.plusminus_dalton, main="normalized")
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117
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118 assign(paste("normalized",calibrant, sep="_"), currentimage)
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119 }
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120
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121
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122 #end if
0
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123
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124 #elif str( $method.methods_conditional.preprocessing_method ) == 'Baseline_reduction':
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125 print('Baseline_reduction')
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126 ##baseline reduction
2
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127 msidata = reduceBaseline(msidata, method="median", blocks=$method.methods_conditional.blocks_baseline)
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128
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129 #if $outputs.outputs_select == "quality_control":
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130 maxfeatures = length(features(msidata))
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131 medianpeaks = median(colSums(spectra(msidata)[]>0))
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132 medint = round(median(spectra(msidata)[]), digits=2)
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133 TICs = round(mean(colSums(spectra(msidata)[])), digits=1)
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134 baseline= c(maxfeatures, medianpeaks, medint, TICs)
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135 QC_numbers= cbind(QC_numbers, baseline)
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136 ### preparation for QC plots
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137 vectorofactions = append(vectorofactions, "baseline_rem")
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138
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139 for (calibrant in inputcalibrants)
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140 {
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141 currentimage = image(msidata , mz=calibrant, strip = strip.custom(bg="lightgrey",
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142 par.strip.text=list(col="black", cex=.9)),lattice=TRUE,
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143 scales = list(draw = FALSE), plusminus = $outputs.plusminus_dalton, main="baseline removed")
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144
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145 assign(paste("baseline_rem",calibrant, sep="_"), currentimage)
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146 }
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147 #end if
0
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148
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149 #elif str( $method.methods_conditional.preprocessing_method ) == 'Smoothing':
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150 print('Smoothing')
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151 ## Smoothing
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152
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153 #if str( $method.methods_conditional.methods_for_smoothing.smoothing_method) == 'gaussian':
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154 print('gaussian smoothing')
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155 msidata <- smoothSignal(msidata, method="$method.methods_conditional.methods_for_smoothing.smoothing_method", window=$method.methods_conditional.window_smoothing, sd = $method.methods_conditional.methods_for_smoothing.sd_gaussian)
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156 #elif str( $method.methods_conditional.methods_for_smoothing.smoothing_method) == 'sgolay':
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157 print('sgolay smoothing')
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158 msidata <- smoothSignal(msidata, method="$method.methods_conditional.methods_for_smoothing.smoothing_method", window=$method.methods_conditional.window_smoothing, order = $method.methods_conditional.methods_for_smoothing.order_of_filters)
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159 #elif str($method.methods_conditional.methods_for_smoothing.smoothing_method) == 'ma':
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160 print('sgolay smoothing')
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161 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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162 #end if
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163
2
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164 #if $outputs.outputs_select == "quality_control":
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165 maxfeatures = length(features(msidata))
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166 medianpeaks = median(colSums(spectra(msidata)[]>0))
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167 medint = round(median(spectra(msidata)[]), digits=2)
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168 TICs = round(mean(colSums(spectra(msidata)[])), digits=1)
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169 smoothed= c(maxfeatures, medianpeaks, medint, TICs)
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170 QC_numbers= cbind(QC_numbers, smoothed)
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171 ### preparation for QC plots
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172 vectorofactions = append(vectorofactions, "smoothed")
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173
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174 for (calibrant in inputcalibrants)
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175 {
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176 currentimage = image(msidata , mz=calibrant, strip = strip.custom(bg="lightgrey",
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177 par.strip.text=list(col="black", cex=.9)),lattice=TRUE,
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178 scales = list(draw = FALSE), plusminus = $outputs.plusminus_dalton, main="smoothed")
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179
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180 assign(paste("smoothed",calibrant, sep="_"), currentimage)
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181 }
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182 #end if
1
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183
0
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184 #elif str( $method.methods_conditional.preprocessing_method) == 'Peak_picking':
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185 print('Peak_picking')
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186 ## Peakpicking
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187
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188 #if str( $method.methods_conditional.methods_for_picking.picking_method) == 'adaptive':
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189 print('adaptive peakpicking')
2
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190 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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191
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192 #elif str( $method.methods_conditional.methods_for_picking.picking_method) == 'limpic':
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193 print('limpic peakpicking')
2
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194 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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195
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196 #elif str( $method.methods_conditional.methods_for_picking.picking_method) == 'simple':
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197 print('simple peakpicking')
2
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198 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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199 #end if
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200
2
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201 #if $outputs.outputs_select == "quality_control":
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202 maxfeatures = length(features(msidata))
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203 medianpeaks = median(colSums(spectra(msidata)[]>0))
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204 medint = round(median(spectra(msidata)[]), digits=2)
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205 TICs = round(mean(colSums(spectra(msidata)[])), digits=1)
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206 picked= c(maxfeatures, medianpeaks, medint, TICs)
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207 QC_numbers= cbind(QC_numbers, picked)
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208 ### preparation for QC plots
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209 vectorofactions = append(vectorofactions, "picked")
1
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210
2
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211 for (calibrant in inputcalibrants)
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212 {
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213 currentimage = image(msidata , mz=calibrant, strip = strip.custom(bg="lightgrey",
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214 par.strip.text=list(col="black", cex=.9)),lattice=TRUE,
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215 scales = list(draw = FALSE), plusminus = $outputs.plusminus_dalton, main="picked")
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216
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217 assign(paste("picked",calibrant, sep="_"), currentimage)
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218 }
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219 #end if
1
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220
0
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221 #elif str( $method.methods_conditional.preprocessing_method ) == 'Peak_alignment':
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222 print('Peak_alignment')
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223 ## Peakalignment
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224
2
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225 #if str( $method.methods_conditional.align_ref_type.align_reference_datatype) == 'align_noref':
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226 align_peak_reference = msidata
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227
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228 #elif str( $method.methods_conditional.align_ref_type.align_reference_datatype) == 'align_table':
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229 align_reference_table = read.delim("$method.methods_conditional.align_ref_type.align_peaks_table", header = FALSE, na.strings=c("","NA"), stringsAsFactors = FALSE)
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230
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231 align_reference_column = align_reference_table[,$method.methods_conditional.align_ref_type.align_mass_column]
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232
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233 align_peak_reference = align_reference_column[align_reference_column>=min(mz(msidata)) & align_reference_column<=max(mz(msidata))]
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234 if (length(align_peak_reference) == 0)
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235 {align_peak_reference = 0
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236 }
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237
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238
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239
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240 #### if length <0: align_peak_reference = 0
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241
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242
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243 #elif str( $method.methods_conditional.align_ref_type.align_reference_datatype) == 'align_msidata_ref':
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244 loadRData <- function(fileName){
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245 #loads an RData file, and returns it
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246 load(fileName)
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247 get(ls()[ls() != "fileName"])
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248 }
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249 align_peak_reference = loadRData('$method.methods_conditional.align_ref_type.align_peaks_msidata')
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250 #end if
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251
0
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252 #if str( $method.methods_conditional.methods_for_alignment.alignment_method) == 'diff':
2
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253 print('diff peakalignment')
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254 msidata = peakAlign(msidata, method='$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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255
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256 #elif str( $method.methods_conditional.methods_for_alignment.alignment_method) == 'DP':
2
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257 print('DPpeakalignment')
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258 msidata = peakAlign(msidata, method='$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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259 #end if
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260
2
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261 #if $outputs.outputs_select == "quality_control":
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262 maxfeatures = length(features(msidata))
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263 medianpeaks = median(colSums(spectra(msidata)[]>0))
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264 medint = round(median(spectra(msidata)[]), digits=2)
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265 TICs = round(mean(colSums(spectra(msidata)[])), digits=1)
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266 aligned= c(maxfeatures, medianpeaks, medint, TICs)
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267 QC_numbers= cbind(QC_numbers, aligned)
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268 ### preparation for QC plots
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269 vectorofactions = append(vectorofactions, "aligned")
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270
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271 for (calibrant in inputcalibrants)
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272 {
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273 currentimage = image(msidata , mz=calibrant, strip = strip.custom(bg="lightgrey",
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274 par.strip.text=list(col="black", cex=.9)),lattice=TRUE,
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275 scales = list(draw = FALSE), plusminus = $outputs.plusminus_dalton, main="aligned")
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276
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277 assign(paste("aligned",calibrant, sep="_"), currentimage)
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278 }
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279 #end if
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280
0
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281 #elif str( $method.methods_conditional.preprocessing_method) == 'Peak_filtering':
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282 print('Peak_filtering')
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283 msidata = peakFilter(msidata, method='freq', freq.min = $method.methods_conditional.frequ_filtering)
2
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284
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285 #if $outputs.outputs_select == "quality_control":
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286 maxfeatures = length(features(msidata))
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287 medianpeaks = median(colSums(spectra(msidata)[]>0))
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288 medint = round(median(spectra(msidata)[]), digits=2)
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289 TICs = round(mean(colSums(spectra(msidata)[])), digits=1)
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290 filtered= c(maxfeatures, medianpeaks, medint, TICs)
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291 QC_numbers= cbind(QC_numbers, filtered)
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292 ### preparation for QC plots
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293 vectorofactions = append(vectorofactions, "filtered")
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294
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295 for (calibrant in inputcalibrants)
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296 {
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297 currentimage = image(msidata , mz=calibrant, strip = strip.custom(bg="lightgrey",
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298 par.strip.text=list(col="black", cex=.9)),lattice=TRUE,
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299 scales = list(draw = FALSE), plusminus = $outputs.plusminus_dalton, main="filtered")
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300
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301 assign(paste("filtered",calibrant, sep="_"), currentimage)
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302 }
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303 #end if
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304
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305 #elif str( $method.methods_conditional.preprocessing_method) == 'Data_reduction':
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306 print('Data_reduction')
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307
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308 #if str( $method.methods_conditional.methods_for_reduction.reduction_method) == 'bin':
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309 print('bin reduction')
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310 msidata = reduceDimension(msidata, method="bin", width=$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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311
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312 #elif str( $method.methods_conditional.methods_for_reduction.reduction_method) == 'resample':
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313 print('resample reduction')
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314 msidata = reduceDimension(msidata, method="resample", step=$method.methods_conditional.methods_for_reduction.resample_step)
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315
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316 #elif str( $method.methods_conditional.methods_for_reduction.reduction_method) == 'peaks':
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317 print('peaks reduction')
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318
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319 #if str( $method.methods_conditional.methods_for_reduction.ref_type.reference_datatype) == 'table':
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320 reference_table = read.delim("$method.methods_conditional.methods_for_reduction.ref_type.peaks_table", header = FALSE, na.strings=c("","NA"), stringsAsFactors = FALSE)
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321 reference_column = reference_table[,$method.methods_conditional.methods_for_reduction.ref_type.mass_column]
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322 peak_reference = reference_column[reference_column>min(mz(msidata)) & reference_column<max(mz(msidata))]
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323
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324 #elif str( $method.methods_conditional.methods_for_reduction.ref_type.reference_datatype) == 'msidata_ref':
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325 loadRData <- function(fileName){
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326 #loads an RData file, and returns it
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327 load(fileName)
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328 get(ls()[ls() != "fileName"])
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329 }
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330 peak_reference = loadRData('$method.methods_conditional.methods_for_reduction.ref_type.peaks_msidata')
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331 #end if
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332 msidata = reduceDimension(msidata, method="peaks", ref=peak_reference, type="$method.methods_conditional.methods_for_reduction.peaks_type")
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333 #end if
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334
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335 #if $outputs.outputs_select == "quality_control":
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336 maxfeatures = length(features(msidata))
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337 medianpeaks = median(colSums(spectra(msidata)[]>0))
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338 medint = round(median(spectra(msidata)[]), digits=2)
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339 TICs = round(mean(colSums(spectra(msidata)[])), digits=1)
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340 reduced= c(maxfeatures, medianpeaks, medint, TICs)
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341 QC_numbers= cbind(QC_numbers, reduced)
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342 ### preparation for QC plots
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343 vectorofactions = append(vectorofactions, "reduced")
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344
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345 for (calibrant in inputcalibrants)
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346 {
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347 currentimage = image(msidata , mz=calibrant, strip = strip.custom(bg="lightgrey",
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348 par.strip.text=list(col="black", cex=.9)),lattice=TRUE,
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349 scales = list(draw = FALSE), plusminus = $outputs.plusminus_dalton, main="reduced")
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350
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351 assign(paste("reduced",calibrant, sep="_"), currentimage)
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352 }
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353 #end if
0
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354 #end if
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355 #end for
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356
2
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357 ####################################################### Outputs: RData, tabular and QC report ######################################################
1
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358
2
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359
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360 ## save as (.RData)
0
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361 save(msidata, file="$msidata_preprocessed")
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362
2
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363
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364 #if $output_matrix:
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365
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366
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367 if (length(features(msidata))> 0)
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368 {
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369
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370 ## save as intensity matrix
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371
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372 spectramatrix = spectra(msidata)
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373 rownames(spectramatrix) = mz(msidata)
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374 newmatrix = rbind(pixels(msidata), spectramatrix)
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375 write.table(newmatrix[2:nrow(newmatrix),], file="$matrixasoutput", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t")
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376
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377 }else{
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378 print("file has no features left")
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379 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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380 }
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381
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382 #end if
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383
1
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384
2
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385 #if $outputs.outputs_select == "quality_control":
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386
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387 rownames(QC_numbers) = c("# features", "median # peaks", "median intensity", "median TIC")
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388 grid.table(t(QC_numbers))
1
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389
2
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390 for (calibrant in inputcalibrants)
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391 {
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392 imagelist = list()
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393
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394 for (numberprepro in 1:length(vectorofactions)){
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395
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396 imagelist[[numberprepro]] = get(paste(vectorofactions[numberprepro],calibrant, sep="_"))
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397
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398
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399 }
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diff changeset
400
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
401 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
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
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
404
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
405 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
406
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
407 #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
408
0
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
409
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
410 ]]></configfile>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
411 </configfiles>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
412 <inputs>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
413 <param name="infile" type="data" format="imzml,rdata,analyze75"
2
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
414 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
415 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
416 <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
417 <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
418 <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
419 <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
420 <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
421 <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
422 <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
423 <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
424 <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
425 <option value="Data_reduction">Data reduction</option>
0
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
426 </param>
2
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
427
0
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
428 <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
429 <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
430 <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
431 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
432 </when>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
433 <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
434 <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
435 <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
436 <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
437 <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
438 <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
439 </param>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
440 <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
441 <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
442 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
443 </when>
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="sgolay">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
445 <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
446 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
447 </when>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
448 <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
449 <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
450 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
451 </when>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
452 </conditional>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
453 <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
454 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
455 </when>
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="Peak_picking">
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="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
458 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
459 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
460 <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
461 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
462 <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
463 <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
464 <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
465 <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
466 <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
467 <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
468 </param>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
469 <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
470 <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
471 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
472 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
473 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
474 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
475 </when>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
476 <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
477 <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
478 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
479 </when>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
480 <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
481 </conditional>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
482 </when>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
483 <when value="Peak_alignment">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
484 <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
485 <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
486 <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
487 <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
488 </param>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
489 <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
490 <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
491 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
492 <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
493 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
494 <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
495 <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
496 </param>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
497 </when>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
498 <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
499 <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
500 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
501 </when>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
502 </conditional>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
503 <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
504 <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
505 <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
506 <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
507 <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
508 </param>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
509 <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
510 <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
511 <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
512 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
513 <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
514 </when>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
515 <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
516 <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
517 </when>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
518 </conditional>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
519 </when>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
520 <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
521 <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
522 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
523 </when>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
524 <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
525 <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
526 <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
527 <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
528 <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
529 <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
530 </param>
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="bin">
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="bin_width" type="float" 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
533 label="The width of a bin in mz or ppm" help="Width must be greater than Range of mz values/Number of mz features"/>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
534 <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
535 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
536 <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
537 <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
538 </param>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
539 <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
540 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
541 <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
542 <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
543 </param>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
544 </when>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
545 <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
546 <param name="resample_step" type="float" 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
547 label="The step size in mz" help="Step size must be greater than Range of mz values/Number of mz features"/>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
548 </when>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
549 <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
550 <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
551 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
552 <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
553 <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
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 <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
556 <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
557 <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
558 <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
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 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
561 <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
562 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
563 <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
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="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
566 <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
567 </when>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
568 </conditional>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
569 </when>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
570 </conditional>
0
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
571 </when>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
572 </conditional>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
573 </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
574 <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
575 <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
576 <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
577 <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
578 </param>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
579 <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
580 <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
581 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
582 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
583 <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
584 <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
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 <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
587 </conditional>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
588 <param name="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
589 </inputs>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
590 <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
591 <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
592 <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
593 <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
594 </data>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
595 <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
596 <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
597 </data>
0
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
598 </outputs>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
599 <tests>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
600 <test>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
601 <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
602 <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
603 <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
604 </param>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
605 <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
606 <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
607 <param name="preprocessing_method" value="Normalization" />
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
608 </conditional>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
609 </repeat>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
610 <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
611 <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
612 <param name="preprocessing_method" value="Smoothing" />
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
613 <conditional name="methods_for_smoothing">
1
641316f29395 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 0
diff changeset
614 <param name="smoothing_method" value="gaussian" />
0
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
615 </conditional>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
616 </conditional>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
617 </repeat>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
618 <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
619 <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
620 <param name="preprocessing_method" 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
621 <conditional name="methods_for_picking">
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
622 <param name="picking_method" value="adaptive" />
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
623 </conditional>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
624 <param name="blocks_picking" value="3" />
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
625 <param name="window_picking" value="3" />
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
626 </conditional>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
627 </repeat>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
628 <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
629 <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
630 <param name="preprocessing_method" 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
631 <conditional name="methods_for_alignment">
1
641316f29395 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 0
diff changeset
632 <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
633 </conditional>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
634 </conditional>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
635 </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
636 <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
637 <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
638 <param name="preprocessing_method" 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
639 <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
640 </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
641 </repeat>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
642 <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
643 <param name="output_matrix" value="True"/>
0
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
644 <output name="msidata_preprocessed" file="preprocessing_results1.RData" compare="sim_size" />
1
641316f29395 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 0
diff changeset
645 <output name="matrixasoutput" file="preprocessing_results1.txt" />
0
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
646 </test>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
647 <test>
1
641316f29395 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 0
diff changeset
648 <param name="infile" value="example_continous.RData" ftype="rdata"/>
0
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
649 <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
650 <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
651 <param name="preprocessing_method" 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
652 <param name="blocks_picking" value="3" />
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
653 <param name="window_picking" value="5" />
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
654 <param name="methods_for_picking" value="simple" />
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
655 </conditional>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
656 </repeat>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
657 <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
658 <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
659 <param name="preprocessing_method" 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
660 <param name="methods_for_alignment" value="DP" />
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
661 </conditional>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
662 </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
663 <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
664 <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
665 <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
666 <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
667 <param name="output_matrix" value="True"/>
0
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
668 <output name="msidata_preprocessed" file="preprocessing_results2.RData" compare="sim_size" />
1
641316f29395 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 0
diff changeset
669 <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
670 <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
671 </test>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
672 <test>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
673 <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
674 <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
675 <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
676 <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
677 </param>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
678 <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
679 <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
680 <param name="preprocessing_method" value="Normalization" />
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
681 </conditional>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
682 </repeat>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
683 <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
684 <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
685 <param name="preprocessing_method" 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
686 <param name="blocks_picking" value="3" />
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
687 <param name="window_picking" value="5" />
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
688 <param name="methods_for_picking" value="limpic" />
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
689 </conditional>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
690 </repeat>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
691 <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
692 <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
693 <param name="preprocessing_method" 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
694 <param name="methods_for_alignment" value="diff" />
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
695 </conditional>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
696 </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
697 <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
698 <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
699 <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
700 <param name="plusminus_dalton" value="0.25"/>
0
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
parents:
diff changeset
701 <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
702 <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
703 </test>
2
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
704 <test>
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="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
706 <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
707 <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
708 <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
709 </param>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
710 <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
711 <conditional name="methods_conditional">
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
712 <param name="preprocessing_method" value="Normalization" />
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
713 </conditional>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
714 </repeat>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
715 <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
716 <conditional name="methods_conditional">
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
717 <param name="preprocessing_method" 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
718 <param name="bin_width" value="0.1" />
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
719 </conditional>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
720 </repeat>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
721 <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
722 <param name="output_matrix" value="True"/>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
723 <output name="msidata_preprocessed" file="preprocessing_results4.RData" 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
724 <output name="matrixasoutput" file="preprocessing_results4.txt" />
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
725 </test>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
726 <test>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
diff changeset
727 <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
728 <composite_data value="Example_Continuous.imzML"/>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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729 <composite_data value="Example_Continuous.ibd"/>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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730 </param>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
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731 <repeat name="methods">
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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732 <conditional name="methods_conditional">
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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733 <param name="preprocessing_method" value="Data_reduction" />
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 1
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734 <param name="step_width" value="0.1" />
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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735 </conditional>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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736 </repeat>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
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737 <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
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738 <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
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739 <param name="calibrants_column" value="1"/>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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740 <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
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741 <param name="output_matrix" value="True"/>
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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742 <output name="msidata_preprocessed" file="preprocessing_results5.RData" compare="sim_size" />
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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743 <output name="matrixasoutput" file="preprocessing_results5.txt" />
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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744 <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
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745 </test>
0
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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746 </tests>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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747 <help>
1
641316f29395 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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748 <![CDATA[
0
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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749 Cardinal is an R package that implements statistical & computational tools for analyzing mass spectrometry imaging datasets.
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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750
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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751 **Preprocessing steps:**
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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752
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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753 - Smoothening: Smoothing of the mass peaks reduces noise and improves peak detection
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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754 - 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
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755 - Baseline reduction: Baseline reduction removes backgroundintensity generated by chemical noise (common in MALDI datasets)
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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756 - Peak picking: relevant peaks are picked while noise-peaks are removed
2
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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757 - Peak alignment: after peak picking, mz inaccuracies are removed by alignment of same peaks to a common mz value
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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758 - Peak filtering: after peak picking and alignment, removes peaks that occur infrequently, such as those which only occur in a small proportion of pixels. If not sure which cutoff to chose run qualitycontrol first and decide according to the zero value plot.
55e081b9f6ac planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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759 - Data reduction: binning, resampling or peak filtering to reduce data
0
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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760 ]]>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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761 </help>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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762 <citations>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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763 <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
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764 </citations>
133a921f4ef5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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765 </tool>