Mercurial > repos > galaxyp > cardinal_preprocessing

annotate preprocessing.xml @ 12:274e81434593 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
author galaxyp
date Wed, 19 Apr 2023 22:29:26 +0000
parents aa479a0cfb43
children a9b90620b7a4
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274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
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1 <tool id="cardinal_preprocessing" name="MSI preprocessing" version="@VERSION@.1">
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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 <macros>
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6 <import>macros.xml</import>
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7 </macros>
7
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8 <expand macro="requirements">
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9 <requirement type="package" version="2.3">r-gridextra</requirement>
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10 <requirement type="package" version="3.4.0">r-ggplot2</requirement>
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11 <requirement type="package" version="3.40.0">bioconductor-sva</requirement>
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12 <requirement type="package" version="1.1.0.1">r-randomcolor</requirement>
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13 </expand>
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14 <command detect_errors="exit_code">
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15 <![CDATA[
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17 @INPUT_LINKING@
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18 cat '${cardinal_preprocessing}' &&
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19 Rscript '${cardinal_preprocessing}' &&
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21 mkdir $outfile_imzml.files_path &&
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22 mv ./out.imzML "${os.path.join($outfile_imzml.files_path, 'imzml')}" | true &&
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23 mv ./out.ibd "${os.path.join($outfile_imzml.files_path, 'ibd')}" | true &&
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24 echo "imzML file:" > $outfile_imzml &&
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25 ls -l "$outfile_imzml.files_path" >> $outfile_imzml
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27 ]]>
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28 </command>
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29 <configfiles>
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30 <configfile name="cardinal_preprocessing"><![CDATA[
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32 ################################# load libraries and read file #################
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34 ## set CPU, default = 1
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36 if (Sys.getenv("GALAXY_SLOTS")!="")
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37 {
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38 number_cpu = 1 ## default = 1
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39 }else{
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40 number_cpu = as.numeric(Sys.getenv("GALAXY_SLOTS")) ##cpu set by Galaxy
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41 }
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0
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43 library(Cardinal)
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44 library(gridExtra)
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45 library(ggplot2)
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46 library(sva)
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47 library(randomcoloR)
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50 @READING_MSIDATA_FULLY_COMPATIBLE@
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53 ## remove duplicated coordinates, otherwise peak picking and log2 transformation will fail
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55 ## set variable to False
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56 #set $used_peak_picking = False
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57 #set $used_peak_alignment = False
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58 #set $continuous_format = False
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61 if (ncol(msidata)>0 & nrow(msidata) >0){
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63 ## start QC report
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65 pdf("Preprocessing.pdf", fonts = "Times", pointsize = 12)
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66 plot(0,type='n',axes=FALSE,ann=FALSE)
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67 title(main=paste("Quality control during preprocessing \n", "Filename:", "$infile.display_name"))
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68
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69 ######################### preparations for QC report #################
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71 maxfeatures =nrow(msidata)
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72 pixelcount = ncol(msidata)
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73 minmz = round(min(mz(msidata)), digits=2)
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74 maxmz = round(max(mz(msidata)), digits=2)
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75 QC_numbers= data.frame(inputdata = c(minmz, maxmz,maxfeatures, pixelcount))
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76 vectorofactions = "inputdata"
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77 ## Choose random spectra for QC plots
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78 random_spectra = sample(pixels(msidata), 4, replace=FALSE)
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79 par(oma=c(0,0,2,0))
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80 print(plot(msidata, pixel=random_spectra, col="black"))
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81 title("Input spectra", outer=TRUE, line=0)
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82
0
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83 ############################### Preprocessing steps ###########################
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84 ###############################################################################
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85
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86 #for $method in $methods:
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87
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88 ############################### Normalization ###########################
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89
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90 #if str( $method.methods_conditional.preprocessing_method ) == 'Normalization':
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91 print('Normalization')
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92 ##normalization
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93
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94 msidata = normalize(msidata, method="$method.methods_conditional.methods_for_normalization.normalization_method")
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95 msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))
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96
0
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97
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98 ############################### QC ###########################
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99
2
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100 maxfeatures =nrow(msidata)
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101 pixelcount = ncol(msidata)
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102 minmz = round(min(mz(msidata)), digits=2)
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103 maxmz = round(max(mz(msidata)), digits=2)
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104 normalized = c(minmz, maxmz,maxfeatures, pixelcount)
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105 QC_numbers= cbind(QC_numbers, normalized)
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106 vectorofactions = append(vectorofactions, "normalized")
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107 print(plot(msidata, pixel=random_spectra, col="black"))
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108 title("Spectra after normalization", outer=TRUE, line=0)
0
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109
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110 ############################### Baseline reduction ###########################
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111
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112 #elif str( $method.methods_conditional.preprocessing_method ) == 'Baseline_reduction':
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113 print('Baseline_reduction')
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114 ##baseline reduction
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115
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116 msidata = reduceBaseline(msidata, method="median", blocks=$method.methods_conditional.blocks_baseline, spar=$method.methods_conditional.spar_baseline)
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117 msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))
0
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118
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119 ############################### QC ###########################
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120
2
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121 maxfeatures =nrow(msidata)
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122 pixelcount = ncol(msidata)
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123 minmz = round(min(mz(msidata)), digits=2)
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124 maxmz = round(max(mz(msidata)), digits=2)
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125 baseline = c(minmz, maxmz,maxfeatures, pixelcount)
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126 QC_numbers= cbind(QC_numbers, baseline)
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127 vectorofactions = append(vectorofactions, "baseline red.")
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128 print(plot(msidata, pixel=random_spectra, col="black"))
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129 title("Spectra after baseline reduction", outer=TRUE, line=0)
0
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130
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131 ############################### Smoothing ###########################
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132
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133 #elif str( $method.methods_conditional.preprocessing_method ) == 'Smoothing':
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134 print('Smoothing')
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135 ## Smoothing
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136
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137 #if str( $method.methods_conditional.methods_for_smoothing.smoothing_method) == 'gaussian':
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138 print('gaussian smoothing')
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139
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140 msidata = smoothSignal(msidata, method="$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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141 msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))
0
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142
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143 #elif str( $method.methods_conditional.methods_for_smoothing.smoothing_method) == 'sgolay':
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144 print('sgolay smoothing')
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145
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146 msidata = smoothSignal(msidata, method="$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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147 msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))
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148
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149 ## if selected replace negative intensities with zero
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150 #if $method.methods_conditional.methods_for_smoothing.replace_negatives:
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151 ## bring spectra matrix to disk
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152 spectra_df = as.matrix(spectra(msidata))
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153 spectra_df[spectra_df<0] = 0
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154 spectra(msidata) = spectra_df
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155 #end if
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156
0
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157 #elif str($method.methods_conditional.methods_for_smoothing.smoothing_method) == 'ma':
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158 print('moving average smoothing')
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159
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160 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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161 msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))
0
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162
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163 #end if
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164
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165 ############################### QC ###########################
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166
2
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167 maxfeatures =nrow(msidata)
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168 pixelcount = ncol(msidata)
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169 minmz = round(min(mz(msidata)), digits=2)
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170 maxmz = round(max(mz(msidata)), digits=2)
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171 smoothed = c(minmz, maxmz,maxfeatures, pixelcount)
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172 QC_numbers= cbind(QC_numbers, smoothed)
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173 vectorofactions = append(vectorofactions, "smoothed")
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174 print(plot(msidata, pixel=random_spectra, col="black"))
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175 title("Spectra after smoothing", outer=TRUE, line=0)
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176
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177
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178 ############################### Mz alignment ###########################
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179
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180 #elif str( $method.methods_conditional.preprocessing_method ) == 'mz_alignment':
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181 print('m/z alignment')
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182 ## M/z alignment
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183
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184 #if str( $method.methods_conditional.mzalign_ref_type.align_reference_datatype) == 'align_table':
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185
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186 reference_mz = read.delim("$method.methods_conditional.mzalign_ref_type.mz_tabular", header = $method.methods_conditional.mzalign_ref_type.feature_header, stringsAsFactors = FALSE)
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187 reference_mz = reference_mz[,$method.methods_conditional.mzalign_ref_type.feature_column]
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188
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189 msidata = mzAlign(msidata, ref=reference_mz, tolerance = $method.methods_conditional.alignment_tol, units = "$method.methods_conditional.alignment_units", quantile = $method.methods_conditional.quantile, span = $method.methods_conditional.span)
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190
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191
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192 #elif str( $method.methods_conditional.mzalign_ref_type.align_reference_datatype) == 'align_noref':
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193
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194 msidata = mzAlign(msidata,tolerance = $method.methods_conditional.alignment_tol, units = "$method.methods_conditional.alignment_units", quantile = $method.methods_conditional.quantile, span = $method.methods_conditional.span)
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195
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196 #end if
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197
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198 msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))
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199
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200 ############################### QC ###########################
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201
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202 maxfeatures =nrow(msidata)
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203 pixelcount = ncol(msidata)
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204 minmz = round(min(mz(msidata)), digits=2)
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205 maxmz = round(max(mz(msidata)), digits=2)
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206 mz_aligned = c(minmz, maxmz,maxfeatures, pixelcount)
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207 QC_numbers= cbind(QC_numbers, mz_aligned)
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208 vectorofactions = append(vectorofactions, "mz aligned")
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209 print(plot(msidata, pixel=random_spectra, col="black"))
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210 title("Spectra after m/z alignment", outer=TRUE, line=0)
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211
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212
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213 ############################### Mz recalibration ###########################
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214
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215 #elif str( $method.methods_conditional.preprocessing_method ) == 'mz_recalibration':
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216 print('m/z recalibration')
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217 ## M/z recalibration
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218
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219 reference_mz = read.delim("$method.methods_conditional.mz_tabular", header = $method.methods_conditional.feature_header, stringsAsFactors = FALSE)
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220 reference_mz = reference_mz[,$method.methods_conditional.feature_column]
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221
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222 msidata = mzAlign(msidata, ref=reference_mz, tolerance = $method.methods_conditional.alignment_tol, units = "$method.methods_conditional.alignment_units", quantile = $method.methods_conditional.quantile, span = $method.methods_conditional.span)
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223
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224 msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))
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225
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226 ## remove the reference peaks data to allow proper peak alignment afterwards
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227 metadata(featureData(msidata))['reference peaks'] <- NULL
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228
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229 ############################### QC ###########################
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230
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231 maxfeatures =nrow(msidata)
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232 pixelcount = ncol(msidata)
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233 minmz = round(min(mz(msidata)), digits=2)
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234 maxmz = round(max(mz(msidata)), digits=2)
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235 mz_recal = c(minmz, maxmz,maxfeatures, pixelcount)
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236 QC_numbers= cbind(QC_numbers, mz_recal)
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237 vectorofactions = append(vectorofactions, "mz recalibrated")
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238 print(plot(msidata, pixel=random_spectra, col="black"))
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239 title("Spectra after m/z recalibration", outer=TRUE, line=0)
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240
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241
0
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242 ############################### Peak picking ###########################
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243
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244 #elif str( $method.methods_conditional.preprocessing_method) == 'Peak_picking':
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245 #set $used_peak_picking = True
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246 print('Peak_picking')
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247 ## Peakpicking
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248
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249 #if str( $method.methods_conditional.methods_for_picking.picking_method) == 'adaptive':
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250 print('adaptive peakpicking')
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251
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252 msidata = peakPick(msidata, window = $method.methods_conditional.window_picking, blocks = $method.methods_conditional.blocks_picking, method='$method.methods_conditional.methods_for_picking.picking_method', SNR=$method.methods_conditional.SNR_picking_method, spar=$method.methods_conditional.methods_for_picking.spar_picking)
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253
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254 #elif str( $method.methods_conditional.methods_for_picking.picking_method) == 'mad':
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255 print('mad peakpicking')
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256
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257 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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258
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259 #elif str( $method.methods_conditional.methods_for_picking.picking_method) == 'simple':
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260 print('simple peakpicking')
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261
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262 msidata = peakPick(msidata, window = $method.methods_conditional.window_picking, blocks = $method.methods_conditional.blocks_picking, method='$method.methods_conditional.methods_for_picking.picking_method', SNR=$method.methods_conditional.SNR_picking_method)
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263
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264 #end if
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265 msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))
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266
0
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267
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268 ############################### QC ###########################
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269
2
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270 maxfeatures =nrow(msidata)
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271 pixelcount = ncol(msidata)
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272 minmz = round(min(mz(msidata)), digits=2)
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273 maxmz = round(max(mz(msidata)), digits=2)
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274 picked = c(minmz, maxmz,maxfeatures, pixelcount)
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275 QC_numbers= cbind(QC_numbers, picked)
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276 vectorofactions = append(vectorofactions, "picked")
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277 print(plot(msidata, pixel=random_spectra, col="black"))
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278 title("Spectra after peak picking", outer=TRUE, line=0)
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279
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280 ############################### Peak alignment ###########################
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281
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282 #elif str( $method.methods_conditional.preprocessing_method ) == 'Peak_alignment':
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283 #set $used_peak_alignment = True
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284 print('Peak_alignment')
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285 ## Peakalignment
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286
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287 #if str( $method.methods_conditional.align_ref_type.align_reference_datatype) == 'align_table':
0
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288
3
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289 align_reference_table = read.delim("$method.methods_conditional.align_ref_type.mz_tabular", header = $method.methods_conditional.align_ref_type.feature_header, stringsAsFactors = FALSE)
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290
3
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291 align_reference_column = align_reference_table[,$method.methods_conditional.align_ref_type.feature_column]
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292
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293 align_peak_reference = as.numeric(align_reference_column[align_reference_column>=min(mz(msidata)) & align_reference_column<=max(mz(msidata))])
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294 if (length(align_peak_reference) == 0)
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295 {align_peak_reference = 0}
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296
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297 msidata = peakAlign(msidata,tolerance =$method.methods_conditional.value_diffalignment, units = "$method.methods_conditional.units_diffalignment", ref=align_peak_reference)
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298
0
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299
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300 #elif str( $method.methods_conditional.align_ref_type.align_reference_datatype) == 'align_noref':
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301
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302 msidata = peakAlign(msidata,tolerance =$method.methods_conditional.value_diffalignment, units = "$method.methods_conditional.units_diffalignment")
0
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303
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304 #end if
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305
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306 msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))
0
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307
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308
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309 ############################### QC ###########################
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310
2
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311 maxfeatures =nrow(msidata)
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312 pixelcount = ncol(msidata)
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313 minmz = round(min(mz(msidata)), digits=2)
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314 maxmz = round(max(mz(msidata)), digits=2)
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315 aligned = c(minmz, maxmz,maxfeatures, pixelcount)
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316 QC_numbers= cbind(QC_numbers, aligned)
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317 vectorofactions = append(vectorofactions, "aligned")
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318 print(plot(msidata, pixel=random_spectra, col="black"))
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319 title("Spectra after alignment", outer=TRUE, line=0)
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320
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321 ############################### Peak filtering ###########################
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322
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323 #elif str( $method.methods_conditional.preprocessing_method) == 'Peak_filtering':
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324 print('Peak_filtering')
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325
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326 msidata = peakFilter(msidata, freq.min = $method.methods_conditional.frequ_filtering)
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327 msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))
0
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328
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329 ############################### QC ###########################
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330
2
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331 maxfeatures =nrow(msidata)
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332 pixelcount = ncol(msidata)
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333 minmz = round(min(mz(msidata)), digits=2)
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334 maxmz = round(max(mz(msidata)), digits=2)
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335 filtered = c(minmz, maxmz,maxfeatures, pixelcount)
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336 QC_numbers= cbind(QC_numbers, filtered)
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337 vectorofactions = append(vectorofactions, "filtered")
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338 print(plot(msidata, pixel=random_spectra, col="black"))
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339 title("Spectra after filtering", outer=TRUE, line=0)
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340
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341 ############################### Peak binning ###########################
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342
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343 #elif str( $method.methods_conditional.preprocessing_method) == 'Peak_binning':
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344 print('Peak_binning')
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345
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346 ## reading reference file
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347 reference_table = read.delim("$method.methods_conditional.mz_tabular", header = $method.methods_conditional.feature_header, stringsAsFactors = FALSE)
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348 reference_column = reference_table[,$method.methods_conditional.feature_column]
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349 peak_reference = reference_column[reference_column>min(mz(msidata)) & reference_column<max(mz(msidata))]
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350
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351 msidata = peakBin(msidata, ref = peak_reference, tolerance = $method.methods_conditional.peakbin_tol, units = "$method.methods_conditional.peakbin_units", type="$method.methods_conditional.peaks_type")
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352 msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))
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353
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354 ############################### QC ###########################
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355
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356 maxfeatures =nrow(msidata)
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357 pixelcount = ncol(msidata)
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358 minmz = round(min(mz(msidata)), digits=2)
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359 maxmz = round(max(mz(msidata)), digits=2)
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360 peak_binned = c(minmz, maxmz,maxfeatures, pixelcount)
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361 QC_numbers= cbind(QC_numbers, peak_binned)
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362 vectorofactions = append(vectorofactions, "peak binned")
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363 print(plot(msidata, pixel=random_spectra, col="black"))
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364 title("Spectra after peak binning", outer=TRUE, line=0)
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365
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366
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367 ############################### Mass binning ###########################
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368
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369 #elif str( $method.methods_conditional.preprocessing_method) == 'Mass_binning':
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370 print('mass binning')
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371
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372 #if str($method.methods_conditional.mz_range.features_filtering) == 'change_mz_range':
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373
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374 msidata = mse_bin = mzBin(msidata,resolution=$method.methods_conditional.bin_width, from=$method.methods_conditional.mz_range.min_mz, to=$method.methods_conditional.mz_range.max_mz, units="$method.methods_conditional.bin_units", fun="$method.methods_conditional.bin_fun")
0
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375
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376
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377 #elif str($method.methods_conditional.mz_range.features_filtering) == 'none':
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378
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379 msidata = mse_bin = mzBin(msidata,resolution=$method.methods_conditional.bin_width, units="$method.methods_conditional.bin_units", fun=$method.methods_conditional.bin_fun)
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380
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381 #elif str($method.methods_conditional.mz_range.features_filtering) == 'bin_to_reference':
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382
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383 bin_reference_mz = read.delim("$method.methods_conditional.mz_range.mz_tabular", header = $method.methods_conditional.mz_range.feature_header, stringsAsFactors = FALSE)
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384 bin_reference_mz = bin_reference_mz[,$method.methods_conditional.mz_range.feature_column]
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385
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386 msidata = mse_bin = mzBin(msidata,resolution=$method.methods_conditional.bin_width, units="$method.methods_conditional.bin_units", fun=$method.methods_conditional.bin_fun,
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387 ref=bin_reference_mz)
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388
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diff changeset
389 #end if
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390
e0bbaf9f7da0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
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391 msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))
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392
1
c8ab1b6f3834 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
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393 ## optional: replace NA with 0
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394 #if $method.methods_conditional.replace_NA_bin:
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395 ## count and replace NAs
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396 print(paste0("Number of NA that were set to zero after binning:",sum(is.na(spectra(msidata)))))
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397 spectra(msidata)[is.na(spectra(msidata))] = 0
1
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398 #end if
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399
0
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400 ############################### QC ###########################
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401
2
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402 maxfeatures =nrow(msidata)
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403 pixelcount = ncol(msidata)
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diff changeset
404 minmz = round(min(mz(msidata)), digits=2)
f29109d0d353 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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405 maxmz = round(max(mz(msidata)), digits=2)
f29109d0d353 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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406 reduced = c(minmz, maxmz,maxfeatures, pixelcount)
f29109d0d353 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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407 QC_numbers= cbind(QC_numbers, reduced)
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408 vectorofactions = append(vectorofactions, "reduced")
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409 print(plot(msidata, pixel=random_spectra, col="black"))
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410 title("Spectra after m/z binning", outer=TRUE, line=0)
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411
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412 ############################### Transformation ###########################
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
413
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
414 #elif str( $method.methods_conditional.preprocessing_method) == 'Transformation':
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
415 print('Transformation')
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
416
6
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
417 if (class(msidata) == "MSProcessedImagingExperiment"){
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
418 msidata = as(msidata, "MSContinuousImagingExperiment")
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
419 }
2
f29109d0d353 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
420
0
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
421 #if str( $method.methods_conditional.transf_conditional.trans_type) == 'log2':
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
422 print('log2 transformation')
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
423
2
f29109d0d353 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
424 ## replace 0 with NA to prevent Inf
10
aa479a0cfb43 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f"
galaxyp
parents: 9
diff changeset
425 spectra_df = as.matrix(spectra(msidata)) ## convert into R matrix
1
c8ab1b6f3834 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
426 spectra_df[spectra_df ==0] = NA
c8ab1b6f3834 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
427 print(paste0("Number of 0 which were converted into NA:",sum(is.na(spectra_df))))
c8ab1b6f3834 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
428 spectra(msidata) = spectra_df
c8ab1b6f3834 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
429 ## log transformation
c8ab1b6f3834 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
430 spectra(msidata) = log2(spectra(msidata))
c8ab1b6f3834 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
431 ## optional: replace NA with 0
c8ab1b6f3834 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
432 #if $method.methods_conditional.transf_conditional.replace_NA_trans:
4
58fb63423b0b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
433 spectra(msidata)[is.na(spectra(msidata))] = 0
1
c8ab1b6f3834 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
434 #end if
0
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
435
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
436 #elif str( $method.methods_conditional.transf_conditional.trans_type) == 'sqrt':
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
437 print('squareroot transformation')
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
438
6
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
439 spectra(msidata) = sqrt(spectra(msidata))
0
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
440
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
441 #end if
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
442
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
443 ############################### QC ###########################
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
444
2
f29109d0d353 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
445 maxfeatures =nrow(msidata)
f29109d0d353 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
446 pixelcount = ncol(msidata)
f29109d0d353 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
447 minmz = round(min(mz(msidata)), digits=2)
f29109d0d353 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
448 maxmz = round(max(mz(msidata)), digits=2)
f29109d0d353 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
449 transformed = c(minmz, maxmz,maxfeatures, pixelcount)
f29109d0d353 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
450 QC_numbers= cbind(QC_numbers, transformed)
f29109d0d353 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
451 vectorofactions = append(vectorofactions, "transformed")
9
e0bbaf9f7da0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents: 8
diff changeset
452 print(plot(msidata, pixel=random_spectra, col="black"))
3
0b6f4c09b6eb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2
galaxyp
parents: 2
diff changeset
453 title("Spectra after transformation", outer=TRUE, line=0)
0
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
454
12
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
455
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
456
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
457
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
458 ############################### ComBat batch correction ###########################
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
459
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
460 #elif str( $method.methods_conditional.preprocessing_method) == 'ComBat_batch_correction':
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
461 print('ComBat batch correction of centroided data')
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
462
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
463 ## load annotation tabular and define batch and condition column
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
464 annotation = read.delim("$method.methods_conditional.annotation_file", header=$method.methods_conditional.feature_header, sep="\t")
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
465 annotation_x = annotation[,$method.methods_conditional.x_column]
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
466 annotation_y = annotation[,$method.methods_conditional.y_column]
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
467 batch = annotation[,$method.methods_conditional.batch_column]
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
468 condition = annotation[,$method.methods_conditional.condition_column]
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
469
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
470 ### stop if not enough batches provided
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
471 tryCatch(
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
472 {
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
473
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
474 if (unique(batch<2))
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
475 {
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
476 stop(call.=FALSE)
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
477 }
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
478 },
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
479 error=function(cond) {
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
480 ## in case user provided an annotation tabular with less than two batches
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
481 message("Error in annotation tabular")
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
482 message("Possible problems: Annotation tabular file has not enough batch levels - to perform ComBat at least 2 batches and 2 pixels per batch are necessary)")
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
483 stop(call.=FALSE)
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
484 }
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
485 )
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
486
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
487 ## get intensity matrix from imzml file
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
488 intensity_matrix = as.matrix(iData(msidata))
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
489 mz_names = paste0("mz_", mz(msidata))
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
490 pixel_names = paste0("xy_", msidata@elementMetadata@coord@listData[["x"]], "_", msidata@elementMetadata@coord@listData[["y"]])
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
491 rownames(intensity_matrix) = mz_names
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
492 colnames(intensity_matrix) = pixel_names
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
493
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
494 ## reorder columns of intensity matrix to row order of batch column
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
495 rownames(annotation) = paste0("xy_", annotation_x, "_", annotation_y)
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
496 col_order = rownames(annotation)
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
497
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
498 ### stop if pixel/sample names (columns) in intensity matrix from imzml file don't match samples names (rows) in annotation tabular file
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
499 tryCatch(
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
500 {
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
501
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
502 if (all(colnames(intensity_matrix) %in% col_order == FALSE))
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
503 {
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
504 stop(call.=FALSE)
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
505 }
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
506 },
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
507 error=function(cond) {
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
508 ## in case pixel names (columns) from the imzml file don't match the pixel names in the annotation tabular file
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
509 message("Error in annotation tabular")
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
510 message("Possible problems: Annotation tabular file does not contain the correct pixel names (columns) from the imzml file)")
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
511 stop(call.=FALSE)
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
512 }
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
513 )
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
514
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
515 intensity_matrix = intensity_matrix[, col_order]
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
516 print("columns have been ordered to annotation row order")
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
517
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
518 ## execution of ComBat algorithm from sva package
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
519 combat_data = ComBat(dat = intensity_matrix, batch = batch, mod = NULL, par.prior = TRUE, prior.plots = FALSE)
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
520 print("Combat has been executed")
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
521
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
522 ## change intensity data of loaded imzml file after combat has been performed
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
523 iData(msidata) = as.matrix(combat_data)
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
524
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
525 ############################### QC ###########################
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
526
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
527 maxfeatures =nrow(msidata)
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
528 pixelcount = ncol(msidata)
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
529 minmz = round(min(mz(msidata)), digits=2)
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
530 maxmz = round(max(mz(msidata)), digits=2)
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
531 batch_corrected = c(minmz, maxmz, maxfeatures, pixelcount)
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
532 QC_numbers= cbind(QC_numbers, batch_corrected)
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
533 vectorofactions = append(vectorofactions, "batch_corrected")
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
534 print(plot(msidata, pixel=random_spectra, col="black"))
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
535 title("Spectra after ComBat batch correction", outer=TRUE, line=0)
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
536
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
537
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
538 ## PCA plot function and execution
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
539 combat_data = as.data.frame(combat_data)
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
540 intensity_data = as.data.frame(intensity_matrix)
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
541
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
542 ## PCA function
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
543 plot_PCA = function(input_data, condition, batch, title, color){
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
544 data <- input_data
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
545 pca_data <- prcomp(t(data[, seq_len(ncol(input_data))]))
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
546 pca_sdev <- pca_data[["sdev"]]
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
547 pca_data_perc <- round(100 * pca_sdev^2 / sum(pca_sdev^2), 1)
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
548 pca_components <- pca_data[["x"]]
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
549 df_pca_data <- data.frame(PC1 = pca_components[, 1], PC2 = pca_components[, 2], sample = colnames(input_data), condition = condition)
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
550 ggplot(df_pca_data, aes(PC1, PC2, color = as.factor(batch), shape = as.factor(condition))) +
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
551 ggtitle(title) +
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
552 geom_point(size = 4) +
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
553 stat_ellipse(aes(PC1, PC2, color = as.factor(batch), group = as.factor(batch)), type = "norm")+
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
554 scale_color_manual(values=color) +
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
555 theme_bw() +
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
556 theme(legend.position = "bottom", legend.box="vertical", plot.title = element_text(size = 12, hjust = 0.5), axis.title = element_text(size = 12), axis.text = element_text(size = 12, color = "black")) +
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
557 labs(x=paste0("PC1 (",pca_data_perc[1],")"), y=paste0("PC2 (",pca_data_perc[2],")")) +
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
558 labs(color = "Batches", shape = "Conditions")}
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
559
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
560 ## define colors
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
561 color_pal = distinctColorPalette(length(levels(as.factor(batch))))
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
562
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
563 ## execution of PCA plots
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
564 PCA_bc = plot_PCA(intensity_data, condition, batch, "before batch correction", color_pal)
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
565 PCA_ac = plot_PCA(combat_data, condition, batch, "batch corrected", color_pal)
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
566 print(PCA_bc)
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
567 print(PCA_ac)
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
568
0
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
569 #end if
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
570 #end for
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
571
1
c8ab1b6f3834 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
572 ############# Outputs: RData, imzml and QC report #############
0
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
573 ################################################################################
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
574
2
f29109d0d353 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
575 ## save msidata as imzML file, will only work if there is at least 1 m/z left
0
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
576
1
c8ab1b6f3834 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
577 if (nrow(msidata) > 0){
3
0b6f4c09b6eb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2
galaxyp
parents: 2
diff changeset
578 ## make sure that coordinates are integers
0b6f4c09b6eb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2
galaxyp
parents: 2
diff changeset
579 coord(msidata)\$y = as.integer(coord(msidata)\$y)
0b6f4c09b6eb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2
galaxyp
parents: 2
diff changeset
580 coord(msidata)\$x = as.integer(coord(msidata)\$x)
10
aa479a0cfb43 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f"
galaxyp
parents: 9
diff changeset
581 ## only continuous files can currently be exported
aa479a0cfb43 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f"
galaxyp
parents: 9
diff changeset
582 msidata = as(msidata, "MSContinuousImagingExperiment")
aa479a0cfb43 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f"
galaxyp
parents: 9
diff changeset
583 writeImzML(msidata, "out")
6
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
584 }
1
c8ab1b6f3834 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
585
0
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
586 plot(0,type='n',axes=FALSE,ann=FALSE)
2
f29109d0d353 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
587 rownames(QC_numbers) = c("min m/z", "max mz", "# features", "# spectra")
0
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
588 grid.table(t(QC_numbers))
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
589 dev.off()
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
590
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
591 }else{
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
592 print("inputfile has no intensities > 0")
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
593 }
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
594
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
595 ]]></configfile>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
596 </configfiles>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
597 <inputs>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
598 <expand macro="reading_msidata"/>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
599 <repeat name="methods" title="Preprocessing" min="1" max="50">
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
600 <conditional name="methods_conditional">
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
601 <param name="preprocessing_method" type="select" label="Preprocessing methods">
6
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
602 <option value="Normalization" selected="True">Intensity Normalization</option>
0
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
603 <option value="Baseline_reduction">Baseline Reduction</option>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
604 <option value="Smoothing">Peak smoothing</option>
8
413a1b74f496 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
galaxyp
parents: 7
diff changeset
605 <option value="mz_alignment">m/z alignment</option>
10
aa479a0cfb43 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f"
galaxyp
parents: 9
diff changeset
606 <option value="mz_recalibration">m/z recalibration</option>
0
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
607 <option value="Peak_picking">Peak picking</option>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
608 <option value="Peak_alignment">Peak alignment</option>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
609 <option value="Peak_filtering">Peak filtering</option>
7
173070dafe95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 6
diff changeset
610 <option value="Peak_binning">Peak binning to reference peaks</option>
9
e0bbaf9f7da0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents: 8
diff changeset
611 <option value="Mass_binning">m/z binning</option>
0
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
612 <option value="Transformation">Transformation</option>
12
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
613 <option value="ComBat_batch_correction">ComBat batch correction of centroided data</option>
0
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
614 </param>
6
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
615 <when value="Normalization">
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
616 <conditional name="methods_for_normalization">
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
617 <param name="normalization_method" type="select" label="Normalization method">
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
618 <option value="tic" selected="True">TIC</option>
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
619 <option value="rms">RMS</option>
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
620 </param>
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
621 <when value="tic"/>
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
622 <when value="rms"/>
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
623 </conditional>
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
624 </when>
0
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
625 <when value="Baseline_reduction">
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
626 <param name="blocks_baseline" type="integer" value="500"
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
627 label="Blocks"/>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
628 <param name="spar_baseline" type="float" value="1.0" label="Spar value"
7
173070dafe95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 6
diff changeset
629 help="Smoothing parameter for the spline smoothing
0
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
630 applied to the spectrum in order to decide the cutoffs
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
631 for throwing away false noise spikes that might occur inside peaks"/>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
632 </when>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
633 <when value="Smoothing">
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
634 <conditional name="methods_for_smoothing">
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
635 <param name="smoothing_method" type="select" label="Smoothing method">
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
636 <option value="gaussian" selected="True">gaussian</option>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
637 <option value="sgolay">Savitsky-Golay</option>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
638 <option value="ma">moving average</option>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
639 </param>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
640 <when value="gaussian">
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
641 <param name="sd_gaussian" type="float" value="2"
4
58fb63423b0b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
642 label="The standard deviation for the Gaussian kernel. Default = window/4"/>
0
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
643 </when>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
644 <when value="sgolay">
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
645 <param name="order_of_filters" type="integer" value="3"
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
646 label="The order of the smoothing filter, must be smaller than window size"/>
4
58fb63423b0b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
647 <param name="replace_negatives" type="boolean" label="Replace negative intensities with 0" truevalue="TRUE" falsevalue="FALSE" checked="True" help="Savitzky golay smoothing can introduce negative intensity values it is recommended to replace them with zero"/>
0
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
648 </when>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
649 <when value="ma">
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
650 <param name="coefficients_ma_filter" type="float" value="1"
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
651 label="The coefficients for the moving average filter"/>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
652 </when>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
653 </conditional>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
654 <param name="window_smoothing" type="float" value="8"
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
655 label="Window size"/>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
656 </when>
8
413a1b74f496 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
galaxyp
parents: 7
diff changeset
657 <when value="mz_alignment">
413a1b74f496 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
galaxyp
parents: 7
diff changeset
658 <param name="alignment_tol" type="text" value="NA"
413a1b74f496 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
galaxyp
parents: 7
diff changeset
659 label="tolerance" help="The tolerance to be used when matching the peaks in the unaligned spectra to the reference spectrum. If this is NA, then automatically guess a tolerance from the data.">
413a1b74f496 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
galaxyp
parents: 7
diff changeset
660 <sanitizer>
413a1b74f496 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
galaxyp
parents: 7
diff changeset
661 <valid initial="string.digits">
413a1b74f496 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
galaxyp
parents: 7
diff changeset
662 <add value="N" />
413a1b74f496 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
galaxyp
parents: 7
diff changeset
663 <add value="A" />
413a1b74f496 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
galaxyp
parents: 7
diff changeset
664 </valid>
413a1b74f496 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
galaxyp
parents: 7
diff changeset
665 </sanitizer>
413a1b74f496 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
galaxyp
parents: 7
diff changeset
666 </param>
413a1b74f496 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
galaxyp
parents: 7
diff changeset
667 <param name="alignment_units" type="select" display="radio" optional="False" label="The units to use for the tolerance.">
413a1b74f496 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
galaxyp
parents: 7
diff changeset
668 <option value="ppm" selected="True">ppm</option>
413a1b74f496 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
galaxyp
parents: 7
diff changeset
669 <option value="mz">m/z</option>
413a1b74f496 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
galaxyp
parents: 7
diff changeset
670 </param>
413a1b74f496 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
galaxyp
parents: 7
diff changeset
671 <conditional name="mzalign_ref_type">
413a1b74f496 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
galaxyp
parents: 7
diff changeset
672 <param name="align_reference_datatype" type="select" label="Choose reference">
413a1b74f496 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
galaxyp
parents: 7
diff changeset
673 <option value="align_noref" selected="True">use mean spectrum as reference</option>
413a1b74f496 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
galaxyp
parents: 7
diff changeset
674 <option value="align_table" >m/z values from tabular file as reference</option>
413a1b74f496 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
galaxyp
parents: 7
diff changeset
675 </param>
413a1b74f496 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
galaxyp
parents: 7
diff changeset
676 <when value="align_noref"/>
413a1b74f496 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
galaxyp
parents: 7
diff changeset
677 <when value="align_table">
413a1b74f496 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
galaxyp
parents: 7
diff changeset
678 <expand macro="reading_1_column_mz_tabular" label="Tabular file with m/z features to use for alignment. Only the m/z values from the tabular file will be kept."/>
413a1b74f496 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
galaxyp
parents: 7
diff changeset
679 </when>
413a1b74f496 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
galaxyp
parents: 7
diff changeset
680 </conditional>
413a1b74f496 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
galaxyp
parents: 7
diff changeset
681 <param name="quantile" type="float" value="0.2"
413a1b74f496 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
galaxyp
parents: 7
diff changeset
682 label="quantile" help="The top quantile of reference points (peaks detected via local maxima) to use from the reference spectrum."/>
413a1b74f496 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
galaxyp
parents: 7
diff changeset
683 <param name="span" type="float" value="0.75"
413a1b74f496 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
galaxyp
parents: 7
diff changeset
684 label="span" help="The smoothing parameter for the local polynomial regression used to determine the warping function."/>
413a1b74f496 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
galaxyp
parents: 7
diff changeset
685 </when>
10
aa479a0cfb43 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f"
galaxyp
parents: 9
diff changeset
686 <when value="mz_recalibration">
aa479a0cfb43 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f"
galaxyp
parents: 9
diff changeset
687 <param name="alignment_tol" type="text" value="NA"
aa479a0cfb43 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f"
galaxyp
parents: 9
diff changeset
688 label="tolerance" help="The tolerance to be used when matching the peaks in the unaligned spectra to the reference spectrum. If this is NA, then automatically guess a tolerance from the data.">
aa479a0cfb43 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f"
galaxyp
parents: 9
diff changeset
689 <sanitizer>
aa479a0cfb43 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f"
galaxyp
parents: 9
diff changeset
690 <valid initial="string.digits">
aa479a0cfb43 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f"
galaxyp
parents: 9
diff changeset
691 <add value="N" />
aa479a0cfb43 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f"
galaxyp
parents: 9
diff changeset
692 <add value="A" />
aa479a0cfb43 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f"
galaxyp
parents: 9
diff changeset
693 </valid>
aa479a0cfb43 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f"
galaxyp
parents: 9
diff changeset
694 </sanitizer>
aa479a0cfb43 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f"
galaxyp
parents: 9
diff changeset
695 </param>
aa479a0cfb43 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f"
galaxyp
parents: 9
diff changeset
696 <param name="alignment_units" type="select" display="radio" optional="False" label="The units to use for the tolerance.">
aa479a0cfb43 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f"
galaxyp
parents: 9
diff changeset
697 <option value="ppm" selected="True">ppm</option>
aa479a0cfb43 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f"
galaxyp
parents: 9
diff changeset
698 <option value="mz">m/z</option>
aa479a0cfb43 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f"
galaxyp
parents: 9
diff changeset
699 </param>
aa479a0cfb43 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f"
galaxyp
parents: 9
diff changeset
700 <expand macro="reading_1_column_mz_tabular" label="Tabular file with m/z features to use for alignment. Only the m/z values from the tabular file will be kept."/>
aa479a0cfb43 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f"
galaxyp
parents: 9
diff changeset
701 <param name="quantile" type="float" value="0.2"
aa479a0cfb43 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f"
galaxyp
parents: 9
diff changeset
702 label="quantile" help="The top quantile of reference points (peaks detected via local maxima) to use from the reference spectrum."/>
aa479a0cfb43 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f"
galaxyp
parents: 9
diff changeset
703 <param name="span" type="float" value="0.75"
aa479a0cfb43 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f"
galaxyp
parents: 9
diff changeset
704 label="span" help="The smoothing parameter for the local polynomial regression used to determine the warping function."/>
aa479a0cfb43 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f"
galaxyp
parents: 9
diff changeset
705 </when>
0
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
706 <when value="Peak_picking">
6
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
707 <param name="SNR_picking_method" type="float" value="6"
0
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
708 label="Signal to noise ratio"
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
709 help="The minimal signal to noise ratio for peaks to be considered as a valid peak."/>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
710 <param name="blocks_picking" type="integer" value="100" label = "Number of blocks"
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
711 help="Number of blocks in which to divide mass spectrum to calculate noise"/>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
712 <param name="window_picking" type="float" value="5" label= "Window size" help="Window width for seeking local maxima"/>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
713 <conditional name="methods_for_picking">
6
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
714 <param name="picking_method" type="select" label="Peak picking method">
0
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
715 <option value="adaptive" selected="True">adaptive</option>
6
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
716 <option value="mad">mad</option>
0
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
717 <option value="simple">simple</option>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
718 </param>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
719 <when value="adaptive">
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
720 <param name="spar_picking" type="float" value="1.0"
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
721 label="Spar value"
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
722 help = "Smoothing parameter for the spline smoothing
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
723 applied to the spectrum in order to decide the cutoffs
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
724 for throwing away false noise spikes that might occur inside peaks"/>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
725 </when>
6
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
726 <when value="mad"/>
0
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
727 <when value="simple"/>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
728 </conditional>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
729 </when>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
730 <when value="Peak_alignment">
6
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
731 <param name="value_diffalignment" type="float" value="200"
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
732 label="tolerance" help="Peaks that differ less than this value will be aligned together"/>
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
733 <param name="units_diffalignment" type="select" display="radio" optional="False" label="units">
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
734 <option value="ppm" selected="True">ppm</option>
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
735 <option value="mz">m/z</option>
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
736 </param>
0
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
737 <conditional name="align_ref_type">
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
738 <param name="align_reference_datatype" type="select" label="Choose reference">
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
739 <option value="align_noref" selected="True">no reference</option>
8
413a1b74f496 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
galaxyp
parents: 7
diff changeset
740 <option value="align_table" >m/z values from tabular file as reference</option>
0
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
741 </param>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
742 <when value="align_noref"/>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
743 <when value="align_table">
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
744 <expand macro="reading_1_column_mz_tabular" label="Tabular file with m/z features to use for alignment. Only the m/z values from the tabular file will be kept."/>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
745 </when>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
746 </conditional>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
747 </when>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
748 <when value="Peak_filtering">
6
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
749 <param name="frequ_filtering" type="float" value="0.01" max="1" min="0" label="Minimum frequency" help="Peaks that occur in the dataset in lesser proportion than this will be dropped (0.01 --> filtering for 1% of spectra)"/>
0
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
750 </when>
7
173070dafe95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 6
diff changeset
751 <when value="Peak_binning">
173070dafe95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 6
diff changeset
752 <expand macro="reading_1_column_mz_tabular" label="A reference to which the peaks are binned." help="Tabular file with m/z features to extract from input file"/>
173070dafe95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 6
diff changeset
753 <param name="peakbin_tol" value="NA" type="text" label="The tolerance to be used when matching the m/z features in the dataset to the reference. If this is NA, then automatically guess a resolution from the data." >
8
413a1b74f496 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
galaxyp
parents: 7
diff changeset
754 <sanitizer>
7
173070dafe95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 6
diff changeset
755 <valid initial="string.digits">
8
413a1b74f496 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
galaxyp
parents: 7
diff changeset
756 <add value="N" />
413a1b74f496 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
galaxyp
parents: 7
diff changeset
757 <add value="A" />
7
173070dafe95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 6
diff changeset
758 </valid>
173070dafe95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 6
diff changeset
759 </sanitizer>
173070dafe95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 6
diff changeset
760 </param>
173070dafe95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 6
diff changeset
761 <param name="peakbin_units" display="radio" type="select" label="The units to use for the tolerance.">
173070dafe95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 6
diff changeset
762 <option value="mz" >mz</option>
173070dafe95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 6
diff changeset
763 <option value="ppm" selected="True" >ppm</option>
173070dafe95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 6
diff changeset
764 </param>
173070dafe95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 6
diff changeset
765 <param name="peaks_type" type="select" display="radio"
173070dafe95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 6
diff changeset
766 label="Should the peak height or area under the curve be taken as the intensity value?">
173070dafe95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 6
diff changeset
767 <option value="height" selected="True">height</option>
173070dafe95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 6
diff changeset
768 <option value="area">area</option>
173070dafe95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 6
diff changeset
769 </param>
173070dafe95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 6
diff changeset
770 </when>
9
e0bbaf9f7da0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents: 8
diff changeset
771 <when value="Mass_binning">
e0bbaf9f7da0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents: 8
diff changeset
772 <param name="bin_width" type="float" value="1" label="The width of a bin in m/z or ppm" help="Width must be greater than range of m/z values divided by number of m/z features"/>
e0bbaf9f7da0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents: 8
diff changeset
773 <param name="bin_units" type="select" display="radio"
e0bbaf9f7da0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents: 8
diff changeset
774 label="Unit for bin">
e0bbaf9f7da0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents: 8
diff changeset
775 <option value="mz" selected="True">mz</option>
e0bbaf9f7da0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents: 8
diff changeset
776 <option value="ppm">ppm</option>
e0bbaf9f7da0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents: 8
diff changeset
777 </param>
e0bbaf9f7da0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents: 8
diff changeset
778 <param name="bin_fun" type="select" display="radio"
e0bbaf9f7da0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents: 8
diff changeset
779 label="Calculate sum or mean intensity for ions of the same bin">
e0bbaf9f7da0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents: 8
diff changeset
780 <option value="mean" selected="True">mean</option>
e0bbaf9f7da0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents: 8
diff changeset
781 <option value="sum">sum</option>
e0bbaf9f7da0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents: 8
diff changeset
782 </param>
e0bbaf9f7da0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents: 8
diff changeset
783 <param name="replace_NA_bin" type="boolean" label="Replace NA with 0" truevalue="TRUE" falsevalue="FALSE" checked="True" help="Binning can introduce NAs, should they be replaced with 0"/>
e0bbaf9f7da0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents: 8
diff changeset
784 <conditional name="mz_range">
10
aa479a0cfb43 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f"
galaxyp
parents: 9
diff changeset
785 <param name="features_filtering" type="select" label="Select m/z options">
9
e0bbaf9f7da0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents: 8
diff changeset
786 <option value="none" selected="True">none</option>
e0bbaf9f7da0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents: 8
diff changeset
787 <option value="change_mz_range">change m/z range</option>
10
aa479a0cfb43 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f"
galaxyp
parents: 9
diff changeset
788 <option value="bin_to_reference">bin m/z to reference</option>
0
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
789 </param>
9
e0bbaf9f7da0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents: 8
diff changeset
790 <when value="none"/>
e0bbaf9f7da0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents: 8
diff changeset
791 <when value="change_mz_range">
e0bbaf9f7da0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents: 8
diff changeset
792 <param name="min_mz" type="float" value="1" label="Minimum value for m/z"/>
e0bbaf9f7da0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents: 8
diff changeset
793 <param name="max_mz" type="float" value="10000" label="Maximum value for m/z"/>
e0bbaf9f7da0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents: 8
diff changeset
794 </when>
10
aa479a0cfb43 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f"
galaxyp
parents: 9
diff changeset
795 <when value="bin_to_reference">
aa479a0cfb43 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f"
galaxyp
parents: 9
diff changeset
796 <expand macro="reading_1_column_mz_tabular" label="Tabular file with m/z features as reference for binning. Only the m/z values from the tabular file will be kept."/>
aa479a0cfb43 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f"
galaxyp
parents: 9
diff changeset
797 </when>
0
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
798 </conditional>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
799 </when>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
800 <when value="Transformation">
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
801 <conditional name="transf_conditional">
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
802 <param name="trans_type" type="select" label="Intensity transformations" help="logarithm base 2 (log2) or squareroot (sqrt)">
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
803 <option value="log2" selected="True">log2</option>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
804 <option value="sqrt">sqrt</option>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
805 </param>
1
c8ab1b6f3834 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
806 <when value="log2">
4
58fb63423b0b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
807 <param name="replace_NA_trans" type="boolean" label="Replace NA with 0" truevalue="TRUE" falsevalue="FALSE" checked="True" help="0 values are set to NA before log2 transformation, after transformation they can be set back to 0"/>
1
c8ab1b6f3834 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
808 </when>
0
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
809 <when value="sqrt"/>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
810 </conditional>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
811 </when>
12
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
812 <when value="ComBat_batch_correction">
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
813 <param name="annotation_file" type="data" format="tabular" label="Annotation file that contains the pixel x and y coordinates, the batch identifier, and the condition annotation for each spectrum." help="Annotation tabular file that contains the batch identifier for each spectrum in one column."/>
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
814 <param name="x_column" type="data_column" data_ref="annotation_file" label="X coordinates" help="Column with x coordinates of pixels."/>
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
815 <param name="y_column" type="data_column" data_ref="annotation_file" label="Y coordinates" help="Column with y ccordinates of pixels."/>
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
816 <param name="batch_column" type="data_column" data_ref="annotation_file" label="Batch column" help="The column that contains the batch identifier for each spectrum."/>
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
817 <param name="condition_column" type="data_column" data_ref="annotation_file" label="Condition column" help="The column that contains the condition annotation for each spectrum. Typically these are the groups you want to compare. If not applicable, the batch column can be selected again as this information is only used for the QC plot."/>
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
818 <param name="feature_header" type="boolean" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/>
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
819 </when>
0
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
820 </conditional>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
821 </repeat>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
822 </inputs>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
823 <outputs>
6
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
824 <data format="imzml" name="outfile_imzml" label="${tool.name} on ${on_string}: imzML"/>
0
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
825 <data format="pdf" name="QC_overview" from_work_dir="Preprocessing.pdf" label = "${tool.name} on ${on_string}: QC"/>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
826 </outputs>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
827 <tests>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
828 <test>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
829 <expand macro="infile_imzml"/>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
830 <repeat name="methods">
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
831 <conditional name="methods_conditional">
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
832 <param name="preprocessing_method" value="Normalization"/>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
833 <conditional name="methods_for_normalization">
6
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
834 <param name="normalization_method" value="tic"/>
0
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
835 </conditional>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
836 </conditional>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
837 </repeat>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
838 <repeat name="methods">
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
839 <conditional name="methods_conditional">
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
840 <param name="preprocessing_method" value="Smoothing"/>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
841 <conditional name="methods_for_smoothing">
10
aa479a0cfb43 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f"
galaxyp
parents: 9
diff changeset
842 <param name="smoothing_method" value="sgolay"/>
0
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
843 </conditional>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
844 </conditional>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
845 </repeat>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
846 <repeat name="methods">
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
847 <conditional name="methods_conditional">
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
848 <param name="preprocessing_method" value="Peak_picking"/>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
849 <conditional name="methods_for_picking">
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
850 <param name="picking_method" value="adaptive"/>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
851 </conditional>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
852 <param name="blocks_picking" value="3"/>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
853 <param name="window_picking" value="3"/>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
854 <param name="SNR_picking_method" value="3"/>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
855 </conditional>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
856 </repeat>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
857 <repeat name="methods">
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
858 <conditional name="methods_conditional">
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
859 <param name="preprocessing_method" value="Peak_alignment"/>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
860 </conditional>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
861 </repeat>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
862 <repeat name="methods">
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
863 <conditional name="methods_conditional">
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
864 <param name="preprocessing_method" value="Peak_filtering"/>
6
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
865 <param name="frequ_filtering" value="0.3"/>
0
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
866 </conditional>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
867 </repeat>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
868 <repeat name="methods">
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
869 <conditional name="methods_conditional">
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
870 <param name="preprocessing_method" value="Transformation"/>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
871 <conditional name="transf_conditional">
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
872 <param name="trans_type" value="sqrt"/>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
873 </conditional>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
874 </conditional>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
875 </repeat>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
876 <output name="QC_overview" file="preprocessing_results1.pdf" compare="sim_size"/>
2
f29109d0d353 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
877 <output name="outfile_imzml" ftype="imzml" file="preprocessing_results1.imzml.txt" compare="sim_size">
6
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
878 <extra_files type="file" file="preprocessing_results1.imzml" name="imzml" lines_diff="6"/>
2
f29109d0d353 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
879 <extra_files type="file" file="preprocessing_results1.ibd" name="ibd" compare="sim_size"/>
f29109d0d353 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
880 </output>
0
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
881 </test>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
882 <test>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
883 <param name="infile" value="3_files_combined.RData" ftype="rdata"/>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
884 <repeat name="methods">
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
885 <conditional name="methods_conditional">
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
886 <param name="preprocessing_method" value="Peak_picking"/>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
887 <param name="blocks_picking" value="3"/>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
888 <param name="window_picking" value="5"/>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
889 <param name="SNR_picking_method" value="2"/>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
890 <conditional name="methods_for_picking">
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
891 <param name="picking_method" value="adaptive"/>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
892 </conditional>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
893 </conditional>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
894 </repeat>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
895 <repeat name="methods">
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
896 <conditional name="methods_conditional">
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
897 <param name="preprocessing_method" value="Peak_alignment"/>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
898 </conditional>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
899 </repeat>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
900 <output name="QC_overview" file="preprocessing_results2.pdf" compare="sim_size"/>
2
f29109d0d353 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
901 <output name="outfile_imzml" ftype="imzml" file="preprocessing_results2.imzml.txt" compare="sim_size">
6
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
902 <extra_files type="file" file="preprocessing_results2.imzml" name="imzml" lines_diff="6"/>
2
f29109d0d353 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
903 <extra_files type="file" file="preprocessing_results2.ibd" name="ibd" compare="sim_size"/>
f29109d0d353 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
904 </output>
0
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
905 </test>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
906 <test>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
907 <expand macro="infile_analyze75"/>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
908 <repeat name="methods">
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
909 <conditional name="methods_conditional">
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
910 <param name="preprocessing_method" value="Normalization"/>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
911 <conditional name="methods_for_normalization">
6
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
912 <param name="normalization_method" value="rms"/>
0
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
913 </conditional>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
914 </conditional>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
915 </repeat>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
916 <repeat name="methods">
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
917 <conditional name="methods_conditional">
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
918 <param name="preprocessing_method" value="Peak_picking"/>
7
173070dafe95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 6
diff changeset
919 <param name="blocks_picking" value="20"/>
0
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
920 <param name="window_picking" value="5"/>
7
173070dafe95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 6
diff changeset
921 <param name="SNR_picking_method" value="2"/>
6
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
922 <conditional name="methods_for_picking">
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
923 <param name="picking_method" value="mad"/>
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
924 </conditional>
0
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
925 </conditional>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
926 </repeat>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
927 <repeat name="methods">
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
928 <conditional name="methods_conditional">
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
929 <param name="preprocessing_method" value="Peak_alignment"/>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
930 </conditional>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
931 </repeat>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
932 <output name="QC_overview" file="preprocessing_results3.pdf" compare="sim_size"/>
2
f29109d0d353 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
933 <output name="outfile_imzml" ftype="imzml" file="preprocessing_results3.imzml.txt" compare="sim_size">
6
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
934 <extra_files type="file" file="preprocessing_results3.imzml" name="imzml" lines_diff="6"/>
2
f29109d0d353 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
935 <extra_files type="file" file="preprocessing_results3.ibd" name="ibd" compare="sim_size"/>
f29109d0d353 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
936 </output>
0
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
937 </test>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
938 <test>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
939 <expand macro="infile_analyze75"/>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
940 <repeat name="methods">
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
941 <conditional name="methods_conditional">
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
942 <param name="preprocessing_method" value="Normalization"/>
6
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
943 <param name="normalization_method" value="tic"/>
0
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
944 </conditional>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
945 </repeat>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
946 <repeat name="methods">
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
947 <conditional name="methods_conditional">
8
413a1b74f496 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
galaxyp
parents: 7
diff changeset
948 <param name="preprocessing_method" value="mz_alignment"/>
413a1b74f496 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
galaxyp
parents: 7
diff changeset
949 </conditional>
413a1b74f496 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
galaxyp
parents: 7
diff changeset
950 </repeat>
413a1b74f496 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
galaxyp
parents: 7
diff changeset
951 <repeat name="methods">
413a1b74f496 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
galaxyp
parents: 7
diff changeset
952 <conditional name="methods_conditional">
10
aa479a0cfb43 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f"
galaxyp
parents: 9
diff changeset
953 <param name="preprocessing_method" value="mz_recalibration"/>
aa479a0cfb43 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f"
galaxyp
parents: 9
diff changeset
954 <param name="alignment_tol" value="2"/>
aa479a0cfb43 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f"
galaxyp
parents: 9
diff changeset
955 <param name="alignment_units" value="ppm"/>
aa479a0cfb43 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f"
galaxyp
parents: 9
diff changeset
956 <param name="mz_tabular" value="inputcalibrantfile2.txt" ftype="tabular"/>
aa479a0cfb43 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f"
galaxyp
parents: 9
diff changeset
957 <param name="feature_column" value="1"/>
aa479a0cfb43 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f"
galaxyp
parents: 9
diff changeset
958 <param name="feature_header" value="TRUE"/>
aa479a0cfb43 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f"
galaxyp
parents: 9
diff changeset
959 </conditional>
aa479a0cfb43 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f"
galaxyp
parents: 9
diff changeset
960 </repeat>
aa479a0cfb43 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f"
galaxyp
parents: 9
diff changeset
961 <repeat name="methods">
aa479a0cfb43 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f"
galaxyp
parents: 9
diff changeset
962 <conditional name="methods_conditional">
9
e0bbaf9f7da0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents: 8
diff changeset
963 <param name="preprocessing_method" value="Mass_binning"/>
6
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
964 <param name="bin_width" value="0.1"/>
9
e0bbaf9f7da0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents: 8
diff changeset
965 <param name="bin_units" value="mz"/>
0
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
966 </conditional>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
967 </repeat>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
968 <output name="QC_overview" file="preprocessing_results4.pdf" compare="sim_size"/>
2
f29109d0d353 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
969 <output name="outfile_imzml" ftype="imzml" file="preprocessing_results4.imzml.txt" compare="sim_size">
6
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
970 <extra_files type="file" file="preprocessing_results4.imzml" name="imzml" lines_diff="6"/>
2
f29109d0d353 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
971 <extra_files type="file" file="preprocessing_results4.ibd" name="ibd" compare="sim_size"/>
f29109d0d353 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
972 </output>
0
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
973 </test>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
974 <test>
6
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
975 <expand macro="processed_infile_imzml"/>
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
976 <conditional name="processed_cond">
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
977 <param name="processed_file" value="processed"/>
9
e0bbaf9f7da0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents: 8
diff changeset
978 <param name="accuracy" value="200"/>
6
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
979 <param name="units" value="ppm"/>
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
980 </conditional>
0
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
981 <repeat name="methods">
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
982 <conditional name="methods_conditional">
6
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
983 <param name="preprocessing_method" value="Transformation"/>
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
984 <conditional name="transf_conditional">
7
173070dafe95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 6
diff changeset
985 <param name="trans_type" value="log2"/>
0
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
986 </conditional>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
987 </conditional>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
988 </repeat>
6
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
989 <repeat name="methods">
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
990 <conditional name="methods_conditional">
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
991 <param name="preprocessing_method" value="Baseline_reduction"/>
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
992 </conditional>
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
993 </repeat>
8
413a1b74f496 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
galaxyp
parents: 7
diff changeset
994 <output name="QC_overview" file="preprocessing_results5.pdf" compare="sim_size" delta="13000"/>
6
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
995 <output name="outfile_imzml" ftype="imzml" file="preprocessing_results5.imzml.txt" compare="sim_size">
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
996 <extra_files type="file" file="preprocessing_results5.imzml" name="imzml" lines_diff="6"/>
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
997 <extra_files type="file" file="preprocessing_results5.ibd" name="ibd" compare="sim_size"/>
cbd9e4df377d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
998 </output>
0
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
999 </test>
12
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1000 <test>
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1001 <param name="infile" value="" ftype="imzml">
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1002 <composite_data value="Combat_40pixel.imzML" />
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1003 <composite_data value="Combat_40pixel.ibd"/>
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1004 </param>
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1005 <repeat name="methods">
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1006 <conditional name="methods_conditional">
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1007 <param name="preprocessing_method" value="ComBat_batch_correction"/>
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1008 <param name="annotation_file" value="annotation_40pixel.tabular" ftype="tabular"/>
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1009 <param name="feature_header" value="TRUE"/>
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1010 <param name="x_column" value="2"/>
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1011 <param name="y_column" value="3"/>
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1012 <param name="batch_column" value="4"/>
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1013 <param name="condition_column" value="6"/>
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1014 </conditional>
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1015 </repeat>
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1016 <output name="QC_overview" file="preprocessing_results_combat_40pixel.pdf" compare="sim_size"/>
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1017 <output name="outfile_imzml" ftype="imzml" file="preprocessing_results_combat_40pixel.imzml.txt" compare="sim_size">
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1018 <extra_files type="file" file="preprocessing_results_combat_40pixel.imzml" name="imzml" lines_diff="6"/>
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1019 <extra_files type="file" file="preprocessing_results_combat_40pixel.ibd" name="ibd" compare="sim_size"/>
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1020 </output>
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1021 </test>
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1022 <test>
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1023 <expand macro="processed_infile_imzml"/>
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1024 <conditional name="processed_cond">
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1025 <param name="processed_file" value="processed"/>
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1026 <param name="accuracy" value="50"/>
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1027 <param name="units" value="ppm"/>
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1028 </conditional>
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1029 <repeat name="methods">
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1030 <conditional name="methods_conditional">
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1031 <param name="preprocessing_method" value="ComBat_batch_correction"/>
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1032 <param name="annotation_file" value="Example_processed_ComBat_annotation.tabular" ftype="tabular"/>
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1033 <param name="feature_header" value="TRUE"/>
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1034 <param name="x_column" value="2"/>
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1035 <param name="y_column" value="3"/>
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1036 <param name="batch_column" value="4"/>
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1037 <param name="condition_column" value="5"/>
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1038 </conditional>
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1039 </repeat>
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1040 <output name="QC_overview" file="ComBat_results_Example_processed_file_preprocessing.pdf" compare="sim_size"/>
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1041 <output name="outfile_imzml" ftype="imzml" file="ComBat_results_Example_processed_file.imzml.txt" compare="sim_size">
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1042 <extra_files type="file" file="ComBat_results_Example_processed_file.imzml" name="imzml" lines_diff="6"/>
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1043 <extra_files type="file" file="ComBat_results_Example_processed_file.ibd" name="ibd" compare="sim_size"/>
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1044 </output>
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1045 </test>
0
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1046 </tests>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1047 <help>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1048 <![CDATA[
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1049
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1050 @CARDINAL_DESCRIPTION@
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1051
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1052 -----
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1053
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1054 This tool provides multiple Cardinal functions to preprocess mass spectrometry imaging data.
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1055
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1056 @MSIDATA_INPUT_DESCRIPTION@
1
c8ab1b6f3834 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
1057 - Coordinates stored as decimals rather than integers will be rounded to obtain a regular pixel grid. This might lead to duplicated coordinates which will be automatically removed after the data is read by the tool.
0
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1058 @MZ_TABULAR_INPUT_DESCRIPTION@
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1059
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1060 **Options**
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1061
9
e0bbaf9f7da0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents: 8
diff changeset
1062 - Normalization: normalization of intensities to total ion current (TIC) or to root-mean-square (RMS)
e0bbaf9f7da0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents: 8
diff changeset
1063 - Baseline reduction: baseline reduction removes background intensity generated by chemical noise (common in MALDI datasets)
0
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1064 - Smoothing: Smoothing of the peaks reduces noise and improves peak detection
9
e0bbaf9f7da0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents: 8
diff changeset
1065 - m/z alignment: removes small m/z shifts between spectra
0
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1066 - Peak picking: relevant peaks are picked while noise-peaks are removed (needs peak alignment afterwards)
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1067 - Peak alignment: only possible after peak picking, m/z inaccuracies are removed by alignment of same peaks to a common m/z value; if no reference is given the peaks are aligned to the local maxima of the mean spectrum of the current dataset; external reference data can be used from another MSI data file or a tabular file with m/z values, but then only the m/z from the reference will be kept
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1068 - Peak filtering: removes peaks that occur only in a small proportion of pixels. If not sure which cut off to choose run quality control tool first and decide according to the number of peaks per m/z plot
9
e0bbaf9f7da0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents: 8
diff changeset
1069 - Peak binning: extracts peaks intensities, either peak height or area under curve (from a profile dataset) for a list of m/z (reference) values
e0bbaf9f7da0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents: 8
diff changeset
1070 - m/z binning: generates new m/z bins
0
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1071 - Transformation: log2 or squareroot transformation of all intensities; when using log2 transformation zero intensities will become NA, this can lead to compatibility problems.
12
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1072 - ComBat batch correction: corrects the intensity values of picked m/z features according to batches given in an annotation table. For now, it can only be applied to m/z features after peak picking (=centroided data). The annotation table needs to contain the x and y coordinates for each pixel and a batch identifier (e.g. TMA_1, TMA_2, TMA_3). Additionally a condition column can be provided, which is only used for the PCA plots in the pdf file. Example of annotation file for ComBat batch correction:
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1073
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1074 ::
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1075
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1076 x_coord y_coord batch_identifier condition
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1077 10 29 TMA_1 A
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1078 22 14 TMA_1 B
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1079 22 27 TMA_2 A
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1080 23 7 TMA_2 B
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1081 29 45 TMA_3 A
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1082 33 41 TMA_3 B
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
parents: 10
diff changeset
1083 ...
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
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diff changeset
1084 ...
274e81434593 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
galaxyp
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diff changeset
1085
9
e0bbaf9f7da0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents: 8
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1086
0
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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1087
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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parents:
diff changeset
1088 **Output**
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
1089
10
aa479a0cfb43 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f"
galaxyp
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diff changeset
1090 - MSI data as continuous imzML file
4
58fb63423b0b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
1091 - pdf with key values and four random mass spectra after each processing step
0
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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parents:
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1092
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1093 ]]>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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1094 </help>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1095 <expand macro="citations"/>
01d12e7e48d3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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1096 </tool>
2
f29109d0d353 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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parents: 1
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1097