annotate msi_preprocessing.xml @ 0:74fcb3c95a53 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
author galaxyp
date Tue, 31 Oct 2017 15:05:05 -0400
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74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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1 <tool id="mass_spectrometry_imaging_preprocessing" name="MSI preprocessing" version="1.7.0">
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2 <description>
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3 mass spectrometry imaging preprocessing
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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4 </description>
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5 <requirements>
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6 <requirement type="package" version="1.7.0">bioconductor-cardinal</requirement>
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7 </requirements>
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8 <command detect_errors="exit_code">
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9 <![CDATA[
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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10
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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11 #if $infile.ext == 'imzml'
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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12 cp '${infile.extra_files_path}/imzml' infile.imzML &&
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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13 cp '${infile.extra_files_path}/ibd' infile.ibd &&
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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14 #elif $infile.ext == 'analyze75'
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15 cp '${infile.extra_files_path}/hdr' infile.hdr &&
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16 cp '${infile.extra_files_path}/img' infile.img &&
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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17 cp '${infile.extra_files_path}/t2m' infile.t2m &&
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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18 #else
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19 ln -s '$infile' infile.RData &&
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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20 #end if
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21 cat '${cardinal_preprocessing}' &&
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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22 Rscript '${cardinal_preprocessing}'
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23
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24 ]]>
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25 </command>
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26 <configfiles>
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27 <configfile name="cardinal_preprocessing"><![CDATA[
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28 library(Cardinal)
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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29
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30 #if $infile.ext == 'imzml'
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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31 msidata <- readMSIData('infile.imzML')
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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32 #elif $infile.ext == 'analyze75'
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33 msidata <- readMSIData('infile.hdr')
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34 #else
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35 load('infile.RData')
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36 #end if
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37
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38 maxpixel = length(pixels(msidata))
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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39 pixelnumber = c(1:maxpixel)
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40
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41 #for $method in $methods:
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42 #if str( $method.methods_conditional.preprocessing_method ) == 'Normalization':
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43 print('Normalization')
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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44 ##normalization
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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45 msidata <- normalize(msidata, pixel=pixelnumber, method="tic")
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46
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47 #elif str( $method.methods_conditional.preprocessing_method ) == 'Baseline_reduction':
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48 print('Baseline_reduction')
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49 ##baseline reduction
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50 msidata = reduceBaseline(msidata, pixel=pixelnumber, method="median", blocks=$method.methods_conditional.blocks_baseline)
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51
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52 #elif str( $method.methods_conditional.preprocessing_method ) == 'Smoothing':
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53 print('Smoothing')
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54 ## Smoothing
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55
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56 #if str( $method.methods_conditional.methods_for_smoothing.smoothing_method) == 'gaussian':
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57 print('gaussian smoothing')
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58 msidata <- smoothSignal(msidata, method="$method.methods_conditional.methods_for_smoothing.smoothing_method", window=$method.methods_conditional.window_smoothing, sd = $method.methods_conditional.methods_for_smoothing.sd_gaussian)
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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59 #elif str( $method.methods_conditional.methods_for_smoothing.smoothing_method) == 'sgolay':
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60 print('sgolay smoothing')
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61 msidata <- smoothSignal(msidata, method="$method.methods_conditional.methods_for_smoothing.smoothing_method", window=$method.methods_conditional.window_smoothing, order = $method.methods_conditional.methods_for_smoothing.order_of_filters)
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62 #elif str($method.methods_conditional.methods_for_smoothing.smoothing_method) == 'ma':
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63 print('sgolay smoothing')
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64 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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65 #end if
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66
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67 #elif str( $method.methods_conditional.preprocessing_method) == 'Peak_picking':
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68 print('Peak_picking')
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69 ## Peakpicking
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70
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71 #if str( $method.methods_conditional.methods_for_picking.picking_method) == 'adaptive':
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72 print('adaptive peakpicking')
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73 msidata = peakPick(msidata, pixel=pixelnumber, 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)
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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74
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75 #elif str( $method.methods_conditional.methods_for_picking.picking_method) == 'limpic':
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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76 print('limpic peakpicking')
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77 msidata = peakPick(msidata, pixel=pixelnumber, window = $method.methods_conditional.window_picking, blocks = $method.methods_conditional.blocks_picking, method='$method.methods_conditional.methods_for_picking.picking_method', SNR=$method.methods_conditional.SNR_picking_method, thresh=$method.methods_conditional.methods_for_picking.tresh_picking)
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78
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79 #elif str( $method.methods_conditional.methods_for_picking.picking_method) == 'simple':
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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80 print('simple peakpicking')
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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81 msidata = peakPick(msidata, pixel=pixelnumber, 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)
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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82 #end if
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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83
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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84 #elif str( $method.methods_conditional.preprocessing_method ) == 'Peak_alignment':
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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85 print('Peak_alignment')
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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86 ## Peakalignment
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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87
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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88 #if str( $method.methods_conditional.methods_for_alignment.alignment_method) == 'diff':
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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89 print('diff peaklignment')
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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90 msidata = peakAlign(msidata, method='$method.methods_conditional.methods_for_alignment.alignment_method',diff.max =$method.methods_conditional.methods_for_alignment.value_diffalignment, units = "$method.methods_conditional.methods_for_alignment.units_diffalignment")
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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91
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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92 #elif str( $method.methods_conditional.methods_for_alignment.alignment_method) == 'DP':
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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93 print('DPpeaklignment')
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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94 msidata = peakAlign(msidata, method='$method.methods_conditional.methods_for_alignment.alignment_method',gap = $method.methods_conditional.methods_for_alignment.gap_DPalignment )
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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95 #end if
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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96
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97 #elif str( $method.methods_conditional.preprocessing_method) == 'Peak_filtering':
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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98 print('Peak_filtering')
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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99 msidata = peakFilter(msidata, method='freq', freq.min = $method.methods_conditional.frequ_filtering)
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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100 #end if
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101 #end for
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102
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103 ## save as as (.RData)
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104 save(msidata, file="$msidata_preprocessed")
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105
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106 ## save as intensity matrix (.csv)
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107 csvmatrix = spectra(msidata)
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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108 rownames(csvmatrix) = mz(msidata)
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109 newmatrix = rbind(pixels(msidata), csvmatrix)
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110 write.csv(newmatrix[2:nrow(newmatrix),], file="$preprocessed_intensity_matrix")
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111
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112 ]]></configfile>
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113 </configfiles>
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114 <inputs>
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115 <param name="infile" type="data" format="imzml,rdata,analyze75"
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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116 label="MSI rawdata as imzml or Cardinal MSImageSet saved as RData"
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117 help="load imzml and ibd file by uploading composite datatype imzml"/>
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118
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119 <repeat name="methods" title="Preprocessing" min="1" max="50">
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120 <conditional name="methods_conditional">
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121 <param name="preprocessing_method" type="select" label="Select the preprocessing methods you want to apply">
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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122 <option value="Normalization" selected="True">Normalization to TIC</option>
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123 <option value="Baseline_reduction">Baseline Reduction</option>
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124 <option value="Smoothing">Peak smoothing</option>
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125 <option value="Peak_picking">Peak picking</option>
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126 <option value="Peak_alignment">Peak alignment</option>
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127 <option value="Peak_filtering">Peak filtering</option>
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128 </param>
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129 <when value="Normalization"/>
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130 <when value="Baseline_reduction">
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131 <param name="blocks_baseline" type="integer" value="50"
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132 label="blocks"/>
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133 </when>
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134 <when value="Smoothing">
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135 <conditional name="methods_for_smoothing">
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136 <param name="smoothing_method" type="select" label="Smoothing method">
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137 <option value="gaussian" selected="True">gaussian</option>
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138 <option value="sgolay">Savitsky-Golay</option>
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139 <option value="ma">moving average</option>
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140 </param>
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141 <when value="gaussian">
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142 <param name="sd_gaussian" type="float" value="4"
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143 label="The standard deviation for the Gaussian kernel (window/sd)"/>
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144 </when>
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145 <when value="sgolay">
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146 <param name="order_of_filters" type="integer" value="3"
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147 label="The order of the smoothing filter"/>
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148 </when>
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149 <when value="ma">
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150 <param name="coefficients_ma_filter" type="integer" value="1"
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151 label="The coefficients for the moving average filter"/>
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152 </when>
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153 </conditional>
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154 <param name="window_smoothing" type="integer" value="9"
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155 label="Window size"/>
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156 </when>
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157 <when value="Peak_picking">
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158 <param name="SNR_picking_method" type="integer" value="3"
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159 label="Signal to noise ratio"
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160 help="The minimal signal to noise ratio for peaks to be considered as a valid peak."/>
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161 <param name="blocks_picking" type="integer" value="100" label = "number of blocks"
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162 help="Number of blocks in which to divide mass spectrum to calculate noise"/>
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163 <param name="window_picking" type="integer" value="5" label= "window size" help="Window width for seeking local maxima"/>
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164 <conditional name="methods_for_picking">
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165 <param name="picking_method" type="select" label="Peak picking method" help = "only simple works for processed imzML files">
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166 <option value="adaptive" selected="True">adaptive</option>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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167 <option value="limpic">limpic</option>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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168 <option value="simple">simple</option>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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169 </param>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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170 <when value="adaptive">
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171 <param name="spar_picking" type="float" value="1.0"
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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172 label="spar value"
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173 help = "Smoothing parameter for the spline smoothing
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174 applied to the spectrum in order to decide the cutoffs
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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175 for throwing away false noise spikes that might occur inside peaks"/>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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176 </when>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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177 <when value="limpic">
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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178 <param name="tresh_picking" type="float" value="0.75"
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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179 label="thresh value" help = "The thresholding quantile to use when comparing slopes in order to throw away peaks that are too flat"/>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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180 </when>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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181 <when value="simple"/>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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182 </conditional>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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183 </when>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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184 <when value="Peak_alignment">
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185 <conditional name="methods_for_alignment">
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186 <param name="alignment_method" type="select" label="Alignment method">
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187 <option value="diff" selected="True">diff</option>
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188 <option value="DP">DP</option>
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189 </param>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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190 <when value="diff">
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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191 <param name="value_diffalignment" type="integer" value="200"
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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192 label="diff.max" help="Peaks that differ less than this value will be aligned together"/>
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193 <param name="units_diffalignment" type="select" display = "radio" optional = "False"
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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194 label="units" help= "The coefficients for the moving average filter">
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195 <option value="ppm" selected="True">ppm</option>
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196 <option value="Da">Da</option>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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197 </param>
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198 </when>
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199 <when value="DP">
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200 <param name="gap_DPalignment" type="integer" value="0"
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201 label="gap" help = "The gap penalty for the dynamic programming sequence alignment"/>
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202 </when>
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203 </conditional>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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204 </when>
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205 <when value="Peak_filtering">
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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206 <param name="frequ_filtering" type="float" value="1"
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207 label="freq.min" help = "Peaks that occur in the dataset fewer times than this will be removed"/>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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208 </when>
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209 </conditional>
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210 </repeat>
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211 </inputs>
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212 <outputs>
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213 <data format="rdata" name="msidata_preprocessed" label="Preprocessed_output"/>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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214 <data format="csv" name="preprocessed_intensity_matrix" label="preprocessed intensity matrix" />
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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215 </outputs>
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216 <tests>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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217 <test>
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218 <param name="infile" value="" ftype="imzml">
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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219 <composite_data value="Example_Continuous.imzML" ftype="imzml"/>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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220 <composite_data value="Example_Continuous.ibd" ftype="ibd"/>
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221 </param>
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222 <repeat name="methods">
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223 <conditional name="methods_conditional">
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224 <param name="preprocessing_method" value="Normalization" />
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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225 </conditional>
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226 </repeat>
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227 <repeat name="methods">
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228 <conditional name="methods_conditional">
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229 <param name="preprocessing_method" value="Smoothing" />
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230 <conditional name="methods_for_smoothing">
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231 <param name="smoothing_method" value="sgolay" />
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232 </conditional>
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233 </conditional>
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234 </repeat>
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235 <repeat name="methods">
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236 <conditional name="methods_conditional">
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237 <param name="preprocessing_method" value="Peak_picking" />
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238 <conditional name="methods_for_picking">
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239 <param name="picking_method" value="adaptive" />
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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240 </conditional>
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241 <param name="blocks_picking" value="3" />
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242 <param name="window_picking" value="3" />
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243 </conditional>
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244 </repeat>
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245 <repeat name="methods">
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246 <conditional name="methods_conditional">
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247 <param name="preprocessing_method" value="Peak_alignment" />
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248 <conditional name="methods_for_alignment">
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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249 <param name="alignment_method" value="DP" />
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250 </conditional>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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251 </conditional>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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252 </repeat>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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253 <repeat name="methods">
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
galaxyp
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254 <conditional name="methods_conditional">
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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255 <param name="preprocessing_method" value="Peak_filtering" />
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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256 </conditional>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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257 </repeat>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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258 <output name="msidata_preprocessed" file="preprocessing_results1.RData" compare="sim_size" />
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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259 <output name="preprocessed_intensity_matrix" file="preprocessing_results1.csv" />
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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260 </test>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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261 <test>
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262 <param name="infile" value="LM5_first68pixel.RData" ftype="rdata"/>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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263 <repeat name="methods">
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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264 <conditional name="methods_conditional">
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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265 <param name="preprocessing_method" value="Baseline_reduction" />
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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266 <param name="blocks_baseline" value="50" />
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267 </conditional>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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268 </repeat>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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269 <repeat name="methods">
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270 <conditional name="methods_conditional">
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271 <param name="preprocessing_method" value="Peak_picking" />
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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272 <param name="blocks_picking" value="3" />
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273 <param name="window_picking" value="5" />
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274 <param name="methods_for_picking" value="simple" />
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275 </conditional>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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276 </repeat>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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277 <repeat name="methods">
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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278 <conditional name="methods_conditional">
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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279 <param name="preprocessing_method" value="Peak_alignment" />
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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280 <param name="methods_for_alignment" value="DP" />
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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281 </conditional>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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282 </repeat>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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283 <output name="msidata_preprocessed" file="preprocessing_results2.RData" compare="sim_size" />
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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284 <output name="preprocessed_intensity_matrix" file="preprocessing_results2.csv" lines_diff="2"/>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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285 </test>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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286 <test>
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287 <param name="infile" value="" ftype="analyze75">
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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288 <composite_data value="Analyze75.hdr" ftype="hdr"/>
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289 <composite_data value="Analyze75.img" ftype="img"/>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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290 <composite_data value="Analyze75.t2m" ftype="t2m"/>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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291 </param>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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292 <repeat name="methods">
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293 <conditional name="methods_conditional">
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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294 <param name="preprocessing_method" value="Normalization" />
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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295 </conditional>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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296 </repeat>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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297 <repeat name="methods">
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298 <conditional name="methods_conditional">
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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299 <param name="preprocessing_method" value="Smoothing" />
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300 <conditional name="methods_for_smoothing">
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301 <param name="smoothing_method" value="gaussian" />
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302 </conditional>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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303 </conditional>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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304 </repeat>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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305 <repeat name="methods">
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306 <conditional name="methods_conditional">
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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307 <param name="preprocessing_method" value="Peak_picking" />
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308 <param name="blocks_picking" value="3" />
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309 <param name="window_picking" value="5" />
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310 <param name="methods_for_picking" value="limpic" />
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311 </conditional>
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312 </repeat>
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313 <repeat name="methods">
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314 <conditional name="methods_conditional">
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315 <param name="preprocessing_method" value="Peak_alignment" />
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316 <param name="methods_for_alignment" value="diff" />
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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317 </conditional>
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318 </repeat>
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319 <output name="msidata_preprocessed" file="preprocessing_results3.RData" compare="sim_size" />
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320 <output name="preprocessed_intensity_matrix" file="preprocessing_results3.csv" />
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321 </test>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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322 </tests>
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323 <help>
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324 <![CDATA[
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325 Cardinal is an R package that implements statistical & computational tools for analyzing mass spectrometry imaging datasets.
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326
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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327 **Preprocessing steps:**
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328
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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329 - Smoothening: Smoothing of the mass peaks reduces noise and improves peak detection
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330 - Normalization: Normalization of intensities to total ion current (TIC)
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331 - Baseline reduction: Baseline reduction removes backgroundintensity generated by chemical noise (common in MALDI datasets)
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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332 - Peak picking: relevant peaks are picked while noise-peaks are removed
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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333 - Peak alignment: mz inaccuracies are removed by alignment of same peaks to a common mz value
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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334 - Peak filtering: removes peaks that occur infrequently, such as those which only occur in a small proportion of pixels
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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335 ]]>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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336 </help>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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337 <citations>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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338 <citation type="doi">10.1093/bioinformatics/btv146</citation>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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339 </citations>
74fcb3c95a53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_preprocessing commit c4e490c83537b39418b5f09d624f7d4da3f3ad55
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340 </tool>