Mercurial > repos > galaxyp > msi_spectra_plot

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
author galaxyp
date Wed, 22 Aug 2018 13:36:10 -0400
parents a2097e90d0eb
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1 <tool id="mass_spectrometry_imaging_mzplots" name="MSI plot spectra" version="1.10.0.6">
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2 <description>
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3 mass spectrometry imaging mass spectra plots
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4 </description>
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5 <requirements>
2
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6 <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement>
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7 <requirement type="package" version="2.2.1">r-gridextra</requirement>
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8 <requirement type="package" version="2.2.1">r-ggplot2</requirement>
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9 <requirement type="package" version="0.5.0">r-scales</requirement>
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10 </requirements>
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11 <command detect_errors="exit_code">
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12 <![CDATA[
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13 #if $infile.ext == 'imzml'
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14 ln -s '${infile.extra_files_path}/imzml' infile.imzML &&
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15 ln -s '${infile.extra_files_path}/ibd' infile.ibd &&
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16 #elif $infile.ext == 'analyze75'
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17 ln -s '${infile.extra_files_path}/hdr' infile.hdr &&
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18 ln -s '${infile.extra_files_path}/img' infile.img &&
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19 ln -s '${infile.extra_files_path}/t2m' infile.t2m &&
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20 #else
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21 ln -s $infile infile.RData &&
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22 #end if
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23 cat '${MSI_mzplots}' &&
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24 Rscript '${MSI_mzplots}'
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25 ]]>
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26 </command>
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27 <configfiles>
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28 <configfile name="MSI_mzplots"><![CDATA[
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29
2
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30 ################################# load libraries and read file #################
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31
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32 library(Cardinal)
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33 library(gridExtra)
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34 library(ggplot2)
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35 library(scales)
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36
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37
0
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38 #if $infile.ext == 'imzml'
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39 #if str($processed_cond.processed_file) == "processed":
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40 msidata <- readImzML('infile', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units")
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41 #else
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42 msidata <- readImzML('infile', attach.only=TRUE)
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43 #end if
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44 #elif $infile.ext == 'analyze75'
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45 msidata = readAnalyze('infile', attach.only=TRUE)
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46 #else
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47 loadRData <- function(fileName){
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48 load(fileName)
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49 get(ls()[ls() != "fileName"])
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50 }
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51 msidata = loadRData('infile.RData')
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52 #end if
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53
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54 ###################################### file properties in numbers ##############
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55
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56 ## Number of features (m/z)
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57 maxfeatures = length(features(msidata))
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58 ## Range m/z
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59 minmz = round(min(mz(msidata)), digits=2)
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60 maxmz = round(max(mz(msidata)), digits=2)
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61 ## Number of spectra (pixels)
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62 pixelcount = length(pixels(msidata))
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63 ## Range x coordinates
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64 minimumx = min(coord(msidata)[,1])
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65 maximumx = max(coord(msidata)[,1])
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66 ## Range y coordinates
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67 minimumy = min(coord(msidata)[,2])
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68 maximumy = max(coord(msidata)[,2])
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69 ## Range of intensities
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70 minint = round(min(spectra(msidata)[], na.rm=TRUE), digits=2)
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71 maxint = round(max(spectra(msidata)[], na.rm=TRUE), digits=2)
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72 medint = round(median(spectra(msidata)[], na.rm=TRUE), digits=2)
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73 ## Number of intensities > 0
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74 npeaks= sum(spectra(msidata)[]>0, na.rm=TRUE)
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75 ## Spectra multiplied with m/z (potential number of peaks)
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76 numpeaks = ncol(spectra(msidata)[])*nrow(spectra(msidata)[])
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77 ## Percentage of intensities > 0
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78 percpeaks = round(npeaks/numpeaks*100, digits=2)
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79 ## Number of empty TICs
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80 TICs = colSums(spectra(msidata)[], na.rm=TRUE)
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81 NumemptyTIC = sum(TICs == 0)
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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82
5
bc931322e4d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
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83
0
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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84 ## Processing informations
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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85 processinginfo = processingData(msidata)
4
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86 centroidedinfo = processinginfo@centroided
0
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87
4
dcf79af72c8f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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88 ## if TRUE write processinginfo if FALSE write FALSE
0
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89
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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90 ## normalization
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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91 if (length(processinginfo@normalization) == 0) {
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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92 normalizationinfo='FALSE'
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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93 } else {
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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94 normalizationinfo=processinginfo@normalization
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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95 }
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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96 ## smoothing
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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97 if (length(processinginfo@smoothing) == 0) {
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98 smoothinginfo='FALSE'
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99 } else {
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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100 smoothinginfo=processinginfo@smoothing
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101 }
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102 ## baseline
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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103 if (length(processinginfo@baselineReduction) == 0) {
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104 baselinereductioninfo='FALSE'
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105 } else {
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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106 baselinereductioninfo=processinginfo@baselineReduction
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107 }
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108 ## peak picking
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109 if (length(processinginfo@peakPicking) == 0) {
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110 peakpickinginfo='FALSE'
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111 } else {
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112 peakpickinginfo=processinginfo@peakPicking
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113 }
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114
3
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115 properties = c("Number of m/z features",
4
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116 "Range of m/z values",
0
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117 "Number of pixels",
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118 "Range of x coordinates",
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119 "Range of y coordinates",
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120 "Range of intensities",
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121 "Median of intensities",
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122 "Intensities > 0",
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123 "Number of zero TICs",
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124 "Preprocessing",
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125 "Normalization",
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126 "Smoothing",
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127 "Baseline reduction",
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128 "Peak picking",
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129 "Centroided")
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130
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131 values = c(paste0(maxfeatures),
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132 paste0(minmz, " - ", maxmz),
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133 paste0(pixelcount),
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134 paste0(minimumx, " - ", maximumx),
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135 paste0(minimumy, " - ", maximumy),
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136 paste0(minint, " - ", maxint),
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137 paste0(medint),
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138 paste0(percpeaks, " %"),
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139 paste0(NumemptyTIC),
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140 paste0(" "),
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141 paste0(normalizationinfo),
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142 paste0(smoothinginfo),
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143 paste0(baselinereductioninfo),
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144 paste0(peakpickinginfo),
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145 paste0(centroidedinfo))
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146
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147 property_df = data.frame(properties, values)
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148
2
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149 ######################################## PDF ###################################
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150 ################################################################################
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151 ################################################################################
0
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152
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153
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154 pdf("mzplots.pdf", fonts = "Times", pointsize = 12)
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155 plot(0,type='n',axes=FALSE,ann=FALSE)
3
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156 #if not $filename:
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157 #set $filename = $infile.display_name
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158 #end if
6
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159 title(main=paste0("Mass spectra for file: \n\n","$filename"))
0
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160
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161
2
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162 ############################# I) numbers ######################################
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163 ###############################################################################
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164
0
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165 grid.table(property_df, rows= NULL)
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166
3
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167 if (npeaks > 0){
0
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168
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169 pixeldf = data.frame(matrix(ncol = 2, nrow=0))
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170
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171 ############################# single pixel ################################
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172 ###########################################################################
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173
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174 #if str( $pixel_conditional.pixel_type) == 'single_pixel':
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175 print("single_pixel")
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176
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177 #for $chosenpixel in $pixel_conditional.repeatpixel:
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178
2
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179 pixelisvalid = as.character($chosenpixel.inputx %in% coord(msidata)\$x & $chosenpixel.inputy %in% coord(msidata)\$y)
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180 pixelname = paste0("x=", $chosenpixel.inputx,", ", "y=", $chosenpixel.inputy)
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181 pixeldf = rbind(pixeldf, cbind(pixelname, pixelisvalid))
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182
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183 ############################# II) control image ####################
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184
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185 if (pixelisvalid == "TRUE"){
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186 print(pixelisvalid)
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187
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188 image(msidata, mz=$chosenpixel.inputmz, ylim = c(maximumy+(0.2*maximumy),minimumy-1),
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189 colorkey=FALSE, plusminus = $chosenpixel.plusminusinDalton,
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190 main= paste0("x= ",$chosenpixel.inputx, ", y= ", $chosenpixel.inputy))
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191
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192 abline(v=$chosenpixel.inputx, col ="$chosenpixel.inputcolour", lty="$chosenpixel.inputtype", lwd=$chosenpixel.inputwidth)
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193 abline(h=$chosenpixel.inputy, col ="$chosenpixel.inputcolour", lty="$chosenpixel.inputtype", lwd=$chosenpixel.inputwidth)
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194
2
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195 ##################### III) plot full mass spectrum #################
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196
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197 plot(msidata, coord=list(x=$chosenpixel.inputx, y=$chosenpixel.inputy))
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198
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199 ##################### IV) plot zoom-in mass spectrum ###############
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200
2
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201 #if $chosenpixel.zoomedplot:
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202 iData(msidata) <- iData(msidata)[] ## getting back data on disk
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203
2
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204 #for $token in $chosenpixel.zoomedplot:
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205
2
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206 minmasspixel = features(msidata, mz=$token.xlimmin)
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207 maxmasspixel = features(msidata, mz=$token.xlimmax)
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208
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209 plot(msidata[minmasspixel:maxmasspixel,], coord=list(x=$chosenpixel.inputx, y=$chosenpixel.inputy),
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210 xlim= c($token.xlimmin,$token.xlimmax))
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211
2
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212 #end for
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213 #end if
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214 }else{
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215 print("The pixel coordinates did not correspond to a real pixel")}
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216 #end for
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217
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218 colnames(pixeldf) = c("pixel coordinates", "coordinates were found in this file")
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219
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220 ############################# sample pixel ################################
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221 ###########################################################################
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222
3
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223 #elif str( $pixel_conditional.pixel_type) == 'sample_pixel':
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224 print("sample pixels")
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225
6
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226 ## optional annotation from tabular file to obtain pixel groups (otherwise all pixels are considered to be one sample)
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227
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228 #if str($pixel_conditional.tabular_annotation.load_annotation) == 'yes_annotation':
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229
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230 ## read and extract x,y,annotation information
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231 input_tabular = read.delim("$pixel_conditional.tabular_annotation.annotation_file", header = $pixel_conditional.tabular_annotation.tabular_header, stringsAsFactors = FALSE)
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232 annotation_input = input_tabular[,c($pixel_conditional.tabular_annotation.column_x, $pixel_conditional.tabular_annotation.column_y, $pixel_conditional.tabular_annotation.column_names)]
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233 colnames(annotation_input) = c("x", "y", "annotation")
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234
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235 ## merge with coordinate information of msidata
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236 msidata_coordinates = cbind(coord(msidata)[,1:2], c(1:ncol(msidata)))
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237 colnames(msidata_coordinates)[3] = "pixel_index"
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238 merged_annotation = merge(msidata_coordinates, annotation_input, by=c("x", "y"), all.x=TRUE)
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239 merged_annotation[is.na(merged_annotation)] = "NA"
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240 merged_annotation = merged_annotation[order(merged_annotation\$pixel_index),]
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241 msidata\$annotation = as.factor(merged_annotation[,4])
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242
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243 #end if
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244
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245 ##################### I) Sample: plot full mass spectrum ##############
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246
6
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247 ## coloured plot with mean over all spectra with the same annotation, if no annotation is provided all pixels are considered as one sample
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248
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249 if (!is.null(levels(msidata\$annotation))){
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250 print("annotated samples")
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251
6
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252 ## overview plot over annotated samples
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253 number_combined = length(levels(msidata\$annotation))
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254
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255 ## the more annotation groups a file has the smaller will be the legend
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256 if (number_combined<20){
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257 legend_size = 10
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258 }else if (number_combined>20 && number_combined<40){
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259 legend_size = 9
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260 }else if (number_combined>40 && number_combined<60){
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261 legend_size = 8
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262 }else if (number_combined>60 && number_combined<100){
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263 legend_size = 7
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264 }else{
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265 legend_size = 6
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266 }
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267
6
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268 position_df = cbind(coord(msidata)[,1:2], msidata\$annotation)
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269 colnames(position_df)[3] = "sample_name"
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270
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271 combine_plot = ggplot(position_df, aes(x=x, y=y, fill=sample_name))+
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272 geom_tile() +
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273 coord_fixed()+
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274 ggtitle("Spatial orientation of pixel annotations")+
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275 theme_bw()+
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276 theme(plot.title = element_text(hjust = 0.5))+
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277 theme(text=element_text(family="ArialMT", face="bold", size=12))+
dcf79af72c8f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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278 theme(legend.position="bottom",legend.direction="vertical")+
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279 theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = legend_size))+
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280 guides(fill=guide_legend(ncol=5,byrow=TRUE))
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281
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282 print(combine_plot)
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283
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284 ## print legend only for less than 10 samples
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285 if (length(levels(msidata\$annotation)) < 10){
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286 key_legend = TRUE
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287 }else{key_legend = FALSE}
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288
6
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289 is.na(spectra(msidata)[]) == 0 ## in case of NA values they will be set to zero
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290 plot(msidata, pixel=1:ncol(msidata), pixel.groups=msidata\$annotation, key=key_legend, col=hue_pal()(length(levels(msidata\$annotation))),superpose=TRUE)
4
dcf79af72c8f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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291 }else{
6
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292 is.na(spectra(msidata)[]) == 0 ## in case of NA values they will be set to zero
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293 plot(msidata, pixel=1:ncol(msidata), key=TRUE)}
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294
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295 ##################### II) Sample: plot zoom-in mass spectrum ##########
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296
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297 #if $pixel_conditional.zoomed_sample:
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298 iData(msidata) <- iData(msidata)[] ## getting back data on disk
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299 #for $token in $pixel_conditional.zoomed_sample:
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300 print("zoomed sample pixels")
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301
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302 minmasspixel = features(msidata, mz=$token.xlimmin)
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303 maxmasspixel = features(msidata, mz=$token.xlimmax)
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304
6
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305 ## coloured plot with mean over all spectra for annotation group, otherwise only 1 black plot
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306 if (!is.null(levels(msidata\$annotation))){
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307 print("annotation samples")
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308 plot(msidata[minmasspixel:maxmasspixel,], pixel=1:ncol(msidata),
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309 xlim= c($token.xlimmin,$token.xlimmax),pixel.groups=msidata\$annotation,
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310 key=key_legend,col=hue_pal()(length(levels(msidata\$annotation))), superpose=TRUE)
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diff changeset
311 }else{
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312 plot(msidata[minmasspixel:maxmasspixel,], pixel=1:ncol(msidata), key=TRUE, xlim= c($token.xlimmin,$token.xlimmax))}
0
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313
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diff changeset
314 #end for
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diff changeset
315 #end if
5
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316
6
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diff changeset
317 if (!is.null(levels(msidata\$annotation))){
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diff changeset
318 pixeldf = data.frame(table(msidata\$annotation))
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diff changeset
319 }else{
dcf79af72c8f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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diff changeset
320 pixeldf = data.frame("$filename", ncol(msidata))}
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321 colnames(pixeldf) = c("sample name", "number of pixels")
0
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322
2
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diff changeset
323 #end if
0
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324
5
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diff changeset
325
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diff changeset
326 ############################# pixel table ######################################
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diff changeset
327 ###############################################################################
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diff changeset
328
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329
4
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330 ### overview table of pixels or samples:
0
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331 plot(0,type='n',axes=FALSE,ann=FALSE)
2
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332 title(main="Overview of chosen pixel:")
4
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333
6
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334 ### for more than 20 annotation groups print only 20 samples per page:
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335 if (is.null(levels(msidata\$annotation))){
4
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336 grid.table(pixeldf, rows= NULL)
6
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337 }else if (length(levels(msidata\$annotation)) <= 20){
4
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338 grid.table(pixeldf, rows= NULL)
dcf79af72c8f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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339 }else{
dcf79af72c8f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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340 grid.table(pixeldf[1:20,], rows= NULL)
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diff changeset
341 mincount = 21
dcf79af72c8f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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342 maxcount = 40
dcf79af72c8f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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343 for (count20 in 1:(ceiling(nrow(pixeldf)/20)-1)){
dcf79af72c8f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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344 plot(0,type='n',axes=FALSE,ann=FALSE)
dcf79af72c8f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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345 if (maxcount <= nrow(pixeldf)){
dcf79af72c8f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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346 grid.table(pixeldf[mincount:maxcount,], rows= NULL)
dcf79af72c8f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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347 mincount = mincount+20
dcf79af72c8f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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diff changeset
348 maxcount = maxcount+20
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349 }else{### stop last page with last sample otherwise NA in table
dcf79af72c8f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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350 grid.table(pixeldf[mincount:nrow(pixeldf),], rows= NULL)}
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351 }
dcf79af72c8f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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352 }
0
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353
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354 dev.off()
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355
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
356 }else{
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357 print("Inputfile has no intensities > 0")
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galaxyp
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diff changeset
358 dev.off()
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galaxyp
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359 }
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
360 ]]></configfile>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
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diff changeset
361 </configfiles>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
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diff changeset
362 <inputs>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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diff changeset
363 <param name="infile" type="data" format="imzml,rdata,analyze75" label="Inputfile as imzML, Analyze7.5 or Cardinal MSImageSet saved as RData"
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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diff changeset
364 help="Upload composite datatype imzml (ibd+imzML) or analyze75 (hdr+img+t2m) or regular upload .RData (Cardinal MSImageSet)"/>
5
bc931322e4d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
365 <conditional name="processed_cond">
bc931322e4d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
366 <param name="processed_file" type="select" label="Is the input file a processed imzML file ">
bc931322e4d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
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diff changeset
367 <option value="no_processed" selected="True">not a processed imzML</option>
bc931322e4d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
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diff changeset
368 <option value="processed">processed imzML</option>
bc931322e4d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
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diff changeset
369 </param>
bc931322e4d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
370 <when value="no_processed"/>
bc931322e4d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
371 <when value="processed">
bc931322e4d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
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diff changeset
372 <param name="accuracy" type="float" value="50" label="Mass accuracy to which the m/z values will be binned" help="This should be set to the native accuracy of the mass spectrometer, if known"/>
bc931322e4d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
373 <param name="units" display="radio" type="select" label="Unit of the mass accuracy" help="either m/z or ppm">
bc931322e4d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
374 <option value="mz" >mz</option>
bc931322e4d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
375 <option value="ppm" selected="True" >ppm</option>
bc931322e4d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
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diff changeset
376 </param>
bc931322e4d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
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diff changeset
377 </when>
bc931322e4d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
378 </conditional>
3
693a8efdfdeb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
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parents: 2
diff changeset
379 <param name="filename" type="text" value="" label="Title" help="will appear in the pdf output. If nothing given it will take the dataset name"/>
2
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
380 <conditional name="pixel_conditional">
5
bc931322e4d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
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diff changeset
381 <param name="pixel_type" type="select" label="Select if you want to plot the mass spectrum of a single pixel or the average spectrum of all pixels of a sample">
2
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
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diff changeset
382 <option value="single_pixel" selected="True">Single pixel</option>
5
bc931322e4d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
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diff changeset
383 <option value="sample_pixel">Average spectrum for each sample</option>
0
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
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diff changeset
384 </param>
2
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
385 <when value="single_pixel">
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
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diff changeset
386 <repeat name="repeatpixel" title="Plot mass spectra for pixel of interest" min="1" max="20">
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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diff changeset
387 <param name="inputx" type="integer" value="" label="x-coordinate of pixel of interest" help="x-value of the pixel of interest"/>
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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diff changeset
388 <param name="inputy" type="integer" value="" label="y-coordinate of pixel of interest" help="y-value of the pixel of interest"/>
6
5bc0d3f28895 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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diff changeset
389 <param name="inputmz" type="float" value="1296.7" label="Next parameters are to control heatmap image which will be plotted, define m/z here" help="m/z will be displayed as heatmap and the pixel of interest will be visualized by the intersection of two lines"/>
5bc0d3f28895 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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diff changeset
390 <param name="plusminusinDalton" value="0.25" type="float" label="m/z range for this m/z value" help="plusminus m/z window "/>
2
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
391 <param name="inputcolour" type="select" label="select the colour for the lines at x and y position">
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
392 <option value="white" selected="True">white</option>
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
393 <option value="black">black</option>
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
394 <option value="grey">grey</option>
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
395 <option value="blue">blue</option>
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
396 <option value="red">red</option>
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
397 <option value="green">green</option>
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
398 </param>
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
399 <param name="inputtype" type="select" label="select the line type for the lines at x and y position">
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
400 <option value="solid" selected="True">solid</option>
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
401 <option value="dashed">dashed</option>
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
402 <option value="dotted">dotted</option>
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
403 <option value="longdash">longdash</option>
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
404 </param>
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
405 <param name="inputwidth" type="integer" value="2" label="select the width of the lines at x and y position"/>
3
693a8efdfdeb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
406 <repeat name="zoomedplot" title="Zoomed in plots with m/z min and m/z max to define the plot window" min="0" max="50">
6
5bc0d3f28895 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
407 <param name="xlimmin" type="integer" value="" label="lower m/z boundary for plotting window" help="minimum m/z for zoomed in window"/>
5bc0d3f28895 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
408 <param name="xlimmax" type="integer" value="" label="upper m/z boundary for plotting window" help="maximum m/z for zoomed in window"/>
2
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
409 </repeat>
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
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diff changeset
410 </repeat>
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
411 </when>
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
412 <when value="sample_pixel">
6
5bc0d3f28895 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
413 <conditional name="tabular_annotation">
5bc0d3f28895 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
414 <param name="load_annotation" type="select" label="Use pixel annotation from tabular file for spectra plots">
5bc0d3f28895 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
415 <option value="no_annotation" selected="True">pixels belong into one group only</option>
5bc0d3f28895 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
416 <option value="yes_annotation">group pixels according to annotations</option>
5bc0d3f28895 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
417 </param>
5bc0d3f28895 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
418 <when value="yes_annotation">
5bc0d3f28895 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
419 <param name="annotation_file" type="data" format="tabular" label="Use annotations from tabular file"
5bc0d3f28895 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
420 help="Tabular file with three columns: x values, y values and pixel annotations"/>
5bc0d3f28895 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
421 <param name="column_x" data_ref="annotation_file" label="Column with x values" type="data_column"/>
5bc0d3f28895 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
422 <param name="column_y" data_ref="annotation_file" label="Column with y values" type="data_column"/>
5bc0d3f28895 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
423 <param name="column_names" data_ref="annotation_file" label="Column with pixel annotations" type="data_column"/>
5bc0d3f28895 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
424 <param name="tabular_header" type="boolean" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/>
5bc0d3f28895 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
425 </when>
5bc0d3f28895 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
426 <when value="no_annotation"/>
5bc0d3f28895 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
427 </conditional>
3
693a8efdfdeb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
428 <repeat name="zoomed_sample" title="Zoomed in plots with m/z min and m/z max to define the plot window" min="0" max="50">
6
5bc0d3f28895 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
429 <param name="xlimmin" type="integer" value="" label="lower m/z boundary for plotting window" help="minimum m/z for zoomed in window"/>
5bc0d3f28895 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
430 <param name="xlimmax" type="integer" value="" label="upper m/z boundary for plotting window" help="maximum m/z for zoomed in window"/>
2
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
431 </repeat>
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
432 </when>
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
433 </conditional>
0
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
434 </inputs>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
435 <outputs>
3
693a8efdfdeb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
436 <data format="pdf" name="plots" from_work_dir="mzplots.pdf" label = "$infile.display_name mass_spectra"/>
0
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
437 </outputs>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
438 <tests>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
439 <test>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
440 <param name="infile" value="" ftype="imzml">
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
441 <composite_data value="Example_Continuous.imzML"/>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
442 <composite_data value="Example_Continuous.ibd"/>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
443 </param>
2
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
444 <conditional name="pixel_conditional">
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
445 <param name="pixel_type" value="single_pixel"/>
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
446 <repeat name="repeatpixel">
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
447 <param name="plusminusinDalton" value="0.25"/>
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
448 <param name="inputx" value="3"/>
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
449 <param name="inputy" value="3"/>
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
450 <repeat name="zoomedplot">
3
693a8efdfdeb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
451 <param name="xlimmin" value="310"/>
693a8efdfdeb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
452 <param name="xlimmax" value="320"/>
2
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
453 </repeat>
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
454 <repeat name="zoomedplot">
3
693a8efdfdeb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
455 <param name="xlimmin" value="350"/>
693a8efdfdeb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
456 <param name="xlimmax" value="400"/>
2
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
457 </repeat>
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
458 <repeat name="zoomedplot">
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
459 <param name="xlimmin" value="400"/>
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
460 <param name="xlimmax" value="420"/>
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
461 </repeat>
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
462 </repeat>
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
463 <repeat name="repeatpixel">
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
464 <param name="plusminusinDalton" value="0.25"/>
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
465 <param name="inputx" value="2"/>
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
466 <param name="inputy" value="2"/>
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
467 </repeat>
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
468 <repeat name="repeatpixel">
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
469 <param name="plusminusinDalton" value="0.25"/>
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
470 <param name="inputx" value="1"/>
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
471 <param name="inputy" value="1"/>
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
472 </repeat>
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
473 </conditional>
0
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
474 <output name="plots" file="Plot_imzml.pdf" compare="sim_size" delta="20000"/>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
475 </test>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
476 <test>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
477 <param name="infile" value="" ftype="analyze75">
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
478 <composite_data value="Analyze75.hdr"/>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
479 <composite_data value="Analyze75.img"/>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
480 <composite_data value="Analyze75.t2m"/>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
481 </param>
2
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
482 <conditional name="pixel_conditional">
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
483 <param name="pixel_type" value="single_pixel"/>
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
484 <repeat name="repeatpixel">
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
485 <param name="plusminusinDalton" value="0.25"/>
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
486 <param name="inputx" value="5"/>
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
487 <param name="inputy" value="2"/>
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
488 <repeat name="zoomedplot">
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
489 <param name="xlimmin" value="840"/>
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
490 <param name="xlimmax" value="850"/>
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
491 </repeat>
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
492 </repeat>
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
493 <repeat name="repeatpixel">
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
494 <param name="plusminusinDalton" value="0.25"/>
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
495 <param name="inputx" value="2"/>
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
496 <param name="inputy" value="2"/>
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
497 </repeat>
4
dcf79af72c8f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
498 </conditional>
0
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
499 <output name="plots" file="Plot_analyze75.pdf" compare="sim_size" delta="20000"/>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
500 </test>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
501 <test>
4
dcf79af72c8f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
502 <param name="infile" value="" ftype="analyze75">
dcf79af72c8f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
503 <composite_data value="Analyze75.hdr"/>
dcf79af72c8f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
504 <composite_data value="Analyze75.img"/>
dcf79af72c8f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
505 <composite_data value="Analyze75.t2m"/>
dcf79af72c8f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
506 </param>
dcf79af72c8f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
507 <conditional name="pixel_conditional">
dcf79af72c8f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
508 <param name="pixel_type" value="sample_pixel"/>
6
5bc0d3f28895 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
509 <conditional name="tabular_annotation">
5bc0d3f28895 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
510 <param name="load_annotation" value="yes_annotation"/>
5bc0d3f28895 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
511 <param name="annotation_file" value="annotations.tabular" ftype="tabular"/>
5bc0d3f28895 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
512 <param name="column_x" value="1"/>
5bc0d3f28895 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
513 <param name="column_y" value="2"/>
5bc0d3f28895 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
514 <param name="column_names" value="4"/>
5bc0d3f28895 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
515 <param name="tabular_header" value="TRUE"/>
5bc0d3f28895 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
516 </conditional>
5bc0d3f28895 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
517 <repeat name="zoomed_sample">
5bc0d3f28895 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
518 <param name="xlimmin" value="1250"/>
5bc0d3f28895 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
519 <param name="xlimmax" value="1270"/>
5bc0d3f28895 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
520 </repeat>
4
dcf79af72c8f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
521 </conditional>
dcf79af72c8f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
522 <output name="plots" file="Plot_analyze75_allpixels.pdf" compare="sim_size" delta="20000"/>
dcf79af72c8f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
523 </test>
dcf79af72c8f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
524 <test>
3
693a8efdfdeb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
525 <param name="infile" value="123_combined.RData" ftype="rdata"/>
2
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
526 <conditional name="pixel_conditional">
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
527 <param name="pixel_type" value="sample_pixel"/>
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
528 <repeat name="zoomed_sample">
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
529 <param name="xlimmin" value="350"/>
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
530 <param name="xlimmax" value="360"/>
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
531 </repeat>
4
dcf79af72c8f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
532 </conditional>
2
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
533 <output name="plots" file="Plot_rdata.pdf" compare="sim_size" delta="20000"/>
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
534 </test>
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
535 <test>
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
536 <param name="infile" value="empty_spectra.rdata" ftype="rdata"/>
4
dcf79af72c8f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
537 <conditional name="pixel_conditional">
dcf79af72c8f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
538 <param name="pixel_type" value="single_pixel"/>
dcf79af72c8f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
539 <repeat name="repeatpixel">
dcf79af72c8f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
540 <param name="plusminusinDalton" value="0.1"/>
dcf79af72c8f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
541 <param name="inputx" value="1"/>
dcf79af72c8f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
542 <param name="inputy" value="1"/>
dcf79af72c8f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
543 </repeat>
dcf79af72c8f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
544 </conditional>
2
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
545 <output name="plots" file="Plot_empty_spectra.pdf" compare="sim_size" delta="20000"/>
0
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
546 </test>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
547 </tests>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
548 <help><![CDATA[
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
549
2
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
550 Cardinal is an R package that implements statistical & computational tools for analyzing mass spectrometry imaging datasets. `More information on Cardinal <http://cardinalmsi.org//>`_
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
551
3
693a8efdfdeb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
552 This tool uses the Cardinal plot function to generate (zoomed in) mass spectra plots of mass spectrometry imaging data.
0
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
553
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
554 Input data: 3 types of input data can be used:
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
555
2
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
556 - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/wp/imzml/>`_
0
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
557 - Analyze7.5 (upload hdr, img and t2m file via the "composite" function)
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
558 - Cardinal "MSImageSet" data (with variable name "msidata", saved as .RData)
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
559
2
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
560 Options:
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
561
3
693a8efdfdeb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
562 - "single pixel": Returns a full mass spectrum plot for one pixel, which is defined by its x- and y-coordinates
2
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
563
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
564 - Enter the x and y coordinates of your pixel of interest
3
693a8efdfdeb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
565 - To have a visual control for the selected pixel, a heatmap of a m/z of interest will be drawn. Two intersecting lines will show the pixel location. This procedure requires an m/z of interest together with a m/z range and for the lines the colour and type.
693a8efdfdeb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
566 - Additionally zoom into mass spectra plots is possible by providing the minimum and maximum m/z value to define the limits of the plot
6
5bc0d3f28895 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
567 - "All pixels of a sample": Returns a full average mass spectrum plot with different colours for each pixel annotation group, without annotations the average of all pixels is plotted
3
693a8efdfdeb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
568 - Additionally zoom into mass spectra plots is possible by providing the minimum and maximum m/z value to define the limits of the plot
2
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
569
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
570 Output:
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
571
3
693a8efdfdeb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
572 - Pdf with the selected mass spectra plots and additional control plots
2
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
573
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
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574 Tip:
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
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575
3
693a8efdfdeb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
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576 - Corresponding mass spectra with m/z intensity pairs as tabular output can be obtained with the filtering tool option "ranges for x and y"
2
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
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577
0
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
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578
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
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579 ]]>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
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580 </help>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
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581 <citations>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
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582 <citation type="doi">10.1093/bioinformatics/btv146</citation>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
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583 </citations>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
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584 </tool>