Mercurial > repos > galaxyp > msi_spectra_plot

annotate msi_spectra_plots.xml @ 0:6663b9a52726 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
author galaxyp
date Mon, 27 Nov 2017 13:49:09 -0500
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6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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1 <tool id="mass_spectrometry_imaging_mzplots" name="MSI massspectra" version="1.7.0">
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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>
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6 <requirement type="package" version="1.7.0">bioconductor-cardinal</requirement>
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7 <requirement type="package" version="2.2.1">r-gridextra</requirement>
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8 <requirement type="package" version="2.23-15">r-kernsmooth</requirement>
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9 </requirements>
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10 <command detect_errors="exit_code">
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11 <![CDATA[
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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12 #if $infile.ext == 'imzml'
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13 cp '${infile.extra_files_path}/imzml' infile.imzML &&
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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14 cp '${infile.extra_files_path}/ibd' infile.ibd &&
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15 #elif $infile.ext == 'analyze75'
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16 cp '${infile.extra_files_path}/hdr' infile.hdr &&
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17 cp '${infile.extra_files_path}/img' infile.img &&
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18 cp '${infile.extra_files_path}/t2m' infile.t2m &&
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19 #else
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20 ln -s $infile infile.RData &&
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21 #end if
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22 cat '${MSI_mzplots}' &&
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23 Rscript '${MSI_mzplots}'
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24 ]]>
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25 </command>
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26 <configfiles>
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27 <configfile name="MSI_mzplots"><![CDATA[
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28 ################################# load libraries and read file #########################
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29
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30 library(Cardinal)
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31 library(gridExtra)
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32 library(KernSmooth)
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33
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34 ## Read MALDI Imaging dataset
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35
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36 #if $infile.ext == 'imzml'
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37 msidata <- readMSIData('infile.imzML')
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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38 #elif $infile.ext == 'analyze75'
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39 msidata <- readMSIData('infile.hdr')
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40 #else
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41 load('infile.RData')
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42 #end if
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43
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44 ###################################### file properties in numbers ######################
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45
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46 ## Number of features (mz)
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47 maxfeatures = length(features(msidata))
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48 ## Range mz
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49 minmz = round(min(mz(msidata)), digits=2)
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50 maxmz = round(max(mz(msidata)), digits=2)
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51 ## Number of spectra (pixels)
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52 pixelcount = length(pixels(msidata))
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53 ## Range x coordinates
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54 minimumx = min(coord(msidata)[,1])
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55 maximumx = max(coord(msidata)[,1])
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56 ## Range y coordinates
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57 minimumy = min(coord(msidata)[,2])
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58 maximumy = max(coord(msidata)[,2])
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59 ## Range of intensities
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60 minint = round(min(spectra(msidata)[]), digits=2)
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61 maxint = round(max(spectra(msidata)[]), digits=2)
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62 medint = round(median(spectra(msidata)[]), digits=2)
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63 ## Number of intensities > 0
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64 npeaks= sum(spectra(msidata)[]>0)
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65 ## Spectra multiplied with mz (potential number of peaks)
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66 numpeaks = ncol(spectra(msidata)[])*nrow(spectra(msidata)[])
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67 ## Percentage of intensities > 0
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68 percpeaks = round(npeaks/numpeaks*100, digits=2)
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69 ## Number of empty TICs
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70 TICs = colSums(spectra(msidata)[])
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71 NumemptyTIC = sum(TICs == 0)
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72
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73 ## Processing informations
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74 processinginfo = processingData(msidata)
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75 centroidedinfo = processinginfo@centroided # TRUE or FALSE
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76
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77 ## if TRUE write processinginfo if no write FALSE
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78
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79 ## normalization
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80 if (length(processinginfo@normalization) == 0) {
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81 normalizationinfo='FALSE'
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82 } else {
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83 normalizationinfo=processinginfo@normalization
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84 }
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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85 ## smoothing
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
86 if (length(processinginfo@smoothing) == 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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87 smoothinginfo='FALSE'
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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88 } else {
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
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89 smoothinginfo=processinginfo@smoothing
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
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90 }
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
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91 ## baseline
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
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92 if (length(processinginfo@baselineReduction) == 0) {
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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93 baselinereductioninfo='FALSE'
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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94 } else {
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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95 baselinereductioninfo=processinginfo@baselineReduction
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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96 }
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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97 ## peak picking
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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98 if (length(processinginfo@peakPicking) == 0) {
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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99 peakpickinginfo='FALSE'
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100 } else {
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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101 peakpickinginfo=processinginfo@peakPicking
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102 }
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103
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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104 properties = c("Number of mz features",
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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105 "Range of mz values [Da]",
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106 "Number of pixels",
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107 "Range of x coordinates",
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108 "Range of y coordinates",
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109 "Range of intensities",
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110 "Median of intensities",
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111 "Intensities > 0",
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112 "Number of zero TICs",
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113 "Preprocessing",
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114 "Normalization",
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115 "Smoothing",
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116 "Baseline reduction",
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117 "Peak picking",
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118 "Centroided")
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119
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120 values = c(paste0(maxfeatures),
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121 paste0(minmz, " - ", maxmz),
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122 paste0(pixelcount),
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123 paste0(minimumx, " - ", maximumx),
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124 paste0(minimumy, " - ", maximumy),
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125 paste0(minint, " - ", maxint),
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126 paste0(medint),
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127 paste0(percpeaks, " %"),
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128 paste0(NumemptyTIC),
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129 paste0(" "),
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130 paste0(normalizationinfo),
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131 paste0(smoothinginfo),
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132 paste0(baselinereductioninfo),
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133 paste0(peakpickinginfo),
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134 paste0(centroidedinfo))
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135
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136 property_df = data.frame(properties, values)
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137
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138
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139 ######################################## PDF #############################################
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140 ##########################################################################################
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141 ##########################################################################################
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142
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143
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144 pdf("mzplots.pdf", fonts = "Times", pointsize = 12)
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145 plot(0,type='n',axes=FALSE,ann=FALSE)
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146
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147 title(main=paste0("Plotted mass spectra for file: \n\n", "$infile.display_name"))
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148
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149
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150 ############################# I) numbers ####################################
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151 #############################################################################
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152 grid.table(property_df, rows= NULL)
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153
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154 counting = 2
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155
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156 outputmatrix = matrix(mz(msidata), ncol=1, byrow=TRUE)
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157 colnames(outputmatrix) = "m/z"
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158
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159 if (npeaks > 0)
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160 {
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161 pixeldf = data.frame(matrix(ncol = 2, nrow=0))
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162
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163 #for $chosenpixel in $repeatpixel:
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164
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165
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166 ### is x and y which was put in to define pixel valid coordinates?
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167 pixelisvalid = as.character($chosenpixel.inputx %in% coord(msidata)\$x & $chosenpixel.inputy %in% coord(msidata)\$y)
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168 pixelname = paste0("x=", $chosenpixel.inputx,", ", "y=", $chosenpixel.inputy)
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169 pixeldf = rbind(pixeldf, cbind(pixelname, pixelisvalid))
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170
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171
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172 ############################# II) control image #############################
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173 #############################################################################
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174
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175
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176 if (pixelisvalid == "TRUE")
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177 {
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178
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179
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180 image(msidata, mz=$chosenpixel.inputmz,
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181 ylim = c(maximumy+(0.2*maximumy),minimumy-1),colorkey=FALSE, plusminus = $chosenpixel.plusminusinDalton, contrast.enhance = "histogram",
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182 main= paste0("x= ",$chosenpixel.inputx, ", y= ", $chosenpixel.inputy))
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183
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184 abline(v=$chosenpixel.inputx, col ="$chosenpixel.inputcolour", lty="$chosenpixel.inputtype", lwd=$chosenpixel.inputwidth)
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185 abline(h=$chosenpixel.inputy, col ="$chosenpixel.inputcolour", lty="$chosenpixel.inputtype", lwd=$chosenpixel.inputwidth)
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186
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187
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188 ##################### III) plot full mass spectrum ##########################
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189 #############################################################################
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190
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191 plot(msidata, coord=list(x=$chosenpixel.inputx, y=$chosenpixel.inputy))
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192
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193
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194
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195 ##################### IV) plot zoom-in mass spectrum ##########################
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196 #############################################################################
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197
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198 #if $chosenpixel.zoomedplot:
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199 #for $token in $chosenpixel.zoomedplot:
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200
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201 minmasspixel = features(msidata, mz=$token.xlimmin)
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202 maxmasspixel = features(msidata, mz=$token.xlimmax)
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203
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204 plot(msidata[minmasspixel:maxmasspixel,], coord=list(x=$chosenpixel.inputx, y=$chosenpixel.inputy),
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205 xlim= c($token.xlimmin,$token.xlimmax))
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206
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207 #end for
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208 #end if
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209
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210 ##################### V) Output with mz and intensities #####################
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211 #############################################################################
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212
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213
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214 ### for each repeat a new intensity column for the new pixel is added
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215 outputmatrix = cbind(outputmatrix, spectra(msidata)[,pixels(msidata, coord=list(x=$chosenpixel.inputx, y=$chosenpixel.inputy))])
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216 colnames(outputmatrix)[counting] = paste0("x= ",$chosenpixel.inputx, ", y= ", $chosenpixel.inputy, " intensity")
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217 counting = counting+1
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218
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219 }else{
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220 print("These pixel coordinates did not correspond to a real pixel")}
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221
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222 #end for
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223
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224 colnames(pixeldf) = c("pixel coordinates", "coordinates were found in this file")
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225 plot(0,type='n',axes=FALSE,ann=FALSE)
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226 title(main=paste0("Overview of chosen pixel for file:\n", "$infile.display_name"))
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227 grid.table(pixeldf, rows= NULL)
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228
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229 dev.off()
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230
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231 write.table(outputmatrix, file="$tabularmatrix", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
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232 }else{
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233 print("Inputfile has no intensities > 0")
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234 dev.off()
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235 }
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236 ]]></configfile>
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237 </configfiles>
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238 <inputs>
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239 <param name="infile" type="data" format="imzml,rdata,analyze75" label="Inputfile as imzML, Analyze7.5 or Cardinal MSImageSet saved as RData"
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240 help="Upload composite datatype imzml (ibd+imzML) or analyze75 (hdr+img+t2m) or regular upload .RData (Cardinal MSImageSet)"/>
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241 <repeat name="repeatpixel" title="Plot mass spectra for pixel of interest" min="1" max="20">
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242 <param name="inputx" type="integer" value="" label="x-coordinate of pixel of interest" help="x-value of the pixel of interest"/>
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243 <param name="inputy" type="integer" value="" label="y-coordinate of pixel of interest" help="y-value of the pixel of interest"/>
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244 <param name="inputmz" type="float" value="1296.7" label="Next parameters are to control heatmap image which will be plotted, here mz in Dalton" help="mz will be displayed as heatmap and the pixel of interest will be visualized by the intersection of two lines"/>
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245 <param name="plusminusinDalton" value="0.25" type="float" label="mass range for this mz value" help="plusminus mass window in Dalton"/>
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246 <param name="inputcolour" type="select" label="select the colour for the lines at x and y position">
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247 <option value="white" selected="True">white</option>
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248 <option value="black">black</option>
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249 <option value="grey">grey</option>
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250 <option value="blue">blue</option>
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251 <option value="red">red</option>
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252 <option value="green">green</option>
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253 </param>
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254 <param name="inputtype" type="select" label="select the line type for the lines at x and y position">
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255 <option value="solid" selected="True">solid</option>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
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256 <option value="dashed">dashed</option>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
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257 <option value="dotted">dotted</option>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
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258 <option value="longdash">longdash</option>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
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259 </param>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
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260 <param name="inputwidth" type="integer" value="2" label="select the width of the lines at x and y position"/>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
261 <repeat name="zoomedplot" title="Zoomed in plots with mz min and mz max to define the plot window" min="0" max="50">
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
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262 <param name="xlimmin" type="integer" value="" label="lower boundary in Dalton for plotting window" help="minimum mz for zoomed in window"/>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
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263 <param name="xlimmax" type="integer" value="" label="upper boundary in Dalton for plotting window" help="maximum mz for zoomed in window"/>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
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264 </repeat>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
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265 </repeat>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
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266 </inputs>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
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267 <outputs>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
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268 <data format="pdf" name="plots" from_work_dir="mzplots.pdf" label = "${tool.name} on $infile.display_name"/>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
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269 <data format="tabular" name="tabularmatrix" label="${tool.name} on $infile.display_name" />
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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270 </outputs>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
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271 <tests>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
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272 <test>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
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273 <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
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274 <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
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275 <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
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276 </param>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
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277 <repeat name="repeatpixel">
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
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278 <param name="plusminusinDalton" value="0.25"/>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
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279 <param name="inputx" value="3"/>
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
280 <param name="inputy" value="3"/>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
281 <repeat name="zoomedplot">
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
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282 <param name="xlimmin" value="550"/>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
283 <param name="xlimmax" value="555"/>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
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284 </repeat>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
285 <repeat name="zoomedplot">
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
286 <param name="xlimmin" value="750"/>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
287 <param name="xlimmax" value="800"/>
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
288 </repeat>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
289 <repeat name="zoomedplot">
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
290 <param name="xlimmin" value="400"/>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
291 <param name="xlimmax" value="420"/>
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
292 </repeat>
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
293 </repeat>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
294 <repeat name="repeatpixel">
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
295 <param name="plusminusinDalton" value="0.25"/>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
296 <param name="inputx" value="2"/>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
297 <param name="inputy" value="2"/>
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
298 </repeat>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
299 <repeat name="repeatpixel">
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
300 <param name="plusminusinDalton" value="0.25"/>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
301 <param name="inputx" value="1"/>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
302 <param name="inputy" value="1"/>
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
303 </repeat>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
304 <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
305 <output name="tabularmatrix" file="Matrix_imzml.txt"/>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
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306 </test>
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
307
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
308 <test>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
309 <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
310 <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
311 <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
312 <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
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diff changeset
313 </param>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
314 <repeat name="repeatpixel">
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
315 <param name="plusminusinDalton" value="0.25"/>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
316 <param name="inputx" value="5"/>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
317 <param name="inputy" value="2"/>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
318 <repeat name="zoomedplot">
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
319 <param name="xlimmin" value="840"/>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
320 <param name="xlimmax" value="850"/>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
321 </repeat>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
322 </repeat>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
323 <repeat name="repeatpixel">
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
324 <param name="plusminusinDalton" value="0.25"/>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
325 <param name="inputx" value="2"/>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
326 <param name="inputy" value="2"/>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
327 </repeat>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
328 <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
329 <output name="tabularmatrix" file="Matrix_analyze75.txt"/>
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
330 </test>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
331
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
332 <test>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
333 <param name="infile" value="preprocessing_results1.RData" ftype="rdata"/>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
334 <repeat name="repeatpixel">
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
335 <param name="plusminusinDalton" value="0.25"/>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
336 <param name="inputx" value="2"/>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
337 <param name="inputy" value="2"/>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
338 <repeat name="zoomedplot">
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
339 <param name="xlimmin" value="222"/>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
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340 <param name="xlimmax" value="244"/>
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341 </repeat>
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342 </repeat>
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343 <output name="plots" file="Plot_rdata.pdf" compare="sim_size" delta="20000"/>
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344 <output name="tabularmatrix" file="Matrix_rdata.txt"/>
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345 </test>
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346 <test>
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347 <param name="infile" value="LM8_file16.rdata" ftype="rdata"/>
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348 <param name="plusminusinDalton" value="0.1"/>
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349 <param name="inputx" value="1"/>
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350 <param name="inputy" value="1"/>
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351 <repeat name="repeatpixel">
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352 <param name="plusminusinDalton" value="0.25"/>
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353 <param name="inputx" value="2"/>
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354 <param name="inputy" value="2"/>
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355 <repeat name="zoomedplot">
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356 <param name="xlimmin" value="1000"/>
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357 <param name="xlimmax" value="1050"/>
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358 </repeat>
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359 </repeat>
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360 <output name="plots" file="Plot_LM8_file16.pdf" compare="sim_size" delta="20000"/>
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361 <output name="tabularmatrix" file="Matrix_LM8.txt"/>
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362 </test>
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363 </tests>
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364 <help><![CDATA[
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365
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366 Returns a full mass-spectrum plot and peaklist output with masses and intensities for the chosen pixel. Input needs the x and the y coordinates of the pixel of interest.
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367 Additionally zoom into mass-spectra plots is possible by providing the minimum and maximum mz value to define the limits of the plot.
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368 To have a visual control that the right pixel was chosen, a heatmap of a mass in Dalton which can be specified will be plotted and two intersecting lines will show where the chosen pixel is located in the ion image.
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369
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370 Input data: 3 types of input data can be used:
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371
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372 - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <http://ms-imaging.org/wp/introduction/>`_
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373 - Analyze7.5 (upload hdr, img and t2m file via the "composite" function)
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374 - Cardinal "MSImageSet" data (with variable name "msidata", saved as .RData)
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375
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376 The output of this tool contains a heatmap of the mass of interest with two lines intersecting at the pixel of interest. Then the full mass-spectrum plot is obtained and if chosen also several zoomed in mass spectra. A peaklist with masses and intensities for this pixel is exported as tabular file.
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377
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378 ]]>
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379 </help>
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380 <citations>
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381 <citation type="doi">10.1093/bioinformatics/btv146</citation>
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382 </citations>
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383 </tool>