Mercurial > repos > galaxyp > msi_spectra_plot

annotate msi_spectra_plots.xml @ 4:dcf79af72c8f draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
author galaxyp
date Tue, 19 Jun 2018 18:06:46 -0400
parents 693a8efdfdeb
children bc931322e4d6
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dcf79af72c8f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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1 <tool id="mass_spectrometry_imaging_mzplots" name="MSI plot spectra" version="1.10.0.2">
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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 #if $infile.ext == 'imzml'
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38 msidata <- readImzML('infile', mass.accuracy=$accuracy, units.accuracy = "$units")
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39 #elif $infile.ext == 'analyze75'
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40 msidata = readAnalyze('infile')
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41 #else
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42 load('infile.RData')
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43 #end if
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44
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45 ###################################### file properties in numbers ##############
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46
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47 ## Number of features (m/z)
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48 maxfeatures = length(features(msidata))
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49 ## Range m/z
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50 minmz = round(min(mz(msidata)), digits=2)
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51 maxmz = round(max(mz(msidata)), digits=2)
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52 ## Number of spectra (pixels)
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53 pixelcount = length(pixels(msidata))
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54 ## Range x coordinates
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55 minimumx = min(coord(msidata)[,1])
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56 maximumx = max(coord(msidata)[,1])
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57 ## Range y coordinates
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58 minimumy = min(coord(msidata)[,2])
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59 maximumy = max(coord(msidata)[,2])
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60 ## Range of intensities
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61 minint = round(min(spectra(msidata)[]), digits=2)
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62 maxint = round(max(spectra(msidata)[]), digits=2)
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63 medint = round(median(spectra(msidata)[]), digits=2)
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64 ## Number of intensities > 0
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65 npeaks= sum(spectra(msidata)[]>0)
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66 ## Spectra multiplied with m/z (potential number of peaks)
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67 numpeaks = ncol(spectra(msidata)[])*nrow(spectra(msidata)[])
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68 ## Percentage of intensities > 0
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69 percpeaks = round(npeaks/numpeaks*100, digits=2)
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70 ## Number of empty TICs
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71 TICs = colSums(spectra(msidata)[])
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72 NumemptyTIC = sum(TICs == 0)
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73
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74 ## Processing informations
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75 processinginfo = processingData(msidata)
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76 centroidedinfo = processinginfo@centroided
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77
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78 ## if TRUE write processinginfo if FALSE write FALSE
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79
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80 ## normalization
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81 if (length(processinginfo@normalization) == 0) {
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82 normalizationinfo='FALSE'
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
83 } else {
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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84 normalizationinfo=processinginfo@normalization
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
85 }
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
86 ## smoothing
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
87 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
parents:
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88 smoothinginfo='FALSE'
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
89 } else {
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 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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91 }
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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92 ## baseline
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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93 if (length(processinginfo@baselineReduction) == 0) {
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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94 baselinereductioninfo='FALSE'
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
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95 } else {
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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96 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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97 }
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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98 ## peak picking
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
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99 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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100 peakpickinginfo='FALSE'
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101 } else {
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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102 peakpickinginfo=processinginfo@peakPicking
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103 }
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104
3
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105 properties = c("Number of m/z features",
4
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106 "Range of m/z values",
0
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107 "Number of pixels",
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108 "Range of x coordinates",
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109 "Range of y coordinates",
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110 "Range of intensities",
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111 "Median of intensities",
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112 "Intensities > 0",
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113 "Number of zero TICs",
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114 "Preprocessing",
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115 "Normalization",
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116 "Smoothing",
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117 "Baseline reduction",
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118 "Peak picking",
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119 "Centroided")
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120
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121 values = c(paste0(maxfeatures),
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122 paste0(minmz, " - ", maxmz),
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123 paste0(pixelcount),
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124 paste0(minimumx, " - ", maximumx),
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125 paste0(minimumy, " - ", maximumy),
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126 paste0(minint, " - ", maxint),
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127 paste0(medint),
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128 paste0(percpeaks, " %"),
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129 paste0(NumemptyTIC),
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130 paste0(" "),
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131 paste0(normalizationinfo),
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132 paste0(smoothinginfo),
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133 paste0(baselinereductioninfo),
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134 paste0(peakpickinginfo),
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135 paste0(centroidedinfo))
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136
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137 property_df = data.frame(properties, values)
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138
2
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139 ######################################## PDF ###################################
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140 ################################################################################
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141 ################################################################################
0
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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)
3
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diff changeset
146 #if not $filename:
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147 #set $filename = $infile.display_name
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148 #end if
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149 title(main=paste0("Plotted mass spectra for file: \n\n","$filename"))
0
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150
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151
2
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152 ############################# I) numbers ######################################
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153 ###############################################################################
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154
0
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155 grid.table(property_df, rows= NULL)
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156
3
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diff changeset
157 if (npeaks > 0){
0
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158
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159 pixeldf = data.frame(matrix(ncol = 2, nrow=0))
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160
3
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galaxyp
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161 ############################# single pixel ################################
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162 ###########################################################################
2
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163
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164 #if str( $pixel_conditional.pixel_type) == 'single_pixel':
3
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165 print("single_pixel")
2
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166
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167 #for $chosenpixel in $pixel_conditional.repeatpixel:
0
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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168
2
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169 pixelisvalid = as.character($chosenpixel.inputx %in% coord(msidata)\$x & $chosenpixel.inputy %in% coord(msidata)\$y)
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170 pixelname = paste0("x=", $chosenpixel.inputx,", ", "y=", $chosenpixel.inputy)
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171 pixeldf = rbind(pixeldf, cbind(pixelname, pixelisvalid))
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172
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173 ############################# II) control image ####################
0
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174
3
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175 if (pixelisvalid == "TRUE"){
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176 print(pixelisvalid)
2
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177
3
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178 image(msidata, mz=$chosenpixel.inputmz, ylim = c(maximumy+(0.2*maximumy),minimumy-1),
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179 colorkey=FALSE, plusminus = $chosenpixel.plusminusinDalton, contrast.enhance = "histogram",
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180 main= paste0("x= ",$chosenpixel.inputx, ", y= ", $chosenpixel.inputy))
2
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181
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182 abline(v=$chosenpixel.inputx, col ="$chosenpixel.inputcolour", lty="$chosenpixel.inputtype", lwd=$chosenpixel.inputwidth)
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183 abline(h=$chosenpixel.inputy, col ="$chosenpixel.inputcolour", lty="$chosenpixel.inputtype", lwd=$chosenpixel.inputwidth)
0
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184
2
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185 ##################### III) plot full mass spectrum #################
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186
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187 plot(msidata, coord=list(x=$chosenpixel.inputx, y=$chosenpixel.inputy))
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188
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189 ##################### IV) plot zoom-in mass spectrum ###############
0
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190
2
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191 #if $chosenpixel.zoomedplot:
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192 #for $token in $chosenpixel.zoomedplot:
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193
2
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194 minmasspixel = features(msidata, mz=$token.xlimmin)
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195 maxmasspixel = features(msidata, mz=$token.xlimmax)
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196
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197 plot(msidata[minmasspixel:maxmasspixel,], coord=list(x=$chosenpixel.inputx, y=$chosenpixel.inputy),
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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198 xlim= c($token.xlimmin,$token.xlimmax))
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199
2
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200 #end for
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201 #end if
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202 }else{
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203 print("The pixel coordinates did not correspond to a real pixel")}
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204 #end for
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205
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206 colnames(pixeldf) = c("pixel coordinates", "coordinates were found in this file")
0
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207
3
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208
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209 ############################# sample pixel ################################
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210 ###########################################################################
0
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211
3
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212 #elif str( $pixel_conditional.pixel_type) == 'sample_pixel':
4
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213 print("sample pixels")
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214
3
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215 ##################### I) Sample: plot full mass spectrum ##############
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216
4
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217 ## coloured plot with mean over all spectra for combined_sample, otherwise only 1 black plot
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218 if (!is.null(levels(msidata\$combined_sample))){
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219 print("combined samples")
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220
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221 ## overview plot over combined sample, in case more than 10 combined_samples legend has to be taken from this plot
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222 number_combined = length(levels(msidata\$combined_sample))
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223
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224 ## the more combined_samples a file has the smaller will be the legend
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225 if (number_combined<20){
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226 legend_size = 10
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227 }else if (number_combined>20 && number_combined<40){
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228 legend_size = 9
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229 }else if (number_combined>40 && number_combined<60){
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230 legend_size = 8
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231 }else if (number_combined>60 && number_combined<100){
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232 legend_size = 7
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233 }else{
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234 legend_size = 6
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235 }
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236
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237 position_df = cbind(coord(msidata)[,1:2], msidata\$combined_sample)
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238 colnames(position_df)[3] = "sample_name"
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239
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240 combine_plot = ggplot(position_df, aes(x=x, y=y, fill=sample_name))+
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241 geom_tile() +
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242 coord_fixed()+
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243 ggtitle("Spatial orientation of combined data")+
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244 theme_bw()+
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245 theme(plot.title = element_text(hjust = 0.5))+
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246 theme(text=element_text(family="ArialMT", face="bold", size=12))+
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247 theme(legend.position="bottom",legend.direction="vertical")+
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248 theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = legend_size))+
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249 guides(fill=guide_legend(ncol=5,byrow=TRUE))
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250 coord_labels = aggregate(cbind(x,y)~sample_name, data=position_df, mean)
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251 coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$sample_name)
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252 for(file_count in 1:nrow(coord_labels))
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253 {combine_plot = combine_plot + annotate("text",x=coord_labels[file_count,"x"],
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254 y=coord_labels[file_count,"y"],label=toString(coord_labels[file_count,4]))}
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255
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256 print(combine_plot)
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257
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258 ## print legend only for less than 10 samples
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259 if (length(levels(msidata\$combined_sample)) < 10){
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260 key_legend = TRUE
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261 }else{key_legend = FALSE}
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262
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263 plot(msidata, pixel=1:ncol(msidata), pixel.groups=msidata\$combined_sample, key=key_legend, col=hue_pal()(length(levels(msidata\$combined_sample))),superpose=TRUE)
dcf79af72c8f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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264 }else{
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265 plot(msidata, pixel=1:ncol(msidata), key=TRUE)}
3
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266
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267 ##################### II) Sample: plot zoom-in mass spectrum ##########
2
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268
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269 #if $pixel_conditional.zoomed_sample:
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270 #for $token in $pixel_conditional.zoomed_sample:
4
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271 print("zoomed sample pixels")
0
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272
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273 minmasspixel = features(msidata, mz=$token.xlimmin)
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274 maxmasspixel = features(msidata, mz=$token.xlimmax)
3
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275
4
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276 ## coloured plot with mean over all spectra for combined_sample, otherwise only 1 black plot
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277 if (!is.null(levels(msidata\$combined_sample))){
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278 print("combined samples")
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279 plot(msidata[minmasspixel:maxmasspixel,], pixel=1:ncol(msidata),
dcf79af72c8f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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280 xlim= c($token.xlimmin,$token.xlimmax),pixel.groups=msidata\$combined_sample,
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281 key=key_legend,col=hue_pal()(length(levels(msidata\$combined_sample))), superpose=TRUE)
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282 }else{
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283 plot(msidata[minmasspixel:maxmasspixel,], pixel=1:ncol(msidata), key=TRUE, xlim= c($token.xlimmin,$token.xlimmax))}
0
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284
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285 #end for
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286 #end if
4
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287 if (!is.null(levels(msidata\$combined_sample))){
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288 pixeldf = data.frame(table(msidata\$combined_sample))
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289 }else{
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290 pixeldf = data.frame("$filename", ncol(msidata))}
2
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291 colnames(pixeldf) = c("sample name", "number of pixels")
0
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292
2
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293 #end if
0
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294
4
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295 ### overview table of pixels or samples:
0
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296 plot(0,type='n',axes=FALSE,ann=FALSE)
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297 title(main="Overview of chosen pixel:")
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298
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299 ### for more than 20 combined samples print only 20 samples per page:
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300 if (is.null(levels(msidata\$combined_sample))){
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301 grid.table(pixeldf, rows= NULL)
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302 }else if (length(levels(msidata\$combined_sample)) <= 20){
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303 grid.table(pixeldf, rows= NULL)
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304 }else{
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305 grid.table(pixeldf[1:20,], rows= NULL)
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306 mincount = 21
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307 maxcount = 40
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308 for (count20 in 1:(ceiling(nrow(pixeldf)/20)-1)){
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309 plot(0,type='n',axes=FALSE,ann=FALSE)
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310 if (maxcount <= nrow(pixeldf)){
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311 grid.table(pixeldf[mincount:maxcount,], rows= NULL)
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312 mincount = mincount+20
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313 maxcount = maxcount+20
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314 }else{### stop last page with last sample otherwise NA in table
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315 grid.table(pixeldf[mincount:nrow(pixeldf),], rows= NULL)}
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316 }
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317 }
0
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318
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319 dev.off()
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320
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321 }else{
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322 print("Inputfile has no intensities > 0")
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323 dev.off()
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324 }
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325 ]]></configfile>
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326 </configfiles>
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327 <inputs>
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328 <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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329 help="Upload composite datatype imzml (ibd+imzML) or analyze75 (hdr+img+t2m) or regular upload .RData (Cardinal MSImageSet)"/>
4
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330 <param name="accuracy" type="float" value="50" label="Only for processed imzML files: enter 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"/>
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331 <param name="units" display="radio" type="select" label="Only for processed imzML files: unit of the mass accuracy" help="either m/z or ppm">
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diff changeset
332 <option value="mz" >mz</option>
dcf79af72c8f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
333 <option value="ppm" selected="True" >ppm</option>
dcf79af72c8f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
334 </param>
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
335 <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
336 <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
337 <param name="pixel_type" type="select" label="Select if you want to plot the mass spectrum of a single pixel or of all pixels of a 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
338 <option value="single_pixel" selected="True">Single pixel</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
339 <option value="sample_pixel">All pixels of a sample</option>
0
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
340 </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
341 <when 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
342 <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
galaxyp
parents: 1
diff changeset
343 <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
galaxyp
parents: 1
diff changeset
344 <param name="inputy" type="integer" value="" label="y-coordinate of pixel of interest" help="y-value of the 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
345 <param name="inputmz" type="float" value="1296.7" label="Next parameters are to control heatmap image which will be plotted, here m/z in Dalton" help="m/z will be displayed as heatmap and the pixel of interest will be visualized by the intersection of two lines"/>
693a8efdfdeb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
346 <param name="plusminusinDalton" value="0.25" type="float" label="m/z range for this m/z value" help="plusminus m/z window in Dalton"/>
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
347 <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
348 <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
349 <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
350 <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
351 <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
352 <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
353 <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
354 </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
355 <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
356 <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
357 <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
358 <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
359 <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
360 </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
361 <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
362 <repeat name="zoomedplot" title="Zoomed in plots with m/z min and m/z max to define the plot window" min="0" max="50">
693a8efdfdeb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
363 <param name="xlimmin" type="integer" value="" label="lower boundary in Dalton for plotting window" help="minimum m/z for zoomed in window"/>
693a8efdfdeb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
364 <param name="xlimmax" type="integer" value="" label="upper boundary in Dalton 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
365 </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
366 </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
367 </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
368 <when value="sample_pixel">
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
369 <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">
693a8efdfdeb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
370 <param name="xlimmin" type="integer" value="" label="lower boundary in Dalton for plotting window" help="minimum m/z for zoomed in window"/>
693a8efdfdeb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 2
diff changeset
371 <param name="xlimmax" type="integer" value="" label="upper boundary in Dalton 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
372 </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
373 </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
374 </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
375 </inputs>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
376 <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
377 <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
378 </outputs>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
379 <tests>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
380 <test>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
381 <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
382 <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
383 <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
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 <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
386 <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
387 <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
388 <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
389 <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
390 <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
391 <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
392 <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
393 <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
394 </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
395 <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
396 <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
397 <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
398 </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
399 <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
400 <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
401 <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
402 </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
403 </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
404 <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
405 <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
406 <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
407 <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
408 </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
409 <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
410 <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
411 <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
412 <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
413 </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
414 </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
415 <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
416 </test>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
417 <test>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
418 <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
419 <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
420 <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
421 <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
422 </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
423 <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
424 <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
425 <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
426 <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
427 <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
428 <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
429 <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
430 <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
431 <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
432 </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
433 </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
434 <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
435 <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
436 <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
437 <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
438 </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
439 </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
440 <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
441 </test>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
442 <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
443 <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
444 <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
445 <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
446 <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
447 </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
448 <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
449 <param name="pixel_type" value="sample_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
450 <repeat name="zoomed_sample">
dcf79af72c8f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
451 <param name="xlimmin" value="1250"/>
dcf79af72c8f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
452 <param name="xlimmax" value="1270"/>
dcf79af72c8f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
453 </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
454 </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
455 <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
456 </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
457 <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
458 <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
459 <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
460 <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
461 <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
462 <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
463 <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
464 </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
465 </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
466 <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
467 </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
468 <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
469 <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
470 <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
471 <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
472 <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
473 <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
474 <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
475 <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
476 </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
477 </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
478 <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
479 </test>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
480 </tests>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
481 <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
482
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
483 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
484
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
485 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
486
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
galaxyp
parents:
diff changeset
487 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
488
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
489 - 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
490 - 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
491 - 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
492
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
493 Options:
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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494
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693a8efdfdeb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
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495 - "single pixel": Returns a full mass spectrum plot for one pixel, which is defined by its x- and y-coordinates
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7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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496
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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497 - Enter the x and y coordinates of your pixel of interest
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693a8efdfdeb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
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498 - 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
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499 - Additionally zoom into mass spectra plots is possible by providing the minimum and maximum m/z value to define the limits of the plot
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dcf79af72c8f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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500 - "All pixels of a sample": Returns a full average mass spectrum plot with different colours for the sample/each combined sample
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7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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501
3
693a8efdfdeb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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502 - 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
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503
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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504 Output:
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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505
3
693a8efdfdeb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
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506 - Pdf with the selected mass spectra plots and additional control plots
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7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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507
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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508 Tip:
7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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509
3
693a8efdfdeb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
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510 - Corresponding mass spectra with m/z intensity pairs as tabular output can be obtained with the filtering tool option "ranges for x and y"
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7e4797d9f7ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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511
0
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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512
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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513 ]]>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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514 </help>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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515 <citations>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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516 <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
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517 </citations>
6663b9a52726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_spectra_plot commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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518 </tool>