Mercurial > repos > galaxyp > msi_ion_images

annotate msi_ion_images.xml @ 0:8ae9894fc55f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_ion_images commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
author galaxyp
date Mon, 27 Nov 2017 13:48:44 -0500
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8ae9894fc55f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_ion_images commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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1 <tool id="mass_spectrometry_imaging_ion_images" name="MSI ion images" version="1.7.0">
8ae9894fc55f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_ion_images commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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2 <description>
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3 mass spectrometry imaging heatmaps
8ae9894fc55f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_ion_images commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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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>
8ae9894fc55f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_ion_images commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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8 <requirement type="package" version="2.23-15">r-kernsmooth</requirement>
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9 <requirement type="package" version="0.20-35">r-lattice</requirement>
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10 </requirements>
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11 <command detect_errors="aggressive">
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12 <![CDATA[
8ae9894fc55f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_ion_images commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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13 #if $infile.ext == 'imzml'
8ae9894fc55f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_ion_images commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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14 cp '${infile.extra_files_path}/imzml' infile.imzML &&
8ae9894fc55f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_ion_images commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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15 cp '${infile.extra_files_path}/ibd' infile.ibd &&
8ae9894fc55f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_ion_images commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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16 #elif $infile.ext == 'analyze75'
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17 cp '${infile.extra_files_path}/hdr' infile.hdr &&
8ae9894fc55f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_ion_images commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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18 cp '${infile.extra_files_path}/img' infile.img &&
8ae9894fc55f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_ion_images commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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19 cp '${infile.extra_files_path}/t2m' infile.t2m &&
8ae9894fc55f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_ion_images commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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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_heatmaps}' &&
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24 Rscript '${MSI_heatmaps}'
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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_heatmaps"><![CDATA[
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29 ################################# load libraries and read file #########################
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30
8ae9894fc55f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_ion_images commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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31 library(Cardinal)
8ae9894fc55f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_ion_images commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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32 library(gridExtra)
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33 library(KernSmooth)
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34 library(lattice)
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35
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36 ## Read MALDI Imaging dataset
8ae9894fc55f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_ion_images commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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37
8ae9894fc55f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_ion_images commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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38 #if $infile.ext == 'imzml'
8ae9894fc55f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_ion_images commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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39 msidata <- readMSIData('infile.imzML')
8ae9894fc55f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_ion_images commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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40 #elif $infile.ext == 'analyze75'
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41 msidata <- readMSIData('infile.hdr')
8ae9894fc55f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_ion_images commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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42 #else
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43 load('infile.RData')
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44 #end if
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45
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46 #if $massfile:
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47 ### Read tabular file with peptide masses for plots and heatmap images:
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48 input_list = read.delim("$massfile", header = FALSE, na.strings=c("","NA", "#NUM!", "#ZAHL!"), stringsAsFactors = FALSE)
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49 if (ncol(input_list) == 1)
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50 {
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51 input_list = cbind(input_list, input_list)
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52 }
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53 #else
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54 input_list = data.frame(0, 0)
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55 #end if
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56 colnames(input_list)[1:2] = c("mz", "name")
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57
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58 ###################################### file properties in numbers ######################
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59
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60 ## Number of features (mz)
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61 maxfeatures = length(features(msidata))
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62 ## Range mz
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63 minmz = round(min(mz(msidata)), digits=2)
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64 maxmz = round(max(mz(msidata)), digits=2)
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65 ## Number of spectra (pixels)
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66 pixelcount = length(pixels(msidata))
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67 ## Range x coordinates
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68 minimumx = min(coord(msidata)[,1])
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69 maximumx = max(coord(msidata)[,1])
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70 ## Range y coordinates
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71 minimumy = min(coord(msidata)[,2])
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72 maximumy = max(coord(msidata)[,2])
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73 ## Range of intensities
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74 minint = round(min(spectra(msidata)[]), digits=2)
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75 maxint = round(max(spectra(msidata)[]), digits=2)
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76 medint = round(median(spectra(msidata)[]), digits=2)
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77 ## Number of intensities > 0
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78 npeaks= sum(spectra(msidata)[]>0)
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79 ## Spectra multiplied with mz (potential number of peaks)
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80 numpeaks = ncol(spectra(msidata)[])*nrow(spectra(msidata)[])
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81 ## Percentage of intensities > 0
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82 percpeaks = round(npeaks/numpeaks*100, digits=2)
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83 ## Number of empty TICs
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84 TICs = colSums(spectra(msidata)[])
8ae9894fc55f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_ion_images commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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85 NumemptyTIC = sum(TICs == 0)
8ae9894fc55f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_ion_images commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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86
8ae9894fc55f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_ion_images commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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87 ## Processing informations
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88 processinginfo = processingData(msidata)
8ae9894fc55f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_ion_images commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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89 centroidedinfo = processinginfo@centroided # TRUE or FALSE
8ae9894fc55f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_ion_images commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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90
8ae9894fc55f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_ion_images commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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91 ## if TRUE write processinginfo if no write FALSE
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92
8ae9894fc55f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_ion_images commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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93 ## normalization
8ae9894fc55f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_ion_images commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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94 if (length(processinginfo@normalization) == 0) {
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95 normalizationinfo='FALSE'
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96 } else {
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97 normalizationinfo=processinginfo@normalization
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98 }
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99 ## smoothing
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100 if (length(processinginfo@smoothing) == 0) {
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101 smoothinginfo='FALSE'
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102 } else {
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103 smoothinginfo=processinginfo@smoothing
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104 }
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105 ## baseline
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106 if (length(processinginfo@baselineReduction) == 0) {
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107 baselinereductioninfo='FALSE'
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108 } else {
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109 baselinereductioninfo=processinginfo@baselineReduction
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110 }
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111 ## peak picking
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112 if (length(processinginfo@peakPicking) == 0) {
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113 peakpickinginfo='FALSE'
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114 } else {
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115 peakpickinginfo=processinginfo@peakPicking
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116 }
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117
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118 ### calculate how many input masses are valid:
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119 inputmasses = input_list[input_list[,1]>minmz & input_list[,1]<maxmz,]
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120
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121 inputmz = inputmasses[,1]
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122 inputnames = inputmasses[,2]
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123
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124 properties = c("Number of mz features",
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125 "Range of mz values [Da]",
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126 "Number of pixels",
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127 "Range of x coordinates",
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128 "Range of y coordinates",
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129 "Range of intensities",
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130 "Median of intensities",
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131 "Intensities > 0",
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132 "Number of zero TICs",
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133 "Preprocessing",
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134 "Normalization",
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135 "Smoothing",
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136 "Baseline reduction",
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137 "Peak picking",
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138 "Centroided",
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139 paste0("# valid masses in ", "$filename"))
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140
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141 values = c(paste0(maxfeatures),
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142 paste0(minmz, " - ", maxmz),
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143 paste0(pixelcount),
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144 paste0(minimumx, " - ", maximumx),
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145 paste0(minimumy, " - ", maximumy),
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146 paste0(minint, " - ", maxint),
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147 paste0(medint),
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148 paste0(percpeaks, " %"),
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149 paste0(NumemptyTIC),
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150 paste0(" "),
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151 paste0(normalizationinfo),
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152 paste0(smoothinginfo),
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153 paste0(baselinereductioninfo),
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154 paste0(peakpickinginfo),
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155 paste0(centroidedinfo),
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156 paste0(length(inputmz), "/", length(input_list[,1])))
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157
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158 property_df = data.frame(properties, values)
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159
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160 ######################################## PDF #############################################
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161 ##########################################################################################
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162 ##########################################################################################
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163
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164
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165 pdf("heatmaps.pdf", fonts = "Times", pointsize = 12)
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166 plot(0,type='n',axes=FALSE,ann=FALSE)
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167 #if not $filename:
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168 #set $filename = $infile.display_name
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169 #end if
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170 title(main=paste("Quality control of MSI data\n\n", "Filename:", "$filename"))
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171
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172 ############################# I) numbers ####################################
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173 #############################################################################
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174
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175 grid.table(property_df, rows= NULL)
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176
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177 if (npeaks > 0)
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178 {
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179 if (length(inputmz) != 0)
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180 {
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181 for (mass in 1:length(inputmz))
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182 {
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183 print(image(msidata, mz=inputmz[mass], strip = strip.custom(bg="lightgrey", par.strip.text=list(col="black", cex=.9)),
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184 lattice=TRUE, ylim = c(maximumy+1,minimumy-1), plusminus = $plusminusinDalton, contrast.enhance = "histogram",
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185 main= paste0(mass, ") ", inputnames[mass], " (", round(inputmz[mass], digits = 2)," ± ", $plusminusinDalton, " Da)")))
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186 }
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187 } else {print("The input masses were outside the mass range")}
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188
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189 dev.off()
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190
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191 }else{
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192 print("inputfile has no intensities > 0")
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193 dev.off()
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194 }
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195 ]]></configfile>
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196 </configfiles>
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197 <inputs>
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198 <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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199 help="Upload composite datatype imzml (ibd+imzML) or analyze75 (hdr+img+t2m) or regular upload .RData (Cardinal MSImageSet)"/>
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200 <param name="filename" type="text" value="" label="Title" help="will appear in the quality report. If nothing given it will take the dataset name."/>
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201 <param name="massfile" type="data" optional="true" format="tabular" label="Text file with masses and names"
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202 help="first column mass (m/z), second column mass name, tab separated file"/>
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203 <param name="plusminusinDalton" value="0.25" type="float" label="Mass range" help="plusminus mass window in Dalton"/>
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204 </inputs>
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205 <outputs>
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206 <data format="pdf" name="plots" from_work_dir="heatmaps.pdf" label = "${tool.name} on $infile.display_name"/>
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207 </outputs>
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208 <tests>
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209 <test>
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210 <param name="infile" value="" ftype="imzml">
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211 <composite_data value="Example_Continuous.imzML"/>
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212 <composite_data value="Example_Continuous.ibd"/>
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213 </param>
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214 <param name="massfile" value="inputpeptides.csv" ftype="tabular"/>
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215 <param name="plusminusinDalton" value="0.25"/>
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216 <param name="filename" value="Testfile_imzml"/>
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217 <output name="plots" file="Heatmaps_imzml.pdf" compare="sim_size" delta="20000"/>
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218 </test>
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219
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220 <test>
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221 <param name="infile" value="" ftype="analyze75">
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222 <composite_data value="Analyze75.hdr"/>
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223 <composite_data value="Analyze75.img"/>
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224 <composite_data value="Analyze75.t2m"/>
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225 </param>
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226 <param name="massfile" value="inputpeptides.txt" ftype="tabular"/>
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227 <param name="plusminusinDalton" value="0.5"/>
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228 <param name="filename" value="Testfile_analyze75"/>
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229 <output name="plots" file="Heatmaps_analyze75.pdf" compare="sim_size" delta="20000"/>
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230 </test>
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231 <test>
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232 <param name="infile" value="preprocessing_results1.RData" ftype="rdata"/>
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233 <param name="massfile" value="inputpeptides.csv" ftype="tabular"/>
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234 <param name="plusminusinDalton" value="0.1"/>
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235 <param name="filename" value="Testfile_rdata"/>
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236 <output name="plots" file="Heatmaps_rdata.pdf" compare="sim_size" delta="20000"/>
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237 </test>
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238 <test>
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239 <param name="infile" value="LM8_file16.rdata" ftype="rdata"/>
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240 <param name="massfile" value="inputpeptides.txt" ftype="tabular"/>
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241 <param name="plusminusinDalton" value="0.1"/>
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242 <param name="filename" value="Testfile_rdata"/>
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243 <output name="plots" file="Heatmaps_LM8_file16.pdf" compare="sim_size" delta="20000"/>
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244 </test>
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245 </tests>
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246 <help><![CDATA[
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247
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248 Heatmaps for different ion masses in mass-spectrometry imaging data.
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249
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250 Input data: 3 types of input data can be used:
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251
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252 - 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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253 - Analyze7.5 (upload hdr, img and t2m file via the "composite" function)
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254 - Cardinal "MSImageSet" data (with variable name "msidata", saved as .RData)
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255
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256 The output of this tool contains heatmaps for every ion mass of interest as pdf.
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257
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258 ]]>
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259 </help>
8ae9894fc55f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_ion_images commit 6d271de132f364b1e16b0222ad2d6e315586f0dd
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260 <citations>
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261 <citation type="doi">10.1093/bioinformatics/btv146</citation>
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262 </citations>
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263 </tool>