Mercurial > repos > galaxyp > msi_combine

annotate msi_combine.xml @ 7:72914d913505 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
author galaxyp
date Wed, 22 Aug 2018 13:31:44 -0400
parents 40f177062ba9
children
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72914d913505 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
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1 <tool id="mass_spectrometry_imaging_combine" name="MSI combine" version="1.10.0.5">
0
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2 <description>
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3 combine several mass spectrometry imaging datasets into one
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4 </description>
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5 <requirements>
1
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6 <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement>
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7 <requirement type="package" version="3.0.0">r-ggplot2</requirement>
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8 </requirements>
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9 <command detect_errors="exit_code">
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10 <![CDATA[
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11 #for $i, $infile in enumerate($infiles):
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12 #if $infile.ext == 'imzml'
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13 ln -s '${infile.extra_files_path}/imzml' infile_${i}.imzML &&
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14 ln -s '${infile.extra_files_path}/ibd' infile_${i}.ibd &&
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15 #elif $infile.ext == 'analyze75'
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16 ln -s '${infile.extra_files_path}/hdr' infile_${i}.hdr &&
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17 ln -s '${infile.extra_files_path}/img' infile_${i}.img &&
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18 ln -s '${infile.extra_files_path}/t2m' infile_${i}.t2m &&
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19 #else
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20 ln -s '$infile' infile_${i}.RData &&
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21 #end if
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22 #end for
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23 #for $i, $annotation_file in enumerate($annotation_files):
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24 ln -s '$annotation_file' annotation_file_${i}.tabular &&
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25 #end for
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26
0
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27 cat '${msi_combine}' &&
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28 Rscript '${msi_combine}'
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29
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30 ]]>
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31 </command>
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32 <configfiles>
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33 <configfile name="msi_combine"><![CDATA[
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35 #import re
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36
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37 ################ load libraries and some preparations #################
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38
1
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39 library(Cardinal)
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40 library(ggplot2)
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41
3
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42 ## read tabular file for xy_shift option
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43
1
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44 #if str( $combine_conditional.combine_method ) == 'xy_shifts':
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45 input_list = read.delim("$combine_conditional.coordinates_file", header = FALSE,
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46 stringsAsFactors = FALSE)
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47 #end if
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48
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49 ## load RData and store with new variable name
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50
2
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51 loadRData <- function(fileName){
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52 #loads an RData file, and returns it
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53 load(fileName)
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54 get(ls()[ls() != "fileName"])
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55 }
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56
3
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57 ## preparations for reading files one by one with for loop
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58
0
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59 pixel_vector = numeric()
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60 x_shifts = 0
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61 y_shifts = 0
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62 max_y = numeric()
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63 valid_dataset = logical()
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64 #set $msidata = []
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65 #set $pixelcoords = []
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66 #set $num_infiles = len($infiles)
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67 all_files = $num_infiles
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68
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70 ############## reading files and changing pixel coordinates ###################
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71
0
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72 #for $i, $infile in enumerate($infiles):
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73
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74 ## read MSI data
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75
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76 #if $infile.ext == 'imzml'
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77 #if str($processed_cond.processed_file) == "processed":
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78 msidata_$i <- readImzML('infile_${i}', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units")
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79 #else
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80 msidata_$i <- readImzML('infile_${i}')
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81 #end if
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82 #elif $infile.ext == 'analyze75'
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83 msidata_$i <- readAnalyze('infile_${i}')
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84 #else
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85 msidata_$i = loadRData('infile_${i}.RData')
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86 #end if
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87
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88
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89 ## read annotation data, up to 5 annotations can be used for now
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90
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91 ## read annotation tabular, set first two columns as x and y, merge with coordinates dataframe and order according to pixelorder in msidata
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92 input_annotation = read.delim("annotation_file_${i}.tabular", header = TRUE,
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93 stringsAsFactors = FALSE)
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94
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95 if (class(input_annotation[,1]) == "character"){
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96 annotation_coordinates = matrix(unlist(strsplit(as.character(input_annotation[,1]), "\\,")), ncol=2, byrow=TRUE)
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97 annotation_coordinates2 = cbind(as.numeric(substring(annotation_coordinates[,1], 5, last = 1000000L)), as.numeric(substring(annotation_coordinates[,2], 5, last = 1000000L)))
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98 input_annotation = cbind(annotation_coordinates2, input_annotation[,-1])
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99 }
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100
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101 colnames(input_annotation)[1:2] = c("x", "y")
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102 msidata_coordinates = cbind(coord(msidata_$i)[,1:2], 1:ncol(msidata_$i))
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103 colnames(msidata_coordinates)[3] = "pixel_index"
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104 ## only first 5 annotation columns are kept
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105 if (ncol(input_annotation) > 7){
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106 input_annotation = input_annotation[,1:7]}
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107
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108 annotation_df = merge(msidata_coordinates, input_annotation, by=c("x", "y"), all.x=TRUE)
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109 annotation_df_8 = cbind(annotation_df, data.frame(matrix(NA,ncol=8-ncol(annotation_df), nrow=ncol(msidata_$i))))
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110 annotation_df_8_sorted = annotation_df_8[order(annotation_df_8\$pixel_index),]## orders pixel according to msidata
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111
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112 ## each annotation column is assigned to the pixel in the pData slot of the MSIdata
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113 msidata_$i\$column1 = annotation_df_8_sorted[,4]
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114 msidata_$i\$column2 = annotation_df_8_sorted[,5]
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115 msidata_$i\$column3 = annotation_df_8_sorted[,6]
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116 msidata_$i\$column4 = annotation_df_8_sorted[,7]
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117 msidata_$i\$column5 = annotation_df_8_sorted[,8]
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118
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119 ## same name for MSI data files necessary to combine data in one single coordinate system
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120 sampleNames(msidata_$i) = "msidata"
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121
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122 ################### preparation xy shifts ##########################
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123
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124 #if str( $combine_conditional.combine_method ) == 'xy_shifts':
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125
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126 ## shift coordinates according to input tabular file and store file names
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127 coord(msidata_$i)\$x = coord(msidata_$i)\$x + input_list[$i+1,$combine_conditional.column_x] ## shifts x coordinates according to tabular file
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128 coord(msidata_$i)\$y = coord(msidata_$i)\$y + input_list[$i+1,$combine_conditional.column_y] ## shifts y coordinates according to tabular file
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129 pixel_vector = append(pixel_vector, rep(paste($i+1, input_list[$i+1,$combine_conditional.column_names], sep="_"),times=ncol(msidata_$i))) ## stores file name for each pixel
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130 msidata_$i\$combined_sample = rep(paste($i+1, input_list[$i+1,$combine_conditional.column_names], sep="_"),times=ncol(msidata_$i))
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131 pixelcoords_$i = cbind(coord(msidata_$i)[,1:2], rep($i+1,ncol(msidata_$i)))
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132 #silent $pixelcoords.append('pixelcoords_'+str($i))
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133 colnames(pixelcoords_$i)[3] = "file_number"
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134
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135 ################### preparation automatic combination ##########################
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136
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137 #elif str( $combine_conditional.combine_method ) == 'automatic_combine':
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138 names_vector = character()
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139 #set escaped_element_identifier = re.sub('[^\w\-\s\[/]]', '_', str($infile.element_identifier)) ## use name of inputfile from Galaxy
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140 if (sum(spectra(msidata_$i)[],na.rm=TRUE)>0) ## use only valid files
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141 {
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142 if (is.null(levels(msidata_$i\$combined_sample)))
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143 {
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144 names_vector = append(names_vector, rep(paste($i+1, "$escaped_element_identifier", sep="_"),ncol(msidata_$i)))
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145 msidata_$i\$combined_sample = as.factor(names_vector)
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146 }
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147 }
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148
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149 ## Number of input files define grid which is row-wise filled with files
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150
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151 coord(msidata_$i)\$x = coord(msidata_$i)\$x - (min(coord(msidata_$i)\$x-1)) + x_shifts
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152 coord(msidata_$i)\$y = coord(msidata_$i)\$y - (min(coord(msidata_$i)\$y-1)) + y_shifts
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153 x_shifts = max(coord(msidata_$i)\$x) + 5
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154 max_y = append(max_y, max(coord(msidata_$i)\$y))
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155 all_files = $num_infiles
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156 new_row = ($i+1)/ceiling(sqrt(all_files))
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157 new_row%%1==0
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158 if (new_row%%1==0)
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159 {x_shifts = 0 ### when row is filled: x values start again at zero
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160 y_shifts = max(max_y) + 5 ### when row is filled: y value increases to start a new row
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161 max_y = numeric()}
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162
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163 #end if
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164
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165 ## store files to combine them later and for each file check if it is valid
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166
0
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167 #silent $msidata.append('msidata_'+str($i))
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168 valid_dataset = append(valid_dataset,
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169 (ncol(msidata_$i)>0 & nrow(msidata_$i)>0 & sum(spectra(msidata_$i)[], na.rm=TRUE)>0))
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170
0
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171 #end for
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172
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173 ## extract columnnames from (last) annotation tabular (for QC plot names)
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174 annotation_colnames = colnames(input_annotation)[-c(1,2)]
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175
1
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176 ###################### automatic combination ###################################
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177 ################################################################################
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178
1
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179 #if str( $combine_conditional.combine_method ) == 'automatic_combine':
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180 print("automatic_combine")
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181
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182 ## combine only valid datasets
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183
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184 valid_data = list(#echo ','.join($msidata)#)[valid_dataset]
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185 msidata_combined = do.call(combine, valid_data)
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186 print("Valid datasets in order of input bottom to top:")
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187 print(valid_dataset)
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188
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189 ## create dataframe with x,y,sample_name and show all pixels in PDF as QC
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190
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191 pdf("Combined_qc.pdf", width=15, height=15)
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192 position_df = cbind(coord(msidata_combined)[,1:2], msidata_combined\$combined_sample)
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193 colnames(position_df)[3] = "sample_name"
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194 combine_plot = ggplot(position_df, aes(x=x, y=y, fill=sample_name))+
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195 geom_tile() +
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196 coord_fixed()+
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197 ggtitle("Spatial orientation of combined data (sample names)")+
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198 theme_bw()+
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199 theme(text=element_text(family="ArialMT", face="bold", size=15))+
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200 theme(legend.position="bottom",legend.direction="vertical")+
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201 guides(fill=guide_legend(ncol=4,byrow=TRUE))
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202 coord_labels = aggregate(cbind(x,y)~sample_name, data=position_df, mean, na.rm=TRUE, na.action="na.pass")
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203 coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$sample_name)
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204 for(file_count in 1:nrow(coord_labels))
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205 {combine_plot = combine_plot + annotate("text",x=coord_labels[file_count,"x"],
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206 y=coord_labels[file_count,"y"],label=toString(coord_labels[file_count,4]))}
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207 print(combine_plot)
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208 dev.off()
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209
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210 ## save as (.RData)
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211
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212 msidata = msidata_combined
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213 save(msidata, file="$msidata_combined")
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214
3
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215
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216 ################################## xy shifts ###################################
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217 ################################################################################
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218
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219 #elif str( $combine_conditional.combine_method ) == 'xy_shifts':
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220 print("xy_shifts")
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221
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222 ## find duplicated coordinates
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223 all_coordinates = do.call(rbind, list(#echo ','.join($pixelcoords)#))
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224 duplicated_coordinates= duplicated(all_coordinates[,1:2])| duplicated(all_coordinates[,1:2], fromLast=TRUE)
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225 print(paste0("Number of removed duplicated coordinates: ", sum(duplicated_coordinates)/2))
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226 unique_coordinates = all_coordinates[!duplicated_coordinates,]
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227
6
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228 ## remove duplicated coordinates
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229 datasetlist = list()
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230 count = 1
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231 for (usable_dataset in list(#echo ','.join($msidata)#)){
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232 pixelsofinterest = pixels(usable_dataset)[names(pixels(usable_dataset)) %in% rownames(unique_coordinates)]
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233 filtered_dataset = usable_dataset[,pixelsofinterest]
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234 if (ncol(filtered_dataset) > 0 ){
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235 datasetlist[[count]] = filtered_dataset}
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236 count = count +1}
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237
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238 msidata_combined = do.call(combine, datasetlist)
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239
6
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240 ## save as (.RData)
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241
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242 msidata = msidata_combined
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243 save(msidata, file="$msidata_combined")
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244
6
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245 ## create x,y,sample_name dataframe for QC pdf
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246
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247 position_df = cbind(coord(msidata), msidata\$combined_sample)
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248 colnames(position_df)[3] = "sample_name"
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249
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250 #end if
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251
1
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252
6
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253 ################################## outputs ####################################
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254 ################################################################################
3
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255
6
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256 ########### QC with pixels and their annotations ################################
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257
6
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258 pdf("Combined_qc.pdf", width=15, height=15)
3
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259
6
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260 ## combined plot
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261 combine_plot = ggplot(position_df, aes(x=x, y=y, fill=sample_name))+
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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262 geom_tile() +
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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263 coord_fixed()+
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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264 ggtitle("Spatial orientation of combined data")+
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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265 theme_bw()+
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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266 theme(text=element_text(family="ArialMT", face="bold", size=15))+
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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267 theme(legend.position="bottom",legend.direction="vertical")+
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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268 guides(fill=guide_legend(ncol=5,byrow=TRUE))
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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269 coord_labels = aggregate(cbind(x,y)~sample_name, data=position_df, mean)
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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270 coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$sample_name)
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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271 for(file_count in 1:nrow(coord_labels))
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272 {combine_plot = combine_plot + annotate("text",x=coord_labels[file_count,"x"],
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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273 y=coord_labels[file_count,"y"],label=toString(coord_labels[file_count,4]))}
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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274 print(combine_plot)
5
49c4a97e7e3a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
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275
6
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276
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277 ## annotation plots
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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278
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279 ## plot 1
3
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280
6
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281 column1_df = cbind(coord(msidata), msidata\$column1)
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282 colnames(column1_df)[3] = "column1"
3
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283
6
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284 if (sum(is.na(column1_df[3])) < nrow(column1_df)){
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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285 column1_plot = ggplot(column1_df, aes(x=x, y=y, fill=column1))+
1
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286 geom_tile() +
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287 coord_fixed()+
6
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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288 ggtitle(paste0(annotation_colnames[1]))+
1
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289 theme_bw()+
3
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290 theme(text=element_text(family="ArialMT", face="bold", size=15))+
f07413fa9b58 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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291 theme(legend.position="bottom",legend.direction="vertical")+
6
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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292 guides(fill=guide_legend(ncol=5,byrow=TRUE, title=annotation_colnames[1]))
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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293 print(column1_plot)}
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294 ##rename columnname for output tabular file
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295 colnames(column1_df)[3] = annotation_colnames[1]
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296
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297 ## plot 2
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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298 column2_df = cbind(coord(msidata), msidata\$column2)
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299 colnames(column2_df)[3] = "column2"
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300
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301 if (sum(is.na(column2_df[3])) < nrow(column2_df)){
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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302 column2_plot = ggplot(column2_df, aes(x=x, y=y, fill=column2))+
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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303 geom_tile() +
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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diff changeset
304 coord_fixed()+
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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305 ggtitle(paste0(annotation_colnames[2]))+
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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306 theme_bw()+
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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307 theme(text=element_text(family="ArialMT", face="bold", size=15))+
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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308 theme(legend.position="bottom",legend.direction="vertical")+
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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309 guides(fill=guide_legend(ncol=5,byrow=TRUE, title=annotation_colnames[2]))
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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310 print(column2_plot)}
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311 ##rename columnname for output tabular file
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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312 colnames(column2_df)[3] = annotation_colnames[2]
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313
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314 ## plot 3
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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315 column3_df = cbind(coord(msidata), msidata\$column3)
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316 colnames(column3_df)[3] = "column3"
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317 if (sum(is.na(column3_df[3])) < nrow(column3_df)){
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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318 column3_plot = ggplot(column3_df, aes(x=x, y=y, fill=column3))+
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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319 geom_tile() +
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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diff changeset
320 coord_fixed()+
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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321 ggtitle(paste0(annotation_colnames[3]))+
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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322 theme_bw()+
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323 theme(text=element_text(family="ArialMT", face="bold", size=15))+
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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324 theme(legend.position="bottom",legend.direction="vertical")+
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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diff changeset
325 guides(fill=guide_legend(ncol=5,byrow=TRUE, title=annotation_colnames[3]))
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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diff changeset
326 print(column3_plot)}
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diff changeset
327 ##rename columnname for output tabular file
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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328 colnames(column3_df)[3] = annotation_colnames[3]
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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329
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330 ## plot 4
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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331 column4_df = cbind(coord(msidata), msidata\$column4)
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332 colnames(column4_df)[3] = "column4"
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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333
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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diff changeset
334 if (sum(is.na(column4_df[3])) < nrow(column4_df)){
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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diff changeset
335 column4_plot = ggplot(column4_df, aes(x=x, y=y, fill=column4))+
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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diff changeset
336 geom_tile() +
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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diff changeset
337 coord_fixed()+
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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diff changeset
338 ggtitle(paste0(annotation_colnames[4]))+
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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diff changeset
339 theme_bw()+
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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diff changeset
340 theme(text=element_text(family="ArialMT", face="bold", size=15))+
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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diff changeset
341 theme(legend.position="bottom",legend.direction="vertical")+
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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diff changeset
342 guides(fill=guide_legend(ncol=5,byrow=TRUE, title=annotation_colnames[4]))
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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343 print(column4_plot)}
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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344 ##rename columnname for output tabular file
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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345 colnames(column4_df)[3] = annotation_colnames[4]
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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346
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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347 ## plot5
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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348
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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349 column5_df = cbind(coord(msidata), msidata\$column5)
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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350 colnames(column5_df)[3] = "column5"
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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351 if (sum(is.na(column5_df[3])) < nrow(column5_df)){
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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352 column5_plot = ggplot(column5_df, aes(x=x, y=y, fill=column5))+
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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diff changeset
353 geom_tile() +
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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diff changeset
354 coord_fixed()+
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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diff changeset
355 ggtitle(paste0(annotation_colnames[5]))+
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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diff changeset
356 theme_bw()+
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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diff changeset
357 theme(text=element_text(family="ArialMT", face="bold", size=15))+
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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diff changeset
358 theme(legend.position="bottom",legend.direction="vertical")+
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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diff changeset
359 guides(fill=guide_legend(ncol=5,byrow=TRUE, title=annotation_colnames[5]))
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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diff changeset
360 print(column5_plot)}
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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diff changeset
361 ##rename columnname for output tabular file
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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diff changeset
362 colnames(column5_df)[3] = annotation_colnames[5]
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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diff changeset
363
1
2ff16a066571 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
galaxyp
parents: 0
diff changeset
364 dev.off()
2ff16a066571 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
galaxyp
parents: 0
diff changeset
365
6
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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diff changeset
366 ##################### annotation tabular output ################################
0
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
parents:
diff changeset
367
5
49c4a97e7e3a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
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diff changeset
368 if (length(features(msidata))> 0 & length(pixels(msidata)) > 0){
6
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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diff changeset
369 annotation_df_list = list(position_df, column1_df, column2_df, column3_df, column4_df, column5_df)
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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diff changeset
370 combined_annotations = Reduce(function(...) merge(..., by=c("x", "y"), all=TRUE), annotation_df_list)
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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diff changeset
371 write.table(combined_annotations, file="$annotation_output", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
1
2ff16a066571 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
galaxyp
parents: 0
diff changeset
372 }else{
6
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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373 print("No annotation tabular output because file has no features or pixels left")
1
2ff16a066571 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
galaxyp
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diff changeset
374 }
5
49c4a97e7e3a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
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diff changeset
375
6
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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diff changeset
376 ####################### optional matrix output #################################
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
377
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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diff changeset
378 #if $output_matrix:
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
379
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
380 if (length(features(msidata))> 0 & length(pixels(msidata)) > 0){
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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diff changeset
381 spectramatrix = spectra(msidata)[]
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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diff changeset
382 spectramatrix = cbind(mz(msidata),spectramatrix)
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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diff changeset
383 newmatrix = rbind(c("mz | spectra", names(pixels(msidata))), spectramatrix)
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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diff changeset
384 write.table(newmatrix, file="$matrixasoutput", quote = FALSE, row.names = FALSE, col.names=FALSE, sep = "\t")
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
385 }else{
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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diff changeset
386 print("No intensity matrix output because file has no features or pixels left")
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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diff changeset
387 }
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
diff changeset
388
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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diff changeset
389 #end if
0
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
parents:
diff changeset
390
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
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diff changeset
391 ]]></configfile>
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
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diff changeset
392 </configfiles>
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
parents:
diff changeset
393 <inputs>
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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diff changeset
394 <param name="infiles" type="data" multiple="true" format="imzml,rdata,analyze75"
4
c1c0618fe430 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 3
diff changeset
395 label="MSI data as imzml, analyze7.5 or Cardinal MSImageSet saved as RData"
0
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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diff changeset
396 help="load imzml and ibd file by uploading composite datatype imzml"/>
5
49c4a97e7e3a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
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diff changeset
397 <conditional name="processed_cond">
49c4a97e7e3a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
398 <param name="processed_file" type="select" label="Is the input file a processed imzML file ">
49c4a97e7e3a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
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diff changeset
399 <option value="no_processed" selected="True">not a processed imzML</option>
49c4a97e7e3a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
400 <option value="processed">processed imzML</option>
49c4a97e7e3a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
401 </param>
49c4a97e7e3a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
402 <when value="no_processed"/>
49c4a97e7e3a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
403 <when value="processed">
49c4a97e7e3a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
404 <param name="accuracy" type="float" value="50" label="Mass accuracy to which the m/z values will be binned" help="This should be set to the native accuracy of the mass spectrometer, if known"/>
49c4a97e7e3a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
405 <param name="units" display="radio" type="select" label="Unit of the mass accuracy" help="either m/z or ppm">
49c4a97e7e3a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
406 <option value="mz" >mz</option>
49c4a97e7e3a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
407 <option value="ppm" selected="True" >ppm</option>
49c4a97e7e3a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
408 </param>
49c4a97e7e3a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
409 </when>
49c4a97e7e3a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 4
diff changeset
410 </conditional>
6
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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diff changeset
411 <param name="annotation_files" type="data" multiple="true" format="tabular"
7
72914d913505 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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diff changeset
412 label="Pixel annotations as tabular files, same number and order of files as input files"
72914d913505 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
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diff changeset
413 help="Coordinates in column 1 in format x = 1, y = 1 or first column x values, second column y values. Up to 5 columns with pixel annotations"/>
1
2ff16a066571 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
galaxyp
parents: 0
diff changeset
414 <conditional name="combine_conditional">
2ff16a066571 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
galaxyp
parents: 0
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415 <param name="combine_method" type="select" label="Select the way you want to combine multiple files" help="More detailed help can be found in the help section at the bottom">
2ff16a066571 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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416 <option value="automatic_combine" selected="True" >automatic combination</option>
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417 <option value="xy_shifts">shift xy coordinates with a tabular file</option>
1
2ff16a066571 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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418 </param>
3
f07413fa9b58 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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parents: 2
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419 <when value="automatic_combine"/>
1
2ff16a066571 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
galaxyp
parents: 0
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420 <when value="xy_shifts">
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40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 5
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421 <param name="coordinates_file" type="data" format="tabular" label="datasetnames, x and y values to shift pixel coordinates before combining"
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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422 help="Tabular file with three columns: 1 for the filename, 1 for the x-coordinate shift and 1 for the y-coordinate shift. Pixels with the same coordinates after shifting will be deleted."/>
1
2ff16a066571 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
galaxyp
parents: 0
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423 <param name="column_x" data_ref="coordinates_file" label="Column with values for shift in x direction" type="data_column"/>
2ff16a066571 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
galaxyp
parents: 0
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424 <param name="column_y" data_ref="coordinates_file" label="Column with values for shift in y direction" type="data_column"/>
2ff16a066571 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
galaxyp
parents: 0
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425 <param name="column_names" data_ref="coordinates_file" label="Column with dataset names" type="data_column"/>
2ff16a066571 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
galaxyp
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426 </when>
2ff16a066571 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
galaxyp
parents: 0
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427 </conditional>
2ff16a066571 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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428 <param name="output_matrix" type="boolean" display="radio" label="Intensity matrix output"/>
0
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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429 </inputs>
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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430 <outputs>
3
f07413fa9b58 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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431 <data format="rdata" name="msidata_combined" label="MSI_data_combined"/>
f07413fa9b58 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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432 <data format="pdf" name="combining_qc" from_work_dir="Combined_qc.pdf" label = "Combined_QC"/>
6
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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433 <data format="tabular" name="annotation_output" label="Annotation_tabular"/>
3
f07413fa9b58 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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434 <data format="tabular" name="matrixasoutput" label="Combined_matrix">
0
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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435 <filter>output_matrix</filter>
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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436 </data>
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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437 </outputs>
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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438 <tests>
6
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galaxyp
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439 <test expect_num_outputs="4">
0
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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440 <param name="infiles" value="msidata_1.RData,msidata_2.RData,msidata_3.RData" ftype="rdata"/>
6
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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441 <param name="annotation_files" value="annotations_file1.tabular,annotations_file2.tabular,annotations_file3.tabular" ftype="tabular"/>
1
2ff16a066571 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
galaxyp
parents: 0
diff changeset
442 <param name="combine_method" value="xy_shifts"/>
0
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
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443 <param name="coordinates_file" ftype="tabular" value="xy_coordinates.tabular"/>
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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444 <param name="column_x" value="1"/>
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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445 <param name="column_y" value="2"/>
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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446 <param name="column_names" value="3"/>
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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447 <param name="output_matrix" value="True"/>
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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448 <output name="matrixasoutput" file="123_combined_matrix.tabular"/>
6
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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449 <output name="annotation_output" file="123_annotation_output.tabular"/>
0
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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450 <output name="msidata_combined" file="123_combined.RData" compare="sim_size" />
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451 <output name="combining_qc" file="123_combined_QC.pdf" compare="sim_size" delta="2000"/>
0
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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452 </test>
6
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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453 <test expect_num_outputs="4">
0
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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454 <param name="infiles" value="msidata_1.RData,msidata_2.RData" ftype="rdata"/>
6
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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455 <param name="annotation_files" value="annotations_file1.tabular,annotations_file2.tabular" ftype="tabular"/>
3
f07413fa9b58 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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456 <param name="combine_method" value="automatic_combine"/>
0
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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457 <param name="output_matrix" value="True"/>
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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458 <output name="matrixasoutput" file="12_combined_matrix.tabular"/>
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40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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459 <output name="annotation_output" file="12_annotation_output.tabular"/>
0
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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460 <output name="msidata_combined" file="12_combined.RData" compare="sim_size" />
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galaxyp
parents: 6
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461 <output name="combining_qc" file="12_combined_QC.pdf" compare="sim_size" delta="2000"/>
0
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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462 </test>
6
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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463 <test expect_num_outputs="3">
3
f07413fa9b58 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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parents: 2
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464 <param name="infiles" value="msidata_1.RData,123_combined.RData" ftype="rdata"/>
6
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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465 <param name="annotation_files" value="annotations_file1.tabular,123_annotation.tabular" ftype="tabular"/>
1
2ff16a066571 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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466 <param name="combine_method" value="automatic_combine"/>
3
f07413fa9b58 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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467 <param name="output_matrix" value="False"/>
6
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468 <output name="annotation_output" file="112_annotation_output.tabular"/>
3
f07413fa9b58 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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469 <output name="msidata_combined" file="112_auto_combined.RData" compare="sim_size" />
7
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470 <output name="combining_qc" file="112_auto_combined_QC.pdf" compare="sim_size" delta="2000"/>
1
2ff16a066571 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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471 </test>
0
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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472 </tests>
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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473 <help>
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474 <![CDATA[
1
2ff16a066571 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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475
2
4f46f06e861b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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476 Cardinal is an R package that implements statistical & computational tools for analyzing mass spectrometry imaging datasets. `More information on Cardinal <http://cardinalmsi.org//>`_
1
2ff16a066571 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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parents: 0
diff changeset
477
3
f07413fa9b58 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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478 This tool uses the Cardinal combine function to combine several mass spectrometry imaging data.
0
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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479
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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480 Input data: 3 types of input data can be used:
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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481
2
4f46f06e861b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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482 - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/wp/imzml/>`_
0
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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483 - Analyze7.5 (upload hdr, img and t2m file via the "composite" function)
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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484 - Cardinal "MSImageSet" data (with variable name "msidata", saved as .RData)
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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485
6
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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parents: 5
diff changeset
486
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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diff changeset
487 Input:
2
4f46f06e861b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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parents: 1
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488
6
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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489 - MSI data files with same m/z values (to obtain same m/z values for different files: filtering tool same m/z range and preprocessing tool same binning width)
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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490 - Tabular files with pixel annotations need to have the x values in the first column, y values in the second column and then up to five annotations in the next columns. The order of the annotations in the columns must be the same for all files (x and y in column 1 and 2; annotation1 in column3, annotation2 in column4,...)
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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491 - The order and the number of MSI data files and annotation tabular files must be the same
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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492 - For xy shifts with tabular file: Tabular file with x and y coordinates shift and file name (see below)
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493
4f46f06e861b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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494 Options:
4f46f06e861b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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495
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496 - "automatic combination": files are automatically arranged in a grid (duplicated pixels are allowed), subfiles are named according to the input file name
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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497 - "xy shifts by hand": each file can be moved in x and y direction according to the users need (define one tabular file in the order in which the files are loaded in the history (bottom to top) and define for each file the x and y coordinates shifts in separate columns and the file name in a third column). The xy shift option combines all datasets and removes all duplicated pixels (same x and y coordinates).
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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498
2
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499
4f46f06e861b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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500 Output:
4f46f06e861b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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501
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40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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502 - single imzML file
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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503 - pdf that shows the pixel positions and annotations of the combined files
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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504 - Tabular file with pixel annotations (x,y,column with input file names, up to five annotation columns)
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f07413fa9b58 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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505 - optional: intensity matrix as tabular file (intensities for m/z in rows and pixel in columns)
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506
4f46f06e861b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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507
0
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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508 ]]>
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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509 </help>
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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510 <citations>
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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511 <citation type="doi">10.1093/bioinformatics/btv146</citation>
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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512 </citations>
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513 </tool>