Mercurial > repos > galaxyp > msi_combine

annotate msi_combine.xml @ 6:f4aafc565aa3 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
author galaxyp
date Tue, 24 Jul 2018 04:52:39 -0400
parents ff91e78b5c5c
children 19d8eee15959
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6
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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1 <tool id="mass_spectrometry_imaging_combine" name="MSI combine" version="1.10.0.4">
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>
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6 <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement>
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7 <requirement type="package" version="2.2.1">r-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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34
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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
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39 library(Cardinal)
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40 library(ggplot2)
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41
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42 ## read tabular file for xy_shift option
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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
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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
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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 colnames(input_annotation)[1:2] = c("x", "y")
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95 msidata_coordinates = cbind(coord(msidata_$i)[,1:2], 1:ncol(msidata_$i))
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96 colnames(msidata_coordinates)[3] = "pixel_index"
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97 ## only first 5 annotation columns are kept
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98 if (ncol(input_annotation) > 7){
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99 input_annotation = input_annotation[,1:7]}
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100
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101 annotation_df = merge(msidata_coordinates, input_annotation, by=c("x", "y"), all.x=TRUE)
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102 annotation_df_8 = cbind(annotation_df, data.frame(matrix(NA,ncol=8-ncol(annotation_df), nrow=ncol(msidata_$i))))
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103 annotation_df_8_sorted = annotation_df_8[order(annotation_df_8\$pixel_index),]## orders pixel according to msidata
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104
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105 ## each annotation column is assigned to the pixel in the pData slot of the MSIdata
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106 msidata_$i\$column1 = annotation_df_8_sorted[,4]
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107 msidata_$i\$column2 = annotation_df_8_sorted[,5]
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108 msidata_$i\$column3 = annotation_df_8_sorted[,6]
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109 msidata_$i\$column4 = annotation_df_8_sorted[,7]
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110 msidata_$i\$column5 = annotation_df_8_sorted[,8]
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111
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112 ## same name for MSI data files necessary to combine data in one single coordinate system
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113 sampleNames(msidata_$i) = "msidata"
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114
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115 ################### preparation xy shifts ##########################
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116
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117 #if str( $combine_conditional.combine_method ) == 'xy_shifts':
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118
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119 ## shift coordinates according to input tabular file and store file names
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120 coord(msidata_$i)\$x = coord(msidata_$i)\$x + input_list[$i+1,$combine_conditional.column_x] ## shifts x coordinates according to tabular file
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121 coord(msidata_$i)\$y = coord(msidata_$i)\$y + input_list[$i+1,$combine_conditional.column_y] ## shifts y coordinates according to tabular file
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122 pixel_vector = append(pixel_vector, rep(paste($i+1, input_list[$i+1,$combine_conditional.column_names], sep="_"),times=ncol(msidata_$i))) ## stores file name for each pixel
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123 msidata_$i\$combined_sample = rep(paste($i+1, input_list[$i+1,$combine_conditional.column_names], sep="_"),times=ncol(msidata_$i))
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124 pixelcoords_$i = cbind(coord(msidata_$i)[,1:2], rep($i+1,ncol(msidata_$i)))
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125 #silent $pixelcoords.append('pixelcoords_'+str($i))
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126 colnames(pixelcoords_$i)[3] = "file_number"
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127
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128 ################### preparation automatic combination ##########################
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129
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130 #elif str( $combine_conditional.combine_method ) == 'automatic_combine':
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131 names_vector = character()
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132 #set escaped_element_identifier = re.sub('[^\w\-\s\[/]]', '_', str($infile.element_identifier)) ## use name of inputfile from Galaxy
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133 if (sum(spectra(msidata_$i)[],na.rm=TRUE)>0) ## use only valid files
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134 {
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135 if (is.null(levels(msidata_$i\$combined_sample))) ### if the file was not combined before use input file name, otherwise keep combined_sample name which was assigned before
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136 {
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137 names_vector = append(names_vector, rep(paste($i+1, "$escaped_element_identifier", sep="_"),ncol(msidata_$i)))
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138 msidata_$i\$combined_sample = as.factor(names_vector)
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139 }
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140 }
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141
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142 ## Number of input files define grid which is row-wise filled with files
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143
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144 coord(msidata_$i)\$x = coord(msidata_$i)\$x - (min(coord(msidata_$i)\$x-1)) + x_shifts
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145 coord(msidata_$i)\$y = coord(msidata_$i)\$y - (min(coord(msidata_$i)\$y-1)) + y_shifts
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146 x_shifts = max(coord(msidata_$i)\$x) + 5
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147 max_y = append(max_y, max(coord(msidata_$i)\$y))
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148 all_files = $num_infiles
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149 new_row = ($i+1)/ceiling(sqrt(all_files))
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150 new_row%%1==0
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151 if (new_row%%1==0)
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152 {x_shifts = 0 ### when row is filled: x values start again at zero
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153 y_shifts = max(max_y) + 5 ### when row is filled: y value increases to start a new row
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154 max_y = numeric()}
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155
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156 #end if
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157
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158 ## store files to combine them later and for each file check if it is valid
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159
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160 #silent $msidata.append('msidata_'+str($i))
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161 valid_dataset = append(valid_dataset,
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162 (ncol(msidata_$i)>0 & nrow(msidata_$i)>0 & sum(spectra(msidata_$i)[], na.rm=TRUE)>0))
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163
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164 #end for
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165
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166 ## extract columnnames from (last) annotation tabular (for QC plot names)
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167 annotation_colnames = colnames(input_annotation)[-c(1,2)]
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168
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169 ###################### automatic combination ###################################
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170 ################################################################################
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171
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172 #if str( $combine_conditional.combine_method ) == 'automatic_combine':
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173 print("automatic_combine")
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174
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175 ## combine only valid datasets
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176
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177 valid_data = list(#echo ','.join($msidata)#)[valid_dataset]
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178 msidata_combined = do.call(combine, valid_data)
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179 print("Valid datasets in order of input bottom to top:")
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180 print(valid_dataset)
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181
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182 ## create dataframe with x,y,sample_name and show all pixels in PDF as QC
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183
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184 pdf("Combined_qc.pdf", width=15, height=15)
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185 position_df = cbind(coord(msidata_combined)[,1:2], msidata_combined\$combined_sample)
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186 colnames(position_df)[3] = "sample_name"
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187 combine_plot = ggplot(position_df, aes(x=x, y=y, fill=sample_name))+
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188 geom_tile() +
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189 coord_fixed()+
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190 ggtitle("Spatial orientation of combined data (sample names)")+
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191 theme_bw()+
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192 theme(text=element_text(family="ArialMT", face="bold", size=15))+
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193 theme(legend.position="bottom",legend.direction="vertical")+
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194 guides(fill=guide_legend(ncol=4,byrow=TRUE))
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195 coord_labels = aggregate(cbind(x,y)~sample_name, data=position_df, mean, na.rm=TRUE, na.action="na.pass")
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196 coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$sample_name)
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197 for(file_count in 1:nrow(coord_labels))
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198 {combine_plot = combine_plot + annotate("text",x=coord_labels[file_count,"x"],
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199 y=coord_labels[file_count,"y"],label=toString(coord_labels[file_count,4]))}
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200 print(combine_plot)
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201 dev.off()
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202
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203 ## save as (.RData)
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204
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205 msidata = msidata_combined
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206 save(msidata, file="$msidata_combined")
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207
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208
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209 ################################## xy shifts ###################################
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210 ################################################################################
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211
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212 #elif str( $combine_conditional.combine_method ) == 'xy_shifts':
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213 print("xy_shifts")
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214
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215 ## find duplicated coordinates
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216 all_coordinates = do.call(rbind, list(#echo ','.join($pixelcoords)#))
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217 duplicated_coordinates= duplicated(all_coordinates[,1:2])| duplicated(all_coordinates[,1:2], fromLast=TRUE)
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218 print(paste0("Number of removed duplicated coordinates: ", sum(duplicated_coordinates)/2))
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219 unique_coordinates = all_coordinates[!duplicated_coordinates,]
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220
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221 ## remove duplicated coordinates
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222 datasetlist = list()
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223 count = 1
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224 for (usable_dataset in list(#echo ','.join($msidata)#)){
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225 pixelsofinterest = pixels(usable_dataset)[names(pixels(usable_dataset)) %in% rownames(unique_coordinates)]
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226 filtered_dataset = usable_dataset[,pixelsofinterest]
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227 if (ncol(filtered_dataset) > 0 ){
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228 datasetlist[[count]] = filtered_dataset}
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229 count = count +1}
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230
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231 msidata_combined = do.call(combine, datasetlist)
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232
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233 ## save as (.RData)
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234
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235 msidata = msidata_combined
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236 save(msidata, file="$msidata_combined")
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237
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238 ## create x,y,sample_name dataframe for QC pdf
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239
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240 position_df = cbind(coord(msidata), msidata\$combined_sample)
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241 colnames(position_df)[3] = "sample_name"
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242
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243 #end if
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244
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245
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246 ################################## outputs ####################################
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247 ################################################################################
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248
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249 ########### QC with pixels and their annotations ################################
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250
6
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251 pdf("Combined_qc.pdf", width=15, height=15)
3
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252
6
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253 ## combined plot
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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254 combine_plot = ggplot(position_df, aes(x=x, y=y, fill=sample_name))+
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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255 geom_tile() +
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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256 coord_fixed()+
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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257 ggtitle("Spatial orientation of combined data")+
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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258 theme_bw()+
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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259 theme(text=element_text(family="ArialMT", face="bold", size=15))+
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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260 theme(legend.position="bottom",legend.direction="vertical")+
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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261 guides(fill=guide_legend(ncol=5,byrow=TRUE))
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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262 coord_labels = aggregate(cbind(x,y)~sample_name, data=position_df, mean)
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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263 coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$sample_name)
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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264 for(file_count in 1:nrow(coord_labels))
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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265 {combine_plot = combine_plot + annotate("text",x=coord_labels[file_count,"x"],
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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266 y=coord_labels[file_count,"y"],label=toString(coord_labels[file_count,4]))}
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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267 print(combine_plot)
5
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268
6
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269
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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270 ## annotation plots
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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271
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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272 ## plot 1
3
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273
6
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274 column1_df = cbind(coord(msidata), msidata\$column1)
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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275 colnames(column1_df)[3] = "column1"
3
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276
6
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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277 if (sum(is.na(column1_df[3])) < nrow(column1_df)){
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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278 column1_plot = ggplot(column1_df, aes(x=x, y=y, fill=column1))+
1
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279 geom_tile() +
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galaxyp
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280 coord_fixed()+
6
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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281 ggtitle(paste0(annotation_colnames[1]))+
1
f3f6c32ab690 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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282 theme_bw()+
3
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283 theme(text=element_text(family="ArialMT", face="bold", size=15))+
91bba2486773 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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284 theme(legend.position="bottom",legend.direction="vertical")+
6
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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285 guides(fill=guide_legend(ncol=5,byrow=TRUE, title=annotation_colnames[1]))
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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286 print(column1_plot)}
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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287 ##rename columnname for output tabular file
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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288 colnames(column1_df)[3] = annotation_colnames[1]
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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289
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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290 ## plot 2
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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291 column2_df = cbind(coord(msidata), msidata\$column2)
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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292 colnames(column2_df)[3] = "column2"
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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293
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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294 if (sum(is.na(column2_df[3])) < nrow(column2_df)){
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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295 column2_plot = ggplot(column2_df, aes(x=x, y=y, fill=column2))+
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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296 geom_tile() +
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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297 coord_fixed()+
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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298 ggtitle(paste0(annotation_colnames[2]))+
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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299 theme_bw()+
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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300 theme(text=element_text(family="ArialMT", face="bold", size=15))+
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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301 theme(legend.position="bottom",legend.direction="vertical")+
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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302 guides(fill=guide_legend(ncol=5,byrow=TRUE, title=annotation_colnames[2]))
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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303 print(column2_plot)}
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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304 ##rename columnname for output tabular file
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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305 colnames(column2_df)[3] = annotation_colnames[2]
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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306
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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307 ## plot 3
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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308 column3_df = cbind(coord(msidata), msidata\$column3)
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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309 colnames(column3_df)[3] = "column3"
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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310 if (sum(is.na(column3_df[3])) < nrow(column3_df)){
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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311 column3_plot = ggplot(column3_df, aes(x=x, y=y, fill=column3))+
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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312 geom_tile() +
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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diff changeset
313 coord_fixed()+
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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314 ggtitle(paste0(annotation_colnames[3]))+
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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315 theme_bw()+
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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316 theme(text=element_text(family="ArialMT", face="bold", size=15))+
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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317 theme(legend.position="bottom",legend.direction="vertical")+
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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diff changeset
318 guides(fill=guide_legend(ncol=5,byrow=TRUE, title=annotation_colnames[3]))
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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diff changeset
319 print(column3_plot)}
f4aafc565aa3 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 ##rename columnname for output tabular file
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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diff changeset
321 colnames(column3_df)[3] = annotation_colnames[3]
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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322
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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323 ## plot 4
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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diff changeset
324 column4_df = cbind(coord(msidata), msidata\$column4)
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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325 colnames(column4_df)[3] = "column4"
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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326
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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diff changeset
327 if (sum(is.na(column4_df[3])) < nrow(column4_df)){
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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328 column4_plot = ggplot(column4_df, aes(x=x, y=y, fill=column4))+
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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diff changeset
329 geom_tile() +
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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diff changeset
330 coord_fixed()+
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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331 ggtitle(paste0(annotation_colnames[4]))+
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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332 theme_bw()+
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333 theme(text=element_text(family="ArialMT", face="bold", size=15))+
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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334 theme(legend.position="bottom",legend.direction="vertical")+
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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335 guides(fill=guide_legend(ncol=5,byrow=TRUE, title=annotation_colnames[4]))
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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336 print(column4_plot)}
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337 ##rename columnname for output tabular file
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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338 colnames(column4_df)[3] = annotation_colnames[4]
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339
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340 ## plot5
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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341
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342 column5_df = cbind(coord(msidata), msidata\$column5)
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343 colnames(column5_df)[3] = "column5"
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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344 if (sum(is.na(column5_df[3])) < nrow(column5_df)){
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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345 column5_plot = ggplot(column5_df, aes(x=x, y=y, fill=column5))+
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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346 geom_tile() +
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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347 coord_fixed()+
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348 ggtitle(paste0(annotation_colnames[5]))+
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349 theme_bw()+
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350 theme(text=element_text(family="ArialMT", face="bold", size=15))+
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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351 theme(legend.position="bottom",legend.direction="vertical")+
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352 guides(fill=guide_legend(ncol=5,byrow=TRUE, title=annotation_colnames[5]))
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353 print(column5_plot)}
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354 ##rename columnname for output tabular file
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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355 colnames(column5_df)[3] = annotation_colnames[5]
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356
1
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357 dev.off()
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358
6
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359 ##################### annotation tabular output ################################
0
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360
5
ff91e78b5c5c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
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361 if (length(features(msidata))> 0 & length(pixels(msidata)) > 0){
6
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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362 annotation_df_list = list(position_df, column1_df, column2_df, column3_df, column4_df, column5_df)
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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363 combined_annotations = Reduce(function(...) merge(..., by=c("x", "y"), all=TRUE), annotation_df_list)
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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364 write.table(combined_annotations, file="$annotation_output", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
1
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365 }else{
6
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366 print("No annotation tabular output because file has no features or pixels left")
1
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367 }
5
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368
6
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369 ####################### optional matrix output #################################
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370
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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diff changeset
371 #if $output_matrix:
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372
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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373 if (length(features(msidata))> 0 & length(pixels(msidata)) > 0){
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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374 spectramatrix = spectra(msidata)[]
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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375 spectramatrix = cbind(mz(msidata),spectramatrix)
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376 newmatrix = rbind(c("mz | spectra", names(pixels(msidata))), spectramatrix)
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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377 write.table(newmatrix, file="$matrixasoutput", quote = FALSE, row.names = FALSE, col.names=FALSE, sep = "\t")
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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diff changeset
378 }else{
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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379 print("No intensity matrix output because file has no features or pixels left")
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diff changeset
380 }
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381
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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diff changeset
382 #end if
0
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383
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384 ]]></configfile>
9cbcf48bf60a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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385 </configfiles>
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386 <inputs>
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387 <param name="infiles" type="data" multiple="true" format="imzml,rdata,analyze75"
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388 label="MSI data as imzml, analyze7.5 or Cardinal MSImageSet saved as RData"
0
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389 help="load imzml and ibd file by uploading composite datatype imzml"/>
5
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390 <conditional name="processed_cond">
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391 <param name="processed_file" type="select" label="Is the input file a processed imzML file ">
ff91e78b5c5c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
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392 <option value="no_processed" selected="True">not a processed imzML</option>
ff91e78b5c5c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
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393 <option value="processed">processed imzML</option>
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394 </param>
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395 <when value="no_processed"/>
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396 <when value="processed">
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397 <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"/>
ff91e78b5c5c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
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398 <param name="units" display="radio" type="select" label="Unit of the mass accuracy" help="either m/z or ppm">
ff91e78b5c5c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
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399 <option value="mz" >mz</option>
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400 <option value="ppm" selected="True" >ppm</option>
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401 </param>
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402 </when>
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403 </conditional>
6
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404 <param name="annotation_files" type="data" multiple="true" format="tabular"
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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405 label="Pixel annotations as tabular files"
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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406 help="Tabular files should have the same order as input files"/>
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407 <conditional name="combine_conditional">
f3f6c32ab690 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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408 <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">
f3f6c32ab690 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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409 <option value="automatic_combine" selected="True" >automatic combination</option>
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410 <option value="xy_shifts">shift xy coordinates with a tabular file</option>
1
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411 </param>
3
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412 <when value="automatic_combine"/>
1
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413 <when value="xy_shifts">
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414 <param name="coordinates_file" type="data" format="tabular" label="datasetnames, x and y values to shift pixel coordinates before combining"
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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415 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."/>
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416 <param name="column_x" data_ref="coordinates_file" label="Column with values for shift in x direction" type="data_column"/>
f3f6c32ab690 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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417 <param name="column_y" data_ref="coordinates_file" label="Column with values for shift in y direction" type="data_column"/>
f3f6c32ab690 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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418 <param name="column_names" data_ref="coordinates_file" label="Column with dataset names" type="data_column"/>
f3f6c32ab690 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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419 </when>
f3f6c32ab690 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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420 </conditional>
f3f6c32ab690 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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421 <param name="output_matrix" type="boolean" display="radio" label="Intensity matrix output"/>
0
9cbcf48bf60a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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422 </inputs>
9cbcf48bf60a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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423 <outputs>
3
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424 <data format="rdata" name="msidata_combined" label="MSI_data_combined"/>
91bba2486773 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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425 <data format="pdf" name="combining_qc" from_work_dir="Combined_qc.pdf" label = "Combined_QC"/>
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f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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426 <data format="tabular" name="annotation_output" label="Annotation_tabular"/>
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427 <data format="tabular" name="matrixasoutput" label="Combined_matrix">
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9cbcf48bf60a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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428 <filter>output_matrix</filter>
9cbcf48bf60a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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429 </data>
9cbcf48bf60a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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430 </outputs>
9cbcf48bf60a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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431 <tests>
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432 <test expect_num_outputs="4">
0
9cbcf48bf60a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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433 <param name="infiles" value="msidata_1.RData,msidata_2.RData,msidata_3.RData" ftype="rdata"/>
6
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434 <param name="annotation_files" value="annotations_file1.tabular,annotations_file2.tabular,annotations_file3.tabular" ftype="tabular"/>
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435 <param name="combine_method" value="xy_shifts"/>
0
9cbcf48bf60a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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436 <param name="coordinates_file" ftype="tabular" value="xy_coordinates.tabular"/>
9cbcf48bf60a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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437 <param name="column_x" value="1"/>
9cbcf48bf60a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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438 <param name="column_y" value="2"/>
9cbcf48bf60a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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439 <param name="column_names" value="3"/>
9cbcf48bf60a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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440 <param name="output_matrix" value="True"/>
9cbcf48bf60a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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441 <output name="matrixasoutput" file="123_combined_matrix.tabular"/>
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f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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442 <output name="annotation_output" file="123_annotation_output.tabular"/>
0
9cbcf48bf60a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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443 <output name="msidata_combined" file="123_combined.RData" compare="sim_size" />
9cbcf48bf60a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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444 <output name="combining_qc" file="123_combined_QC.pdf" compare="sim_size" delta="20000"/>
9cbcf48bf60a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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445 </test>
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f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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446 <test expect_num_outputs="4">
0
9cbcf48bf60a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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447 <param name="infiles" value="msidata_1.RData,msidata_2.RData" ftype="rdata"/>
6
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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448 <param name="annotation_files" value="annotations_file1.tabular,annotations_file2.tabular" ftype="tabular"/>
3
91bba2486773 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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449 <param name="combine_method" value="automatic_combine"/>
0
9cbcf48bf60a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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450 <param name="output_matrix" value="True"/>
9cbcf48bf60a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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451 <output name="matrixasoutput" file="12_combined_matrix.tabular"/>
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f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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452 <output name="annotation_output" file="12_annotation_output.tabular"/>
0
9cbcf48bf60a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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453 <output name="msidata_combined" file="12_combined.RData" compare="sim_size" />
9cbcf48bf60a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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454 <output name="combining_qc" file="12_combined_QC.pdf" compare="sim_size" delta="20000"/>
9cbcf48bf60a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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455 </test>
6
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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456 <test expect_num_outputs="3">
3
91bba2486773 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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457 <param name="infiles" value="msidata_1.RData,123_combined.RData" ftype="rdata"/>
6
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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458 <param name="annotation_files" value="annotations_file1.tabular,123_annotation.tabular" ftype="tabular"/>
1
f3f6c32ab690 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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459 <param name="combine_method" value="automatic_combine"/>
3
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460 <param name="output_matrix" value="False"/>
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461 <output name="annotation_output" file="112_annotation_output.tabular"/>
3
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462 <output name="msidata_combined" file="112_auto_combined.RData" compare="sim_size" />
91bba2486773 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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463 <output name="combining_qc" file="112_auto_combined_QC.pdf" compare="sim_size" delta="20000"/>
1
f3f6c32ab690 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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464 </test>
0
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465 </tests>
9cbcf48bf60a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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466 <help>
9cbcf48bf60a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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467 <![CDATA[
1
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468
2
00b6c61f5054 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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469 Cardinal is an R package that implements statistical & computational tools for analyzing mass spectrometry imaging datasets. `More information on Cardinal <http://cardinalmsi.org//>`_
1
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470
3
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471 This tool uses the Cardinal combine function to combine several mass spectrometry imaging data.
0
9cbcf48bf60a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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472
9cbcf48bf60a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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473 Input data: 3 types of input data can be used:
9cbcf48bf60a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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474
2
00b6c61f5054 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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475 - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/wp/imzml/>`_
0
9cbcf48bf60a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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476 - Analyze7.5 (upload hdr, img and t2m file via the "composite" function)
9cbcf48bf60a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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477 - Cardinal "MSImageSet" data (with variable name "msidata", saved as .RData)
9cbcf48bf60a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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478
6
f4aafc565aa3 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
479
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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480 Input:
2
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parents: 1
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481
6
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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482 - 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)
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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483 - 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,...)
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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484 - The order and the number of MSI data files and annotation tabular files must be the same
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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485 - For xy shifts with tabular file: Tabular file with x and y coordinates shift and file name (see below)
2
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parents: 1
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486
00b6c61f5054 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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diff changeset
487 Options:
00b6c61f5054 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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488
6
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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489 - "automatic combination": files are automatically arranged in a grid (duplicated pixels are allowed), subfiles are named according to the input file name
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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490 - "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).
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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491
2
00b6c61f5054 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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492
00b6c61f5054 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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493 Output:
00b6c61f5054 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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494
6
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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495 - single imzML file
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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496 - pdf that shows the pixel positions and annotations of the combined files
f4aafc565aa3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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497 - Tabular file with pixel annotations (x,y,column with input file names, up to five annotation columns)
3
91bba2486773 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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498 - optional: intensity matrix as tabular file (intensities for m/z in rows and pixel in columns)
2
00b6c61f5054 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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499
00b6c61f5054 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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500
0
9cbcf48bf60a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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501 ]]>
9cbcf48bf60a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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502 </help>
9cbcf48bf60a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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503 <citations>
9cbcf48bf60a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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504 <citation type="doi">10.1093/bioinformatics/btv146</citation>
9cbcf48bf60a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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505 </citations>
9cbcf48bf60a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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506 </tool>