Mercurial > repos > galaxyp > msi_combine

annotate msi_combine.xml @ 6:40f177062ba9 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 04:50:51 -0400
parents 49c4a97e7e3a
children 72914d913505
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1 <tool id="mass_spectrometry_imaging_combine" name="MSI combine" version="1.10.0.4">
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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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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
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 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
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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251 pdf("Combined_qc.pdf", width=15, height=15)
3
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252
6
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galaxyp
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253 ## combined plot
40f177062ba9 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))+
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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255 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
256 coord_fixed()+
40f177062ba9 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")+
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
258 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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259 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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diff changeset
260 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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261 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
galaxyp
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262 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
galaxyp
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263 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
galaxyp
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264 for(file_count in 1:nrow(coord_labels))
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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265 {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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266 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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267 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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268
6
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269
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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270 ## annotation plots
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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271
40f177062ba9 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
f07413fa9b58 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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273
6
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274 column1_df = cbind(coord(msidata), msidata\$column1)
40f177062ba9 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
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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277 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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278 column1_plot = ggplot(column1_df, aes(x=x, y=y, fill=column1))+
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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279 geom_tile() +
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galaxyp
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280 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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281 ggtitle(paste0(annotation_colnames[1]))+
1
2ff16a066571 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
galaxyp
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282 theme_bw()+
3
f07413fa9b58 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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283 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
galaxyp
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284 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
galaxyp
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diff changeset
285 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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286 print(column1_plot)}
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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287 ##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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288 colnames(column1_df)[3] = 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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289
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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290 ## plot 2
40f177062ba9 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)
40f177062ba9 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"
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293
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galaxyp
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294 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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295 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
galaxyp
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296 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
297 coord_fixed()+
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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diff changeset
298 ggtitle(paste0(annotation_colnames[2]))+
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
299 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
300 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
301 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
302 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
galaxyp
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303 print(column2_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
304 ##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
305 colnames(column2_df)[3] = 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
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
307 ## plot 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
308 column3_df = cbind(coord(msidata), msidata\$column3)
40f177062ba9 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"
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
310 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
galaxyp
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311 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
galaxyp
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diff changeset
312 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
313 coord_fixed()+
40f177062ba9 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]))+
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
315 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
316 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
317 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
318 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
galaxyp
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diff changeset
319 print(column3_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
320 ##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
321 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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diff changeset
322
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galaxyp
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diff changeset
323 ## plot 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
324 column4_df = cbind(coord(msidata), msidata\$column4)
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 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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diff changeset
326
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
327 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
328 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
329 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
330 coord_fixed()+
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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diff changeset
331 ggtitle(paste0(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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diff changeset
332 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
333 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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334 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
335 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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336 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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337 ##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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338 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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339
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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340 ## plot5
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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341
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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342 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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343 colnames(column5_df)[3] = "column5"
40f177062ba9 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)){
40f177062ba9 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))+
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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346 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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347 coord_fixed()+
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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348 ggtitle(paste0(annotation_colnames[5]))+
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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349 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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350 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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351 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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352 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
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353 print(column5_plot)}
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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354 ##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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355 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
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356
1
2ff16a066571 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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357 dev.off()
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358
6
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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359 ##################### annotation tabular output ################################
0
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
galaxyp
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360
5
49c4a97e7e3a 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
40f177062ba9 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)
40f177062ba9 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)
40f177062ba9 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
2ff16a066571 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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365 }else{
6
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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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
49c4a97e7e3a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
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368
6
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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369 ####################### optional matrix output #################################
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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370
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
371 #if $output_matrix:
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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diff changeset
372
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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diff changeset
373 if (length(features(msidata))> 0 & length(pixels(msidata)) > 0){
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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374 spectramatrix = spectra(msidata)[]
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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diff changeset
375 spectramatrix = cbind(mz(msidata),spectramatrix)
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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diff changeset
376 newmatrix = rbind(c("mz | spectra", names(pixels(msidata))), spectramatrix)
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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377 write.table(newmatrix, file="$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
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diff changeset
378 }else{
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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diff changeset
379 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
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diff changeset
380 }
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
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 #end if
0
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
383
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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diff changeset
384 ]]></configfile>
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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385 </configfiles>
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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diff changeset
386 <inputs>
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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387 <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
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diff changeset
388 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
389 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
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diff changeset
390 <conditional name="processed_cond">
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
391 <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
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diff changeset
392 <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
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diff changeset
393 <option value="processed">processed imzML</option>
49c4a97e7e3a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
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diff changeset
394 </param>
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
395 <when value="no_processed"/>
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
396 <when value="processed">
49c4a97e7e3a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
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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"/>
49c4a97e7e3a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
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diff changeset
398 <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
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diff changeset
399 <option value="mz" >mz</option>
49c4a97e7e3a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
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diff changeset
400 <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
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diff changeset
401 </param>
49c4a97e7e3a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
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diff changeset
402 </when>
49c4a97e7e3a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
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diff changeset
403 </conditional>
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
404 <param name="annotation_files" type="data" multiple="true" format="tabular"
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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diff changeset
405 label="Pixel annotations as tabular files"
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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diff changeset
406 help="Tabular files should have the same order as input files"/>
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
407 <conditional name="combine_conditional">
2ff16a066571 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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diff changeset
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">
2ff16a066571 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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diff changeset
409 <option value="automatic_combine" selected="True" >automatic combination</option>
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
410 <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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diff changeset
411 </param>
3
f07413fa9b58 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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diff changeset
412 <when value="automatic_combine"/>
1
2ff16a066571 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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diff changeset
413 <when value="xy_shifts">
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
414 <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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diff changeset
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."/>
1
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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"/>
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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417 <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
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418 <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
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419 </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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420 </conditional>
2ff16a066571 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
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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422 </inputs>
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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423 <outputs>
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424 <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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425 <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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426 <data format="tabular" name="annotation_output" label="Annotation_tabular"/>
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f07413fa9b58 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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427 <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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428 <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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429 </data>
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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430 </outputs>
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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431 <tests>
6
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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432 <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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433 <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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434 <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
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435 <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
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436 <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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437 <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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438 <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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439 <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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440 <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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441 <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
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442 <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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443 <output name="msidata_combined" file="123_combined.RData" compare="sim_size" />
50ba517b7caa 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"/>
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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445 </test>
6
40f177062ba9 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
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="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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448 <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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449 <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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450 <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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451 <output name="matrixasoutput" file="12_combined_matrix.tabular"/>
6
40f177062ba9 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
50ba517b7caa 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" />
50ba517b7caa 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"/>
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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455 </test>
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
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456 <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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457 <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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458 <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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459 <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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460 <param name="output_matrix" value="False"/>
6
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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461 <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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462 <output name="msidata_combined" file="112_auto_combined.RData" compare="sim_size" />
f07413fa9b58 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
2ff16a066571 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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464 </test>
0
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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465 </tests>
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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466 <help>
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467 <![CDATA[
1
2ff16a066571 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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468
2
4f46f06e861b 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
f07413fa9b58 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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471 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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472
50ba517b7caa 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:
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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474
2
4f46f06e861b 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
50ba517b7caa 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)
50ba517b7caa 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)
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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478
6
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parents: 5
diff changeset
479
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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diff changeset
480 Input:
2
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parents: 1
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481
6
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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)
40f177062ba9 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,...)
40f177062ba9 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
40f177062ba9 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
4f46f06e861b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 1
diff changeset
486
4f46f06e861b 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:
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 - "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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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).
40f177062ba9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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491
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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492
4f46f06e861b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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493 Output:
4f46f06e861b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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494
6
40f177062ba9 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
40f177062ba9 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
40f177062ba9 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
f07413fa9b58 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
4f46f06e861b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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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
0
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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501 ]]>
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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502 </help>
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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503 <citations>
50ba517b7caa 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>
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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505 </citations>
50ba517b7caa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 1e5a87e56e09f01087844f8d2c95002455b1d89d
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506 </tool>