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annotate msi_combine.xml @ 5:ff91e78b5c5c draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
author galaxyp
date Fri, 06 Jul 2018 14:13:08 -0400
parents d05bd881af3d
children f4aafc565aa3
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1 <tool id="mass_spectrometry_imaging_combine" name="MSI combine" version="1.10.0.3">
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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_${i}.RData &&
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21 #end if
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22 #end for
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23 cat '${msi_combine}' &&
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24 Rscript '${msi_combine}'
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26 ]]>
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27 </command>
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28 <configfiles>
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29 <configfile name="msi_combine"><![CDATA[
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31 #import re
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33 ################ load libraries and some preparations #################
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35 library(Cardinal)
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36 library(ggplot2)
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37
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38 ## read tabular file for xy_shift option
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39
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40 #if str( $combine_conditional.combine_method ) == 'xy_shifts':
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41 input_list = read.delim("$combine_conditional.coordinates_file", header = FALSE,
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42 stringsAsFactors = FALSE)
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43 #end if
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44
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45 ## load RData and store with new variable name
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46
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47 loadRData <- function(fileName){
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48 #loads an RData file, and returns it
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49 load(fileName)
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50 get(ls()[ls() != "fileName"])
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51 }
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52
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53 ## preparations for reading files one by one with for loop
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54
0
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55 pixel_vector = numeric()
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56 x_shifts = 0
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57 y_shifts = 0
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58 max_y = numeric()
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59 valid_dataset = logical()
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60 #set $msidata = []
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61 #set $pixelcoords = []
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62 #set $num_infiles = len($infiles)
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63 all_files = $num_infiles
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64
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65
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66 ############## reading files and changing pixel coordinates ###################
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67
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68 #for $i, $infile in enumerate($infiles):
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69
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70 #if $infile.ext == 'imzml'
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71 #if str($processed_cond.processed_file) == "processed":
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72 msidata_$i <- readImzML('infile_${i}', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units")
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73 #else
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74 msidata <- readImzML('infile')
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75 #end if
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76 #elif $infile.ext == 'analyze75'
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77 msidata_$i <- readAnalyze('infile_${i}')
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78 #else
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79 msidata_$i = loadRData('infile_${i}.RData')
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80 #end if
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81
2
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82
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83 sampleNames(msidata_$i) = "msidata" ## same name necessary to combine data in one single coordinate system
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84
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85 ################### preparation xy shifts ##########################
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86
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87 #if str( $combine_conditional.combine_method ) == 'xy_shifts':
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88
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89 coord(msidata_$i)\$x = coord(msidata_$i)\$x + input_list[$i+1,$combine_conditional.column_x] ## shifts x coordinates according to tabular file
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90 coord(msidata_$i)\$y = coord(msidata_$i)\$y + input_list[$i+1,$combine_conditional.column_y] ## shifts y coordinates according to tabular file
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91 pixel_vector = append(pixel_vector, rep(paste($i+1, input_list[$i+1,$combine_conditional.column_names], sep="_"),times=ncol(msidata_$i))) ## stores file name for each pixel
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92 msidata_$i\$combined_sample = rep(paste($i+1, input_list[$i+1,$combine_conditional.column_names], sep="_"),times=ncol(msidata_$i))
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93 pixelcoords_$i = cbind(coord(msidata_$i)[,1:2], rep($i+1,ncol(msidata_$i)))
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94 #silent $pixelcoords.append('pixelcoords_'+str($i))
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95 colnames(pixelcoords_$i)[3] = "file_number"
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96
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97 ################### preparation automatic combination ##########################
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98
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99 #elif str( $combine_conditional.combine_method ) == 'automatic_combine':
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100 names_vector = character()
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101 #set escaped_element_identifier = re.sub('[^\w\-\s\[/]]', '_', str($infile.element_identifier)) ## use name of inputfile from Galaxy
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102 if (sum(spectra(msidata_$i)[],na.rm=TRUE)>0) ## use only valid files
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103 {
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104 if (is.null(levels(msidata_$i\$combined_sample))) ### if the file was not combined before use input file name, otherwise keep combined_sample name which was assigned before
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105 {
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106 names_vector = append(names_vector, rep(paste($i+1, "$escaped_element_identifier", sep="_"),ncol(msidata_$i)))
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107 msidata_$i\$combined_sample = as.factor(names_vector)
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108 }
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109 }
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110
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111 ## Number of input files define grid which is row-wise filled with files
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112
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113 coord(msidata_$i)\$x = coord(msidata_$i)\$x - (min(coord(msidata_$i)\$x-1)) + x_shifts
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114 coord(msidata_$i)\$y = coord(msidata_$i)\$y - (min(coord(msidata_$i)\$y-1)) + y_shifts
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115 x_shifts = max(coord(msidata_$i)\$x) + 5
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116 max_y = append(max_y, max(coord(msidata_$i)\$y))
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117 all_files = $num_infiles
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118 new_row = ($i+1)/ceiling(sqrt(all_files))
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119 new_row%%1==0
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120 if (new_row%%1==0)
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121 {x_shifts = 0 ### when row is filled: x values start again at zero
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122 y_shifts = max(max_y) + 5 ### when row is filled: y value increases to start a new row
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123 max_y = numeric()}
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124
0
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125 #end if
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126
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127 ## store files to combine them later and for each file check if it is valid
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128
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129 #silent $msidata.append('msidata_'+str($i))
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130 valid_dataset = append(valid_dataset,
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131 (ncol(msidata_$i)>0 & nrow(msidata_$i)>0 & sum(spectra(msidata_$i)[], na.rm=TRUE)>0))
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132
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133 #end for
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134
0
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135
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136 ###################### automatic combination ###################################
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137 ################################################################################
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138
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139 #if str( $combine_conditional.combine_method ) == 'automatic_combine':
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140 print("automatic_combine")
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141
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142 ## combine only valid datasets
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143
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144 valid_data = list(#echo ','.join($msidata)#)[valid_dataset]
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145 msidata_combined = do.call(combine, valid_data)
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146 print("Valid datasets in order of input bottom to top:")
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147 print(valid_dataset)
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148
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149 ## create dataframe with x,y,sample_name and show all pixels in PDF as QC
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150
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151 pdf("Combined_qc.pdf", width=15, height=15)
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152 position_df = cbind(coord(msidata_combined)[,1:2], msidata_combined\$combined_sample)
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153 colnames(position_df)[3] = "sample_name"
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154 combine_plot = ggplot(position_df, aes(x=x, y=y, fill=sample_name))+
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155 geom_tile() +
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156 coord_fixed()+
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157 ggtitle("Spatial orientation of combined data")+
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158 theme_bw()+
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159 theme(text=element_text(family="ArialMT", face="bold", size=15))+
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160 theme(legend.position="bottom",legend.direction="vertical")+
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161 guides(fill=guide_legend(ncol=4,byrow=TRUE))
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162 coord_labels = aggregate(cbind(x,y)~sample_name, data=position_df, mean, na.rm=TRUE, na.action="na.pass")
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163 coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$sample_name)
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164 for(file_count in 1:nrow(coord_labels))
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165 {combine_plot = combine_plot + annotate("text",x=coord_labels[file_count,"x"],
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166 y=coord_labels[file_count,"y"],label=toString(coord_labels[file_count,4]))}
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167 print(combine_plot)
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168 dev.off()
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169
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170 ## save as (.RData)
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171
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172 msidata = msidata_combined
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173 save(msidata, file="$msidata_combined")
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174
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175
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176 ################################## xy shifts ###################################
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177 ################################################################################
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178
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179 #elif str( $combine_conditional.combine_method ) == 'xy_shifts':
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180 print("xy_shifts")
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181
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182 #if str($combine_conditional.combination_true) == "yes_combi":
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183 print("combination with xy shifts")
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184
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185 ## find duplicated coordinates
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186 all_coordinates = do.call(rbind, list(#echo ','.join($pixelcoords)#))
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187 duplicated_coordinates= duplicated(all_coordinates[,1:2])| duplicated(all_coordinates[,1:2], fromLast=TRUE)
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188 print(paste0("Number of removed duplicated coordinates: ", sum(duplicated_coordinates)/2))
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189 unique_coordinates = all_coordinates[!duplicated_coordinates,]
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190
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191 ## remove duplicated coordinates
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192 datasetlist = list()
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193 count = 1
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194 for (usable_dataset in list(#echo ','.join($msidata)#)){
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195 pixelsofinterest = pixels(usable_dataset)[names(pixels(usable_dataset)) %in% rownames(unique_coordinates)]
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196 filtered_dataset = usable_dataset[,pixelsofinterest]
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197 if (ncol(filtered_dataset) > 0 ){
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198 datasetlist[[count]] = filtered_dataset}
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199 count = count +1}
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200
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201 msidata_combined = do.call(combine, datasetlist)
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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="$msidata_combined")
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207
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208 ## create x,y,sample_name dataframe for QC pdf
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209
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210 position_df = cbind(coord(msidata), msidata\$combined_sample)
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211 colnames(position_df)[3] = "sample_name"
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212
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213 #else:
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214 print("no combination, only testing xy shifts")
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215
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216 position_df = do.call(rbind, list(#echo ','.join($pixelcoords)#))
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217 position_df\$sample_name = as.factor(pixel_vector)
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218
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219 print(paste0("Number of duplicated coordinates: ", sum(duplicated(position_df[,1:2]))))
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220
3
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221 #end if
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222
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223 ## create PDF to show all pixels in PDF as QC
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224
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225 pdf("Combined_qc.pdf", width=15, height=15)
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226 combine_plot = ggplot(position_df, aes(x=x, y=y, fill=sample_name))+
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227 geom_tile() +
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228 coord_fixed()+
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229 ggtitle("Spatial orientation of combined data")+
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230 theme_bw()+
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231 theme(text=element_text(family="ArialMT", face="bold", size=15))+
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232 theme(legend.position="bottom",legend.direction="vertical")+
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233 guides(fill=guide_legend(ncol=5,byrow=TRUE))
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234 coord_labels = aggregate(cbind(x,y)~sample_name, data=position_df, mean)
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235 coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$sample_name)
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236 for(file_count in 1:nrow(coord_labels))
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237 {combine_plot = combine_plot + annotate("text",x=coord_labels[file_count,"x"],
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238 y=coord_labels[file_count,"y"],label=toString(coord_labels[file_count,4]))}
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239 print(combine_plot)
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240 dev.off()
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241
3
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242 #end if
0
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243
3
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244 ####################### optional matrix output #################################
0
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245
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246 #if $output_matrix:
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247
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248 if (length(features(msidata))> 0 & length(pixels(msidata)) > 0){
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249 spectramatrix = spectra(msidata)[]
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250 spectramatrix = cbind(mz(msidata),spectramatrix)
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251 newmatrix = rbind(c("mz | spectra", names(pixels(msidata))), spectramatrix)
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252 write.table(newmatrix, file="$matrixasoutput", quote = FALSE, row.names = FALSE, col.names=FALSE, sep = "\t")
1
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253 }else{
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254 print("file has no features or pixels left")
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255 }
5
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256
0
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257 #end if
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258
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259 ]]></configfile>
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260 </configfiles>
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261 <inputs>
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262 <param name="infiles" type="data" multiple="true" format="imzml,rdata,analyze75"
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263 label="MSI data as imzml, analyze7.5 or Cardinal MSImageSet saved as RData"
0
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264 help="load imzml and ibd file by uploading composite datatype imzml"/>
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265 <conditional name="processed_cond">
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266 <param name="processed_file" type="select" label="Is the input file a processed imzML file ">
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267 <option value="no_processed" selected="True">not a processed imzML</option>
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268 <option value="processed">processed imzML</option>
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269 </param>
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270 <when value="no_processed"/>
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271 <when value="processed">
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272 <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"/>
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273 <param name="units" display="radio" type="select" label="Unit of the mass accuracy" help="either m/z or ppm">
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274 <option value="mz" >mz</option>
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275 <option value="ppm" selected="True" >ppm</option>
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276 </param>
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277 </when>
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278 </conditional>
1
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279 <conditional name="combine_conditional">
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280 <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">
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281 <option value="automatic_combine" selected="True" >automatic combination</option>
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282 <option value="xy_shifts">xy shifts by hand</option>
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283 </param>
3
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284 <when value="automatic_combine"/>
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285 <when value="xy_shifts">
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286 <param name="coordinates_file" type="data" format="tabular" label="datasetnames, X and y values to shift data before combining"
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287 help="Tabular file with three columns: 1 for the filename, 1 for the x-coordinate shift and 1 for the y-coordinate shift"/>
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288 <param name="column_x" data_ref="coordinates_file" label="Column with values for shift in x direction" type="data_column"/>
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289 <param name="column_y" data_ref="coordinates_file" label="Column with values for shift in y direction" type="data_column"/>
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290 <param name="column_names" data_ref="coordinates_file" label="Column with dataset names" type="data_column"/>
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291 <param name="combination_true" type="boolean" display="radio" truevalue="yes_combi" falsevalue="no_combi" label="Combine datasets" help = "If there are duplicated pixels they will be deleted. If it is not clear if there are duplicated pixels, select No to get an idea about the pixel overlap"/>
1
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292 </when>
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293 </conditional>
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294 <param name="output_matrix" type="boolean" display="radio" label="Intensity matrix output"/>
0
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295 </inputs>
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296 <outputs>
3
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297 <data format="rdata" name="msidata_combined" label="MSI_data_combined"/>
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298 <data format="pdf" name="combining_qc" from_work_dir="Combined_qc.pdf" label = "Combined_QC"/>
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299 <data format="tabular" name="matrixasoutput" label="Combined_matrix">
0
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300 <filter>output_matrix</filter>
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301 </data>
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302 </outputs>
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303 <tests>
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304 <test expect_num_outputs="3">
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305 <param name="infiles" value="msidata_1.RData,msidata_2.RData,msidata_3.RData" ftype="rdata"/>
1
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306 <param name="combine_method" value="xy_shifts"/>
0
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307 <param name="coordinates_file" ftype="tabular" value="xy_coordinates.tabular"/>
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308 <param name="column_x" value="1"/>
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309 <param name="column_y" value="2"/>
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310 <param name="column_names" value="3"/>
3
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311 <param name="combination_true" value="yes_combi"/>
0
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312 <param name="output_matrix" value="True"/>
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313 <output name="matrixasoutput" file="123_combined_matrix.tabular"/>
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314 <output name="msidata_combined" file="123_combined.RData" compare="sim_size" />
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315 <output name="combining_qc" file="123_combined_QC.pdf" compare="sim_size" delta="20000"/>
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316 </test>
3
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317 <test expect_num_outputs="2">
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318 <param name="infiles" value="msidata_1.RData,msidata_2.RData,msidata_3.RData" ftype="rdata"/>
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319 <param name="combine_method" value="xy_shifts"/>
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320 <param name="coordinates_file" ftype="tabular" value="xy_coordinates.tabular"/>
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321 <param name="column_x" value="1"/>
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322 <param name="column_y" value="2"/>
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323 <param name="column_names" value="3"/>
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324 <param name="combination_true" value="no_combi"/>
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325 <output name="msidata_combined" file="123_no_combi.RData" compare="sim_size" />
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326 <output name="combining_qc" file="123_no_combi_QC.pdf" compare="sim_size" delta="20000"/>
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327 </test>
0
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328 <test expect_num_outputs="3">
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329 <param name="infiles" value="msidata_1.RData,msidata_2.RData" ftype="rdata"/>
3
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330 <param name="combine_method" value="automatic_combine"/>
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331 <param name="output_matrix" value="True"/>
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332 <output name="matrixasoutput" file="12_combined_matrix.tabular"/>
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333 <output name="msidata_combined" file="12_combined.RData" compare="sim_size" />
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334 <output name="combining_qc" file="12_combined_QC.pdf" compare="sim_size" delta="20000"/>
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335 </test>
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336 <test expect_num_outputs="2">
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337 <param name="infiles" value="msidata_1.RData,123_combined.RData" ftype="rdata"/>
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338 <param name="combine_method" value="automatic_combine"/>
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339 <param name="output_matrix" value="False"/>
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340 <output name="msidata_combined" file="112_auto_combined.RData" compare="sim_size" />
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341 <output name="combining_qc" file="112_auto_combined_QC.pdf" compare="sim_size" delta="20000"/>
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342 </test>
0
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343 </tests>
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344 <help>
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345 <![CDATA[
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346
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347 Cardinal is an R package that implements statistical & computational tools for analyzing mass spectrometry imaging datasets. `More information on Cardinal <http://cardinalmsi.org//>`_
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348
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349 This tool uses the Cardinal combine function to combine several mass spectrometry imaging data.
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350
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351 Input data: 3 types of input data can be used:
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352
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353 - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/wp/imzml/>`_
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354 - Analyze7.5 (upload hdr, img and t2m file via the "composite" function)
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355 - Cardinal "MSImageSet" data (with variable name "msidata", saved as .RData)
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356
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357 Prerequisite:
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358
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359 - m/z values need to be the same across all datasets (before using this tool), this can be achieved with the filtering tool (use same m/z range) and the preprocessing tool (use same binning parameter)
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360
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361 Options:
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362
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363 - "automatic combination": files are automatically arranged in a grid, subfiles are named according to input file name
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364 - "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). To test if the pixels are correctly shifted use "combine datasets: No".
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365 Combine datasets: Yes - Combines all datasets and removes all duplicated pixels (same x and y coordinates).
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366
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367 Output:
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368
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369 - imzML file containing multiple subfiles
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370 - pdf that shows the pixel positions of the combined files
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371 - optional: intensity matrix as tabular file (intensities for m/z in rows and pixel in columns)
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372
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373
0
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374 ]]>
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375 </help>
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376 <citations>
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377 <citation type="doi">10.1093/bioinformatics/btv146</citation>
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378 </citations>
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379 </tool>