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annotate msi_combine.xml @ 3:91bba2486773 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
author galaxyp
date Mon, 11 Jun 2018 17:33:28 -0400
parents 00b6c61f5054
children d05bd881af3d
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91bba2486773 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7
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1 <tool id="mass_spectrometry_imaging_combine" name="MSI combine" version="1.10.0.1">
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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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38 ## read tabular file for xy_shift option
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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
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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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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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70 #if $infile.ext == 'imzml'
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71 msidata_$i <- readImzML('infile_${i}')
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72 #elif $infile.ext == 'analyze75'
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73 msidata_$i <- readAnalyze('infile_${i}')
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74 #else
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75 msidata_$i = loadRData('infile_${i}.RData')
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76 #end if
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77
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78 sampleNames(msidata_$i) = "msidata" ## same name necessary to combine data in one single coordinate system
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80 ################### preparation xy shifts ##########################
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81
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82 #if str( $combine_conditional.combine_method ) == 'xy_shifts':
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84 coord(msidata_$i)\$x = coord(msidata_$i)\$x + input_list[$i+1,$combine_conditional.column_x] ## shifts x coordinates according to tabular file
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85 coord(msidata_$i)\$y = coord(msidata_$i)\$y + input_list[$i+1,$combine_conditional.column_y] ## shifts y coordinates according to tabular file
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86 pixel_vector = append(pixel_vector, rep(paste($i+1, input_list[$i+1,$combine_conditional.column_names], sep="_"),times=ncol(msidata_$i))) ## stores file name for each pixel
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87
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88 pixelcoords_$i = cbind(coord(msidata_$i)[,1:2], rep($i+1,ncol(msidata_$i)))
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89 #silent $pixelcoords.append('pixelcoords_'+str($i))
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90 colnames(pixelcoords_$i)[3] = "file_number"
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91
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92 ################### preparation automatic combination ##########################
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93
1
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94 #elif str( $combine_conditional.combine_method ) == 'automatic_combine':
3
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95 names_vector = character()
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96 #set escaped_element_identifier = re.sub('[^\w\-\s\[/]]', '_', str($infile.element_identifier)) ## use name of inputfile from Galaxy
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97 if (sum(spectra(msidata_$i))>0) ## use only valid files
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98 {
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99 if (is.null(levels(msidata_$i\$combined_sample))) ### if the file was not combined before use input file name, otherwise keep combined_sample name which was assigned before
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100 {
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101 names_vector = append(names_vector, rep(paste($i+1, "$escaped_element_identifier", sep="_"),ncol(msidata_$i)))
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102 msidata_$i\$combined_sample = as.factor(names_vector)
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103 }
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104 }
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105
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106 ## Number of input files define grid which is row-wise filled with files
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107
1
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108 coord(msidata_$i)\$x = coord(msidata_$i)\$x - (min(coord(msidata_$i)\$x-1)) + x_shifts
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109 coord(msidata_$i)\$y = coord(msidata_$i)\$y - (min(coord(msidata_$i)\$y-1)) + y_shifts
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110 x_shifts = max(coord(msidata_$i)\$x) + 5
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111 max_y = append(max_y, max(coord(msidata_$i)\$y))
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112 all_files = $num_infiles
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113 new_row = ($i+1)/ceiling(sqrt(all_files))
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114 new_row%%1==0
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115 if (new_row%%1==0)
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116 {x_shifts = 0 ### when row is filled: x values start again at zero
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117 y_shifts = max(max_y) + 5 ### when row is filled: y value increases to start a new row
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118 max_y = numeric()}
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119
0
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120 #end if
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121
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122 ## store files to combine them later and for each file check if it is valid
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123
0
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124 #silent $msidata.append('msidata_'+str($i))
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125 valid_dataset = append(valid_dataset,
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126 (ncol(msidata_$i)>0 & nrow(msidata_$i)>0 & sum(spectra(msidata_$i))>0))
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127
0
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128 #end for
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129
0
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130
1
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131 ###################### automatic combination ###################################
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132 ################################################################################
0
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133
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134 #if str( $combine_conditional.combine_method ) == 'automatic_combine':
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135 print("automatic_combine")
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136
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137 ## combine only valid datasets
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138
3
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139 valid_data = list(#echo ','.join($msidata)#)[valid_dataset]
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140 msidata_combined = do.call(combine, valid_data)
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141 print("Valid datasets in order of input bottom to top:")
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142 print(valid_dataset)
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143
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144 ## create dataframe with x,y,sample_name and show all pixels in PDF as QC
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145
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146 pdf("Combined_qc.pdf", width=15, height=15)
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147 position_df = cbind(coord(msidata_combined)[,1:2], msidata_combined\$combined_sample)
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148 colnames(position_df)[3] = "sample_name"
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149 combine_plot = ggplot(position_df, aes(x=x, y=y, fill=sample_name))+
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150 geom_tile() +
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151 coord_fixed()+
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152 ggtitle("Spatial orientation of combined data")+
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153 theme_bw()+
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154 theme(text=element_text(family="ArialMT", face="bold", size=15))+
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155 theme(legend.position="bottom",legend.direction="vertical")+
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156 guides(fill=guide_legend(ncol=4,byrow=TRUE))
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157 coord_labels = aggregate(cbind(x,y)~sample_name, data=position_df, mean)
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158 coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$sample_name)
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159 for(file_count in 1:nrow(coord_labels))
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160 {combine_plot = combine_plot + annotate("text",x=coord_labels[file_count,"x"],
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161 y=coord_labels[file_count,"y"],label=toString(coord_labels[file_count,4]))}
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162 print(combine_plot)
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163 dev.off()
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164
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165 ## save as (.RData)
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166
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167 msidata = msidata_combined
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168 save(msidata, file="$msidata_combined")
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169
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170
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171 ################################## xy shifts ###################################
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172 ################################################################################
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173
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174 #elif str( $combine_conditional.combine_method ) == 'xy_shifts':
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175 print("xy_shifts")
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176
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177 #if str($combine_conditional.combination_true) == "yes_combi":
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178 print("combination with xy shifts")
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179
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180 msidata_combined = do.call(combine, list(#echo ','.join($msidata)#))
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181 sample_names = as.factor(pixel_vector) ## the sample names are assigned to each pixel
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182 msidata_combined\$combined_sample = sample_names ## sample names are stored in $combined_sample slot
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183
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184 ## save as (.RData)
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185
3
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186 msidata = msidata_combined
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187 save(msidata, file="$msidata_combined")
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188
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189 ## create x,y,sample_name dataframe for QC pdf
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190
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191 position_df = cbind(coord(msidata), msidata\$combined_sample)
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192 colnames(position_df)[3] = "sample_name"
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193
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194 #else:
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195 print("no combination, only testing xy shifts")
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196
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197 position_df = do.call(rbind, list(#echo ','.join($pixelcoords)#))
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198 position_df\$sample_name = as.factor(pixel_vector)
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199
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200 #end if
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201
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202 ## create PDF to show all pixels in PDF as QC
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203
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204 pdf("Combined_qc.pdf", width=15, height=15)
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205 combine_plot = ggplot(position_df, aes(x=x, y=y, fill=sample_name))+
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206 geom_tile() +
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207 coord_fixed()+
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208 ggtitle("Spatial orientation of combined data")+
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209 theme_bw()+
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210 theme(text=element_text(family="ArialMT", face="bold", size=15))+
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211 theme(legend.position="bottom",legend.direction="vertical")+
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212 guides(fill=guide_legend(ncol=4,byrow=TRUE))
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213 coord_labels = aggregate(cbind(x,y)~sample_name, data=position_df, mean)
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214 coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$sample_name)
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215 for(file_count in 1:nrow(coord_labels))
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216 {combine_plot = combine_plot + annotate("text",x=coord_labels[file_count,"x"],
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217 y=coord_labels[file_count,"y"],label=toString(coord_labels[file_count,4]))}
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218 print(combine_plot)
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219 dev.off()
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220
3
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221 #end if
0
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222
3
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223 ####################### optional matrix output #################################
0
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224
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225 #if $output_matrix:
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226
1
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227 if (length(features(msidata_combined))> 0 & length(pixels(msidata_combined)) > 0)
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228 {
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229 spectramatrix = spectra(msidata_combined)
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230 rownames(spectramatrix) = mz(msidata_combined)
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231 newmatrix = rbind(pixels(msidata_combined), spectramatrix)
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232 write.table(newmatrix[2:nrow(newmatrix),], file="$matrixasoutput", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t")
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233 }else{
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234 print("file has no features or pixels left")
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235 }
0
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236 #end if
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237
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238 ]]></configfile>
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239 </configfiles>
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240 <inputs>
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241 <param name="infiles" type="data" multiple="true" format="imzml,rdata,analyze75"
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242 label="MSI rawdata as imzml, analyze7.5 or Cardinal MSImageSet saved as RData"
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243 help="load imzml and ibd file by uploading composite datatype imzml"/>
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244 <conditional name="combine_conditional">
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245 <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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246 <option value="automatic_combine" selected="True" >automatic combination</option>
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247 <option value="xy_shifts">xy shifts by hand</option>
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248 </param>
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249 <when value="automatic_combine"/>
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250 <when value="xy_shifts">
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251 <param name="coordinates_file" type="data" format="tabular" label="datasetnames, X and y values to shift data before combining"
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252 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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253 <param name="column_x" data_ref="coordinates_file" label="Column with values for shift in x direction" type="data_column"/>
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254 <param name="column_y" data_ref="coordinates_file" label="Column with values for shift in y direction" type="data_column"/>
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255 <param name="column_names" data_ref="coordinates_file" label="Column with dataset names" type="data_column"/>
3
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256 <param name="combination_true" type="boolean" display="radio" truevalue="yes_combi" falsevalue="no_combi" label="Combine datasets" help = "Combination only works if x and y-shifts lead to unique pixel positions. If this is unknown use the No option to get an idea about the pixel overlap"/>
1
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257 </when>
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258 </conditional>
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259 <param name="output_matrix" type="boolean" display="radio" label="Intensity matrix output"/>
0
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260 </inputs>
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261 <outputs>
3
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262 <data format="rdata" name="msidata_combined" label="MSI_data_combined"/>
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263 <data format="pdf" name="combining_qc" from_work_dir="Combined_qc.pdf" label = "Combined_QC"/>
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264 <data format="tabular" name="matrixasoutput" label="Combined_matrix">
0
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265 <filter>output_matrix</filter>
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266 </data>
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267 </outputs>
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268 <tests>
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269 <test expect_num_outputs="3">
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270 <param name="infiles" value="msidata_1.RData,msidata_2.RData,msidata_3.RData" ftype="rdata"/>
1
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271 <param name="combine_method" value="xy_shifts"/>
0
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272 <param name="coordinates_file" ftype="tabular" value="xy_coordinates.tabular"/>
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273 <param name="column_x" value="1"/>
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274 <param name="column_y" value="2"/>
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275 <param name="column_names" value="3"/>
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276 <param name="combination_true" value="yes_combi"/>
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277 <param name="output_matrix" value="True"/>
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278 <output name="matrixasoutput" file="123_combined_matrix.tabular"/>
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279 <output name="msidata_combined" file="123_combined.RData" compare="sim_size" />
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280 <output name="combining_qc" file="123_combined_QC.pdf" compare="sim_size" delta="20000"/>
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281 </test>
3
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282 <test expect_num_outputs="2">
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283 <param name="infiles" value="msidata_1.RData,msidata_2.RData,msidata_3.RData" ftype="rdata"/>
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284 <param name="combine_method" value="xy_shifts"/>
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285 <param name="coordinates_file" ftype="tabular" value="xy_coordinates.tabular"/>
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286 <param name="column_x" value="1"/>
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287 <param name="column_y" value="2"/>
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288 <param name="column_names" value="3"/>
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289 <param name="combination_true" value="no_combi"/>
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290 <output name="msidata_combined" file="123_no_combi.RData" compare="sim_size" />
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291 <output name="combining_qc" file="123_no_combi_QC.pdf" compare="sim_size" delta="20000"/>
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292 </test>
0
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293 <test expect_num_outputs="3">
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294 <param name="infiles" value="msidata_1.RData,msidata_2.RData" ftype="rdata"/>
3
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295 <param name="combine_method" value="automatic_combine"/>
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296 <param name="output_matrix" value="True"/>
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297 <output name="matrixasoutput" file="12_combined_matrix.tabular"/>
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298 <output name="msidata_combined" file="12_combined.RData" compare="sim_size" />
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299 <output name="combining_qc" file="12_combined_QC.pdf" compare="sim_size" delta="20000"/>
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300 </test>
3
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301 <test expect_num_outputs="2">
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302 <param name="infiles" value="msidata_1.RData,123_combined.RData" ftype="rdata"/>
1
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303 <param name="combine_method" value="automatic_combine"/>
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304 <param name="output_matrix" value="False"/>
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305 <output name="msidata_combined" file="112_auto_combined.RData" compare="sim_size" />
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306 <output name="combining_qc" file="112_auto_combined_QC.pdf" compare="sim_size" delta="20000"/>
1
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307 </test>
0
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308 </tests>
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309 <help>
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310 <![CDATA[
1
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311
2
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312 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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313
3
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314 This tool uses the Cardinal combine function to combine several mass spectrometry imaging data.
0
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315
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316 Input data: 3 types of input data can be used:
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317
2
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318 - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/wp/imzml/>`_
0
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319 - Analyze7.5 (upload hdr, img and t2m file via the "composite" function)
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320 - Cardinal "MSImageSet" data (with variable name "msidata", saved as .RData)
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321
2
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322 Prerequisite:
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323
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324 - 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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325
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326 Options:
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327
3
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328 - "automatic combination": files are automatically arranged in a grid, subfiles are named according to input file name
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329 - "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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330
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331
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332 Output:
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333
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334 - imzML file containing multiple subfiles
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335 - pdf that shows the pixel positions of the combined files
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336 - optional: intensity matrix as tabular file (intensities for m/z in rows and pixel in columns)
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337
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338
0
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339 ]]>
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340 </help>
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341 <citations>
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342 <citation type="doi">10.1093/bioinformatics/btv146</citation>
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343 </citations>
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344 </tool>