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annotate msi_combine.xml @ 1:2ff16a066571 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
author galaxyp
date Tue, 08 May 2018 02:35:41 -0400
parents 50ba517b7caa
children 4f46f06e861b
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2ff16a066571 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
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1 <tool id="mass_spectrometry_imaging_combine" name="MSI combine" version="1.10.0.0">
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2 <description>
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3 combine several mass spectrometry imaging datasets into one
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4 </description>
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5 <requirements>
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6 <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement>
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7 <requirement type="package" version="2.2.1">r-ggplot2</requirement>
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8 </requirements>
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9 <command detect_errors="exit_code">
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10 <![CDATA[
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11 #for $i, $infile in enumerate($infiles):
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12 #if $infile.ext == 'imzml'
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13 ln -s '${infile.extra_files_path}/imzml' infile.imzML &&
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14 ln -s '${infile.extra_files_path}/ibd' infile.ibd &&
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15 #elif $infile.ext == 'analyze75'
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16 ln -s '${infile.extra_files_path}/hdr' infile.hdr &&
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17 ln -s '${infile.extra_files_path}/img' infile.img &&
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18 ln -s '${infile.extra_files_path}/t2m' infile.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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30 #import re
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31 ################ load libraries, read rename and combine files #################
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32
1
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33 library(Cardinal)
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34 library(ggplot2)
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35
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36 #if str( $combine_conditional.combine_method ) == 'xy_shifts':
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37 input_list = read.delim("$combine_conditional.coordinates_file", header = FALSE,
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38 stringsAsFactors = FALSE)
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39 #end if
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40
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41 pixel_vector = numeric()
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42 names_vector = character()
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43 x_shifts = 0
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44 y_shifts = 0
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45 max_y = numeric()
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46
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47 #set $msidata = []
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48 #set $pixelcoords = []
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49 #set $num_infiles = len($infiles)
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50
0
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51 #for $i, $infile in enumerate($infiles):
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52
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53 #if $infile.ext == 'imzml'
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54 msidata_$i <- readImzML('infile_${i}')
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55 sampleNames(msidata_$i) = "msidata"
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56 pixelcoords_$i = cbind(coord(msidata_$i)[,1:2], rep($i+1,ncol(msidata_$i)))
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57 #elif $infile.ext == 'analyze75'
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58 msidata_$i <- readAnalyze('infile_${i}')
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59 sampleNames(msidata_$i) = "msidata"
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60 pixelcoords_$i = cbind(coord(msidata_$i)[,1:2], rep($i+1,ncol(msidata_$i)))
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61 #else
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62 loadRData <- function(fileName){
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63 #loads an RData file, and returns it
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64 load(fileName)
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65 get(ls()[ls() != "fileName"])
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66 }
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67 msidata_$i = loadRData('infile_${i}.RData')
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68 sampleNames(msidata_$i) = "msidata"
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69 pixelcoords_$i = cbind(coord(msidata_$i)[,1:2], rep($i+1,ncol(msidata_$i)))
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70 #end if
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71 colnames(pixelcoords_$i)[3] = "file_number"
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72
1
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73 #if str( $combine_conditional.combine_method ) == 'xy_shifts':
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74 coord(msidata_$i)\$x = coord(msidata_$i)\$x + input_list[$i+1,$combine_conditional.column_x]
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75 coord(msidata_$i)\$y = coord(msidata_$i)\$y + input_list[$i+1,$combine_conditional.column_y]
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76 pixel_vector = append(pixel_vector, rep(input_list[$i+1,$combine_conditional.column_names],times=ncol(msidata_$i)))
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77
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78 #elif str( $combine_conditional.combine_method ) == 'automatic_combine':
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79 #set escaped_element_identifier = re.sub('[^\w\-\s\[/]]', '_', str($infile.element_identifier))
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80 names_vector = append(names_vector, rep(paste($i+1, "$escaped_element_identifier", sep="_"),ncol(msidata_$i)))
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81 coord(msidata_$i)\$x = coord(msidata_$i)\$x - (min(coord(msidata_$i)\$x-1)) + x_shifts
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82 coord(msidata_$i)\$y = coord(msidata_$i)\$y - (min(coord(msidata_$i)\$y-1)) + y_shifts
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83 x_shifts = max(coord(msidata_$i)\$x) + $combine_conditional.x_distance
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84 max_y = append(max_y, max(coord(msidata_$i)\$y))
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85
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86 all_files = $num_infiles
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87 new_row = ($i+1)/ceiling(sqrt(all_files))
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88 new_row%%1==0
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89 if (new_row%%1==0)
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90 {x_shifts = 0 ### x values start again at zero
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91 y_shifts = max(max_y) + $combine_conditional.y_distance
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92 max_y = numeric()}
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93
0
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94 #end if
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95 #silent $msidata.append('msidata_'+str($i))
1
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96 #silent $pixelcoords.append('pixelcoords_'+str($i))
0
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97 #end for
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98
1
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99 ###################### automatic combination ###################################
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100 ################################################################################
0
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101
1
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102 #if str( $combine_conditional.combine_method ) == 'automatic_combine':
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103 print("automatic_combine")
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104 msidata_combined = do.call(combine, list(#echo ','.join($msidata)#))
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105 sample_names = as.factor(names_vector)
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106 pData(msidata_combined)\$sample = sample_names
0
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107
1
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108 ## create PDF to show pixels of each file
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109 pdf("combining_qc.pdf", width=15, height=15)
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110 position_df = cbind(coord(msidata_combined)[,1:2], pData(msidata_combined)\$sample)
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111 colnames(position_df)[3] = "sample_name"
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112
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113 combine_plot = ggplot(position_df, aes(x=x, y=y, fill=sample_name))+
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114 geom_tile() +
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115 coord_fixed()+
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116 ggtitle("Spatial orientation of combined data")+
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117 theme_bw()+
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118 theme(text=element_text(family="ArialMT", face="bold", size=15))+
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119 theme(legend.position="bottom",legend.direction="vertical")+
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120 guides(fill=guide_legend(ncol=4,byrow=TRUE))
0
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121
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122
1
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123 coord_labels = aggregate(cbind(x,y)~sample_name, data=position_df, mean)
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124 coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$sample_name)
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125 for(file_count in 1:nrow(coord_labels))
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126 {
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127 combine_plot = combine_plot + annotate("text",x=coord_labels[file_count,"x"],y=coord_labels[file_count,"y"],label=toString(coord_labels[file_count,4]))
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128 }
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129
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130 print(combine_plot)
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131 dev.off()
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132
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133 ## save as (.RData)
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134 msidata = msidata_combined
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135 save(msidata, file="$msidata_combined")
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136 ################################## xy shifts ###################################
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137 ################################################################################
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138 #elif str( $combine_conditional.combine_method ) == 'xy_shifts':
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139 print("xy_shifts")
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140 msidata_combined = do.call(combine, list(#echo ','.join($msidata)#))
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141
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142 ############# replace NA with 0 and rename pixels according to dataset #########
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143
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144 spectra(msidata_combined)[is.na(spectra(msidata_combined))] <- 0
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145 print(paste0("Number of NAs which were replaced ",sum(is.na(spectra(msidata_combined)))))
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146
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147 sample_names = as.factor(pixel_vector)
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148 pData(msidata_combined)\$sample = sample_names
0
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149
1
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150 ###################################### outputs #################################
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151 ## save as (.RData)
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152 msidata = msidata_combined
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153 save(msidata, file="$msidata_combined")
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154
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155 ## create PDF to show pixels of each file
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156 pdf("combining_qc.pdf")
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157 position_df = cbind(coord(msidata), pData(msidata)\$sample)
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158 colnames(position_df)[3] = "sample_name"
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159
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160 combine_plot = ggplot(position_df, aes(x=x, y=y, fill=sample_name))+
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161 geom_tile() +
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162 coord_fixed()+
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163 ggtitle("Spatial orientation of combined data")+
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164 theme_bw()+
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165 theme(text=element_text(family="ArialMT", face="bold", size=12))
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166
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167 coord_labels = aggregate(cbind(x,y)~sample_name, data=position_df, mean)
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168 for(file_count in 1:nrow(coord_labels))
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169 {
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170 combine_plot = combine_plot + annotate("text",x=coord_labels[file_count,"x"],y=coord_labels[file_count,"y"],label=toString(coord_labels[file_count,"sample_name"]))
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171 }
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172
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173 print(combine_plot)
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174
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175 dev.off()
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176
0
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177
1
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178 ################################## no shifts ###################################
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179 ################################################################################
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180 #elif str( $combine_conditional.combine_method ) == 'no_shifts':
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181 print("no_shifts")
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182 msidata_combined = do.call(combine, list(#echo ','.join($msidata)#))
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183
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184 ############# replace NA with 0 and rename pixels according to dataset #########
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185
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186 spectra(msidata_combined)[is.na(spectra(msidata_combined))] <- 0
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187 print(paste0("Number of NAs which were replaced ",sum(is.na(spectra(msidata_combined)))))
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188
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189 ###################################### outputs #################################
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190 ## save as (.RData)
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191 msidata = msidata_combined
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192 save(msidata, file="$msidata_combined")
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193
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194 ## create PDF to show pixels of each file
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195 pdf("combining_qc.pdf")
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196 position_df = cbind(coord(msidata), pData(msidata)\$sample)
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197 colnames(position_df)[3] = "sample_name"
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198
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199 ggplot(position_df, aes(x=x, y=y, fill=sample_name))+
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200 geom_tile() +
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201 coord_fixed()+
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202 ggtitle("Spatial orientation of combined data")+
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203 theme_bw()+
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204 theme(text=element_text(family="ArialMT", face="bold", size=12))
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205
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206 dev.off()
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207
0
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208
1
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209 ################################## no combination ##############################
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210 ################################################################################
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211 #elif str( $combine_conditional.combine_method ) == 'no_combine':
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212 print("no_combine")
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213
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214 ## create PDF to show pixels of each file
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215 pdf("combining_qc.pdf")
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216 position_df = do.call(rbind, list(#echo ','.join($pixelcoords)#))
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217 position_df[duplicated(position_df[,1:2]),3] = 0
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218 position_df\$file_number = as.factor(position_df\$file_number)
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219
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220 combine_plot = ggplot(position_df, aes(x=x, y=y, fill=file_number))+
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221 geom_tile() +
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222 coord_fixed()+
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223 ggtitle("Spatial orientation before combination")+
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224 theme_bw()+
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225 theme(text=element_text(family="ArialMT", face="bold", size=12))+
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226 theme(panel.grid.major = element_line(colour = "black")) +
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227 scale_x_continuous(minor_breaks = seq(min(position_df\$x-50), max(position_df\$x+50, 1))) +
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228 scale_y_continuous(minor_breaks = seq(min(position_df\$y-50), max(position_df\$y+50, 1)))
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229
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230
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231 coord_labels = aggregate(cbind(x,y)~file_number, data=position_df, mean)
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232 for(file_count in 1:nrow(coord_labels))
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233 {
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234 combine_plot = combine_plot + annotate("text",x=coord_labels[file_count,"x"],y=coord_labels[file_count,"y"],label=toString(coord_labels[file_count,"file_number"]))
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235 }
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236
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237 print(combine_plot)
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238
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239 dev.off()
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240 #end if
0
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241
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242 #if $output_matrix:
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243
1
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244 if (length(features(msidata_combined))> 0 & length(pixels(msidata_combined)) > 0)
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245 {
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246 spectramatrix = spectra(msidata_combined)
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247 rownames(spectramatrix) = mz(msidata_combined)
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248 newmatrix = rbind(pixels(msidata_combined), spectramatrix)
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249 write.table(newmatrix[2:nrow(newmatrix),], file="$matrixasoutput", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t")
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250 }else{
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251 print("file has no features or pixels left")
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252 }
0
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253 #end if
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254
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255 ]]></configfile>
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256 </configfiles>
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257 <inputs>
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258 <param name="infiles" type="data" multiple="true" format="imzml,rdata,analyze75"
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259 label="MSI rawdata as imzml, analyze7.5 or Cardinal MSImageSet saved as RData"
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260 help="load imzml and ibd file by uploading composite datatype imzml"/>
1
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261 <conditional name="combine_conditional">
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262 <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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263 <option value="automatic_combine" selected="True" >automatic combination</option>
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264 <option value="no_shifts" >no coordinates shift</option>
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265 <option value="xy_shifts">xy shifts by hand</option>
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266 <option value="no_combine">check pixels before combination</option>
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267 </param>
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268 <when value="no_shifts">
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269 </when>
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270 <when value="automatic_combine">
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271 <param name="x_distance" type="integer" value="10" label="How many pixels in x direction should be between files?"/>
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272 <param name="y_distance" type="integer" value="10" label="How many pixels in y direction should be between files?"/>
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273 </when>
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274 <when value="xy_shifts">
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275 <param name="coordinates_file" type="data" format="tabular" label="datasetnames, X and y values to shift data before combining"
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276 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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277 <param name="column_x" data_ref="coordinates_file" label="Column with values for shift in x direction" type="data_column"/>
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278 <param name="column_y" data_ref="coordinates_file" label="Column with values for shift in y direction" type="data_column"/>
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279 <param name="column_names" data_ref="coordinates_file" label="Column with dataset names" type="data_column"/>
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280 </when>
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281 <when value="no_combine"/>
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282 </conditional>
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283 <param name="output_matrix" type="boolean" display="radio" label="Intensity matrix output"/>
0
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284 </inputs>
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285 <outputs>
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286 <data format="rdata" name="msidata_combined" label="Combined MSI data"/>
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287 <data format="pdf" name="combining_qc" from_work_dir="combining_qc.pdf" label = "Combined image of pixels"/>
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288 <data format="tabular" name="matrixasoutput" label="Combined matrix">
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289 <filter>output_matrix</filter>
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290 </data>
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291 </outputs>
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292 <tests>
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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,msidata_3.RData" ftype="rdata"/>
1
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295 <param name="combine_method" value="xy_shifts"/>
0
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296 <param name="coordinates_file" ftype="tabular" value="xy_coordinates.tabular"/>
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297 <param name="column_x" value="1"/>
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298 <param name="column_y" value="2"/>
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299 <param name="column_names" value="3"/>
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300 <param name="output_matrix" value="True"/>
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301 <output name="matrixasoutput" file="123_combined_matrix.tabular"/>
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302 <output name="msidata_combined" file="123_combined.RData" compare="sim_size" />
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303 <output name="combining_qc" file="123_combined_QC.pdf" compare="sim_size" delta="20000"/>
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304 </test>
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305 <test expect_num_outputs="3">
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306 <param name="infiles" value="msidata_1.RData,msidata_2.RData" ftype="rdata"/>
1
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307 <param name="combine_method" value="no_shifts"/>
0
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308 <param name="output_matrix" value="True"/>
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309 <output name="matrixasoutput" file="12_combined_matrix.tabular"/>
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310 <output name="msidata_combined" file="12_combined.RData" compare="sim_size" />
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311 <output name="combining_qc" file="12_combined_QC.pdf" compare="sim_size" delta="20000"/>
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312 </test>
1
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313 <test expect_num_outputs="3">
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314 <param name="infiles" value="msidata_1.RData,msidata_2.RData" ftype="rdata"/>
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315 <param name="combine_method" value="automatic_combine"/>
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316 <param name="x_distance" value="1"/>
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317 <param name="y_distance" value="1"/>
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318 <param name="output_matrix" value="True"/>
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319 <output name="matrixasoutput" file="12_auto_combined_matrix.tabular"/>
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320 <output name="msidata_combined" file="12_auto_combined.RData" compare="sim_size" />
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321 <output name="combining_qc" file="12_auto_combined_QC.pdf" compare="sim_size" delta="20000"/>
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322 </test>
0
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323 </tests>
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324 <help>
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325 <![CDATA[
1
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326 This tool can combine several mass-spectrometry imaging files.
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327 1) m/z values need to be the same across all datasets
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328 2) pixels (defined by x and y coordinates) must be unique
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329
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330 1) Same m/z values/axis can be achieved with the filtering tool to get all datasets to the same m/z range and afterwards binning in the preprocessing tool to obtain the same bins for all dataset.
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331 2) The pixels (defined by x and y coordinates) must be unique across all datasets, therefore the option "Select the way you want to combine multiple files" is helpful:
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332
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333 - "automatic combination": files are arranged in a grid with a distance in x and y direction which can be given by the user
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334 - "no coordinates shift": this option can only be used if all pixels are unique across datasets
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335 - "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
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336 - "check pixels before combination": no combination takes place. You will only get a pdf which shows the arrangement of the pixels (with or without additional xy shifts)
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337
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338 Input data: 3 types of input data can be used:
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339
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340 - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <http://ms-imaging.org/wp/introduction/>`_
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341 - Analyze7.5 (upload hdr, img and t2m file via the "composite" function)
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342 - Cardinal "MSImageSet" data (with variable name "msidata", saved as .RData)
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343
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344 The output of this tool is a Cardinal "MSImageSet" with the variable name "msidata" saved as .RData.
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345 ]]>
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346 </help>
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347 <citations>
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348 <citation type="doi">10.1093/bioinformatics/btv146</citation>
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349 </citations>
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350 </tool>