Mercurial > repos > galaxyp > cardinal_combine

annotate combine.xml @ 4:48c07268f341 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
author galaxyp
date Fri, 22 Mar 2019 08:18:29 -0400
parents 129cddd02600
children b41107d8fe89
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48c07268f341 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
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1 <tool id="cardinal_combine" name="MSI combine" version="@VERSION@.3">
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 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="requirements">
1
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9 <requirement type="package" version="3.0">r-ggplot2</requirement>
0
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10 </expand>
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11 <command detect_errors="exit_code">
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12 <![CDATA[
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13 #for $i, $infile in enumerate($infiles):
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14 #if $infile.ext == 'imzml'
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15 ln -s '${infile.extra_files_path}/imzml' infile_${i}.imzML &&
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16 ln -s '${infile.extra_files_path}/ibd' infile_${i}.ibd &&
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17 #elif $infile.ext == 'analyze75'
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18 ln -s '${infile.extra_files_path}/hdr' infile_${i}.hdr &&
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19 ln -s '${infile.extra_files_path}/img' infile_${i}.img &&
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20 ln -s '${infile.extra_files_path}/t2m' infile_${i}.t2m &&
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21 #else
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22 ln -s '$infile' infile_${i}.RData &&
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23 #end if
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24 #end for
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25 #if $annotation_cond.annotation_tabular == 'annotation'
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26 #for $i, $annotation_file in enumerate($annotation_cond.annotation_files):
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27 ln -s '$annotation_file' annotation_file_${i}.tabular &&
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28 #end for
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29 #end if
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31 cat '${msi_combine}' &&
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32 Rscript '${msi_combine}' &&
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33 #if str($imzml_output) == "imzml_format":
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34 mkdir $outfile_imzml.files_path &&
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35 mv ./out.imzML "${os.path.join($outfile_imzml.files_path, 'imzml')}" | true &&
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36 mv ./out.ibd "${os.path.join($outfile_imzml.files_path, 'ibd')}" | true &&
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37 #end if
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38 echo "imzML file:" > $outfile_imzml &&
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39 ls -l "$outfile_imzml.files_path" >> $outfile_imzml
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40
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41 ]]>
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42 </command>
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43 <configfiles>
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44 <configfile name="msi_combine"><![CDATA[
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45
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46 #import re
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47
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48 ################ load libraries and some preparations #################
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49
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50 library(Cardinal)
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51 library(ggplot2)
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52
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53 ## read tabular file for xy_shift option
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54 #if str( $combine_conditional.combine_method ) == 'xy_shifts':
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55 input_list = read.delim("$combine_conditional.coordinates_file", header = $combine_conditional.xy_header,
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56 stringsAsFactors = FALSE)
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57 #end if
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58
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59 ## function to load RData and store with new variable name
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60 loadRData <- function(fileName){
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61 load(fileName)
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62 get(ls()[ls() != "fileName"])
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63 }
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64
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65 ## preparations for reading files one by one with for loop
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66 pixel_vector = numeric()
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67 x_shifts = 0
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68 y_shifts = 0
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69 max_y = numeric()
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70 valid_dataset = logical()
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71 #set $msidata = []
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72 #set $pixelcoords = []
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73 #set $num_infiles = len($infiles)
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74 all_files = $num_infiles
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75
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76
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77 ############## reading files and changing pixel coordinates ###################
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78
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79 #for $i, $infile in enumerate($infiles):
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80
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81 ## read and manipulate MSI data
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82
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83 #if $infile.ext == 'imzml'
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84 #if str($processed_cond.processed_file) == "processed":
1
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85 msidata_$i <- readImzML('infile_${i}', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units", attach.only=TRUE)
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86 centroided(msidata_$i) = $centroids
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87 #else
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88 msidata_$i <- readImzML('infile_${i}', attach.only=TRUE)
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89 centroided(msidata_$i) = $centroids
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90 #end if
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91 #elif $infile.ext == 'analyze75'
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92 msidata_$i <- readAnalyze('infile_${i}', attach.only=TRUE)
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93 centroided(msidata_$i) = $centroids
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94 #else
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95 msidata_$i = loadRData('infile_${i}.RData')
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96 #end if
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97
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98 ## remove duplicated coordinates, otherwise combine will fail
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99 print(paste0(sum(duplicated(coord(msidata_$i))), " duplicated coordinates were removed from input file"))
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100 msidata_${i} <- msidata_${i}[,!duplicated(coord(msidata_${i}))]
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101
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102 ## same name for MSI data files necessary to combine data in one single coordinate system
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103 sampleNames(msidata_$i) = "msidata"
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104
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105
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106 ## read and process annotation tabular or automatically use name of infile as annotation
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107
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108 ## set all pixel annotations to NA, necessary in case files were combined before with different annotations
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109 msidata_$i\$column1 = rep(NA, ncol(msidata_$i))
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110 msidata_$i\$column2 = rep(NA, ncol(msidata_$i))
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111 msidata_$i\$column3 = rep(NA, ncol(msidata_$i))
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112 msidata_$i\$column4 = rep(NA, ncol(msidata_$i))
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113 msidata_$i\$column5 = rep(NA, ncol(msidata_$i))
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114 msidata_$i\$combined_sample = rep(NA, ncol(msidata_$i))
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115
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116
0
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117 #if str($annotation_cond.annotation_tabular) == 'annotation'
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118 print("annotations")
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119
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120 ## read annotation tabular, set first two columns as x and y, merge with coordinates dataframe and order according to pixelorder in msidata
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121 input_annotation = read.delim("annotation_file_${i}.tabular", header = $annotation_cond.tabular_header, stringsAsFactors = FALSE)
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122
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123 colnames(input_annotation)[1:2] = c("x", "y")
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124 msidata_coordinates = cbind(coord(msidata_$i)[,1:2], 1:ncol(msidata_$i))
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125 colnames(msidata_coordinates)[3] = "pixel_index"
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126
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127 ## only first 5 annotation columns are kept
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128 if (ncol(input_annotation) > 7){
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129 input_annotation = input_annotation[,1:7]}
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130
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131 annotation_df = merge(msidata_coordinates, input_annotation, by=c("x", "y"), all.x=TRUE)
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132 annotation_df_8 = cbind(annotation_df, data.frame(matrix(NA,ncol=8-ncol(annotation_df), nrow=ncol(msidata_$i))))
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133 annotation_df_8_sorted = annotation_df_8[order(annotation_df_8\$pixel_index),]## orders pixel according to msidata
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134
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135 ## each annotation column is assigned to the pixel in the pData slot of the MSIdata
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136 msidata_$i\$column1 = annotation_df_8_sorted[,4]
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137 msidata_$i\$column2 = annotation_df_8_sorted[,5]
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138 msidata_$i\$column3 = annotation_df_8_sorted[,6]
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139 msidata_$i\$column4 = annotation_df_8_sorted[,7]
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140 msidata_$i\$column5 = annotation_df_8_sorted[,8]
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141
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142
0
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143 ## extract columnnames from (last) annotation tabular (for QC plot names)
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144 annotation_colnames = colnames(input_annotation)[-c(1,2)]
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145
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146 #end if
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147
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148
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149 ################### preparation xy shifts ##########################
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150
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151 #if str( $combine_conditional.combine_method ) == 'xy_shifts':
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152
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153 ## shift coordinates according to input tabular file and store file names
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154 coord(msidata_$i)\$x = as.integer(coord(msidata_$i)\$x + input_list[$i+1,$combine_conditional.column_x]) ## shifts x coordinates according to tabular file
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155 coord(msidata_$i)\$y = as.integer(coord(msidata_$i)\$y + input_list[$i+1,$combine_conditional.column_y]) ## shifts y coordinates according to tabular file
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156 pixel_vector = append(pixel_vector, rep(paste($i+1, input_list[$i+1,$combine_conditional.column_names], sep="_"),times=ncol(msidata_$i))) ## stores file name for each pixel
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157 msidata_$i\$combined_sample = rep(paste($i+1, input_list[$i+1,$combine_conditional.column_names], sep="_"),times=ncol(msidata_$i))
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158 ## store number of file
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159 pixelcoords_$i = cbind(coord(msidata_$i)[,1:2], rep($i+1,ncol(msidata_$i)))
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160 #silent $pixelcoords.append('pixelcoords_'+str($i))
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161 colnames(pixelcoords_$i)[3] = "file_number"
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162
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163 ################### preparation automatic combination ##########################
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164
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165 #elif str( $combine_conditional.combine_method ) == 'automatic_combine':
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166
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167 ## use name of Galaxy inputfile as combined sample annotation
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168 names_vector = character()
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169 #set escaped_element_identifier = re.sub('[^\w\-\s\[/]]', '_', str($infile.element_identifier))
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170
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171 if (ncol(msidata_$i)>0 & nrow(msidata_$i) >0)
0
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172 {
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173 if (is.null(levels(msidata_$i\$combined_sample)))
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174 {
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175 names_vector = append(names_vector, rep(paste($i+1, "$escaped_element_identifier", sep="_"),ncol(msidata_$i)))
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176 msidata_$i\$combined_sample = as.factor(names_vector)
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177 }
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178 }
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179
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180 ## Number of input files define grid which is row-wise filled with files
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181 coord(msidata_$i)\$x = as.integer(coord(msidata_$i)\$x - (min(coord(msidata_$i)\$x-1)) + x_shifts)
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182 coord(msidata_$i)\$y = as.integer(coord(msidata_$i)\$y - (min(coord(msidata_$i)\$y-1)) + y_shifts)
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183 x_shifts = max(coord(msidata_$i)\$x) + 5
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184 max_y = append(max_y, max(coord(msidata_$i)\$y))
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185 all_files = $num_infiles
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186 new_row = ($i+1)/ceiling(sqrt(all_files))
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187 new_row%%1==0
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188 if (new_row%%1==0)
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189 {x_shifts = 0 ### when row is filled: x values start again at zero
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190 y_shifts = max(max_y) + 5 ### when row is filled: y value increases to start a new row
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191 max_y = numeric()}
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192
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193 #end if
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194
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195 ## store files to combine them later and for each file check if it is valid
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196
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197 #silent $msidata.append('msidata_'+str($i))
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198 valid_dataset = append(valid_dataset, ncol(msidata_$i)>0 & nrow(msidata_$i)>0) ## file with no intensities is considered valid
0
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199
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200 #end for
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201
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202
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203 ###################### automatic combination ###################################
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204 ################################################################################
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205
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206 #if str( $combine_conditional.combine_method ) == 'automatic_combine':
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207 print("automatic_combine")
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208
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209 ## combine only valid datasets
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210
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211 valid_data = list(#echo ','.join($msidata)#)[valid_dataset]
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212 msidata_combined = do.call(combine, valid_data)
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213 print("Valid datasets in order of input bottom to top:")
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214 print(valid_dataset)
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215
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216 ## create dataframe with x,y,sample_name and show all pixels in PDF as QC
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217 position_df = cbind(coord(msidata_combined)[,1:2], msidata_combined\$combined_sample)
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218 colnames(position_df)[3] = "sample_name"
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219
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220 msidata = msidata_combined
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221
1
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222 ## save msidata as imzML file
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223 #if str($imzml_output) == "imzml_format":
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224 writeImzML(msidata, "out")
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225 #elif str($imzml_output) == "rdata_format":
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226 ## save as (.RData)
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227 iData(msidata) = iData(msidata)[]
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228 save(msidata, file="$outfile_rdata")
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229 #end if
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230
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231
0
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232 ################################## xy shifts ###################################
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233 ################################################################################
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234
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235 #elif str( $combine_conditional.combine_method ) == 'xy_shifts':
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236 print("xy_shifts")
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237
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238 ## in case user made mistake with xy shifts: find duplicated coordinates
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239 all_coordinates = do.call(rbind, list(#echo ','.join($pixelcoords)#))
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240 duplicated_coordinates= duplicated(all_coordinates[,1:2])| duplicated(all_coordinates[,1:2], fromLast=TRUE)
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241 print(paste0("Number of removed duplicated coordinates after combination: ", sum(duplicated_coordinates)/2))
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242 unique_coordinates = all_coordinates[!duplicated_coordinates,]
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243
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244 ## remove duplicated coordinates
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245 datasetlist = list()
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246 count = 1
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247 for (usable_dataset in list(#echo ','.join($msidata)#)){
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248 pixelsofinterest = pixels(usable_dataset)[names(pixels(usable_dataset)) %in% rownames(unique_coordinates)]
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249 filtered_dataset = usable_dataset[,pixelsofinterest]
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250 if (ncol(filtered_dataset) > 0 ){
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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251 datasetlist[[count]] = filtered_dataset}
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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252 count = count +1}
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253
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254 msidata_combined = do.call(combine, datasetlist)
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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255
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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256 msidata = msidata_combined
4
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257
1
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258 ## save msidata as imzML file
2
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259 #if str($imzml_output) == "imzml_format":
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260 writeImzML(msidata, "out")
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261 #elif str($imzml_output) == "rdata_format":
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262 ## save as (.RData)
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263 iData(msidata) = iData(msidata)[]
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264 save(msidata, file="$outfile_rdata")
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265 #end if
1
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266
0
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267 ## create x,y,sample_name dataframe for QC pdf
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268
2
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269 position_df = cbind(coord(msidata)[,1:2], msidata\$combined_sample)
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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270 colnames(position_df)[3] = "sample_name"
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271
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272 #end if
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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273
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274
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275 ################################## outputs ####################################
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276 ################################################################################
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277
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278 ########### QC with pixels and their annotations ################################
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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279
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280 pdf("Combined_qc.pdf", width=15, height=15)
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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281
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282 ## combined plot
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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283 combine_plot = ggplot(position_df, aes(x=x, y=y, fill=sample_name))+
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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284 geom_tile() +
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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285 coord_fixed()+
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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286 ggtitle("Spatial orientation of combined data")+
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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287 theme_bw()+
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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288 theme(text=element_text(family="ArialMT", face="bold", size=15))+
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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289 theme(legend.position="bottom",legend.direction="vertical")+
2
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290 guides(fill=guide_legend(ncol=4,byrow=TRUE))
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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291 coord_labels = aggregate(cbind(x,y)~sample_name, data=position_df, mean)
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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292 coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$sample_name)
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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293 for(file_count in 1:nrow(coord_labels))
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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294 {combine_plot = combine_plot + annotate("text",x=coord_labels[file_count,"x"],
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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295 y=coord_labels[file_count,"y"],label=toString(coord_labels[file_count,4]))}
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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296 print(combine_plot)
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297
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298 #if str($annotation_cond.annotation_tabular) == 'annotation'
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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299 ## annotation plots
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300
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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301 ## plot 1
2
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302 column1_df = cbind(coord(msidata)[,1:2], msidata\$column1)
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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303 colnames(column1_df)[3] = "column1"
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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304
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galaxyp
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305 if (sum(is.na(column1_df[3])) < nrow(column1_df)){
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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306 column1_plot = ggplot(column1_df, aes(x=x, y=y, fill=column1))+
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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307 geom_tile() +
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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308 coord_fixed()+
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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309 ggtitle(paste0(annotation_colnames[1]))+
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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310 theme_bw()+
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galaxyp
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311 theme(text=element_text(family="ArialMT", face="bold", size=15))+
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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312 theme(legend.position="bottom",legend.direction="vertical")+
2
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313 guides(fill=guide_legend(ncol=4,byrow=TRUE, title=annotation_colnames[1]))
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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314 print(column1_plot)}
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315 ##rename columnname for output tabular file
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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316 colnames(column1_df)[3] = annotation_colnames[1]
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317
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318 ## plot 2
2
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319 column2_df = cbind(coord(msidata)[,1:2], msidata\$column2)
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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320 colnames(column2_df)[3] = "column2"
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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321
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322 if (sum(is.na(column2_df[3])) < nrow(column2_df)){
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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323 column2_plot = ggplot(column2_df, aes(x=x, y=y, fill=column2))+
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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324 geom_tile() +
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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325 coord_fixed()+
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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326 ggtitle(paste0(annotation_colnames[2]))+
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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327 theme_bw()+
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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328 theme(text=element_text(family="ArialMT", face="bold", size=15))+
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
329 theme(legend.position="bottom",legend.direction="vertical")+
2
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galaxyp
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330 guides(fill=guide_legend(ncol=4,byrow=TRUE, title=annotation_colnames[2]))
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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331 print(column2_plot)}
2
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332
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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333 ##rename columnname for output tabular file
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
334 colnames(column2_df)[3] = annotation_colnames[2]
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
335
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
336 ## plot 3
2
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
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337 column3_df = cbind(coord(msidata)[,1:2], msidata\$column3)
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
338 colnames(column3_df)[3] = "column3"
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
339 if (sum(is.na(column3_df[3])) < nrow(column3_df)){
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
340 column3_plot = ggplot(column3_df, aes(x=x, y=y, fill=column3))+
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
341 geom_tile() +
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
342 coord_fixed()+
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
343 ggtitle(paste0(annotation_colnames[3]))+
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
344 theme_bw()+
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
345 theme(text=element_text(family="ArialMT", face="bold", size=15))+
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
346 theme(legend.position="bottom",legend.direction="vertical")+
2
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
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347 guides(fill=guide_legend(ncol=4,byrow=TRUE, title=annotation_colnames[3]))
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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348 print(column3_plot)}
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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349 ##rename columnname for output tabular file
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
350 colnames(column3_df)[3] = annotation_colnames[3]
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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351
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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352 ## plot 4
2
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
353 column4_df = cbind(coord(msidata)[,1:2], msidata\$column4)
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
354 colnames(column4_df)[3] = "column4"
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
355
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
356 if (sum(is.na(column4_df[3])) < nrow(column4_df)){
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
357 column4_plot = ggplot(column4_df, aes(x=x, y=y, fill=column4))+
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
358 geom_tile() +
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
359 coord_fixed()+
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
360 ggtitle(paste0(annotation_colnames[4]))+
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
361 theme_bw()+
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
362 theme(text=element_text(family="ArialMT", face="bold", size=15))+
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
363 theme(legend.position="bottom",legend.direction="vertical")+
2
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
364 guides(fill=guide_legend(ncol=4,byrow=TRUE, title=annotation_colnames[4]))
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
365 print(column4_plot)}
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
366 ##rename columnname for output tabular file
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
367 colnames(column4_df)[3] = annotation_colnames[4]
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
368
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
369 ## plot5
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
370
2
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
371 column5_df = cbind(coord(msidata)[,1:2], msidata\$column5)
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
372 colnames(column5_df)[3] = "column5"
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
373 if (sum(is.na(column5_df[3])) < nrow(column5_df)){
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
374 column5_plot = ggplot(column5_df, aes(x=x, y=y, fill=column5))+
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
375 geom_tile() +
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
376 coord_fixed()+
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
377 ggtitle(paste0(annotation_colnames[5]))+
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
378 theme_bw()+
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
379 theme(text=element_text(family="ArialMT", face="bold", size=15))+
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
380 theme(legend.position="bottom",legend.direction="vertical")+
2
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
381 guides(fill=guide_legend(ncol=4,byrow=TRUE, title=annotation_colnames[5]))
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
382 print(column5_plot)}
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
383 ##rename columnname for output tabular file
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
384 colnames(column5_df)[3] = annotation_colnames[5]
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
385
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
386 #end if
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
387 dev.off()
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
388
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
389 ##################### annotation tabular output ################################
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
390
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
391 if (length(features(msidata))> 0 & length(pixels(msidata)) > 0){
2
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
392 position_df\$sample_name = gsub("^[^_]*_","",position_df\$sample_name)
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
393
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
394 #if str($annotation_cond.annotation_tabular) == 'no_annotation':
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
395
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
396 write.table(position_df, file="$pixel_annotations", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
397
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
398 #else
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
399 annotation_df_list = list(position_df, column1_df, column2_df, column3_df, column4_df, column5_df)
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
400 combined_annotations = Reduce(function(...) merge(..., by=c("x", "y"), all=TRUE), annotation_df_list)
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
401 write.table(combined_annotations, file="$pixel_annotations", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
402 #end if
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
403
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
404 }else{
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
405 print("No annotation tabular output because file has no features or pixels left")
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
406 }
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
407
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
408
1
65245dc812c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
409
65245dc812c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
410
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
411 ]]></configfile>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
412 </configfiles>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
413 <inputs>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
414 <param name="infiles" type="data" multiple="true" format="imzml,rdata,analyze75"
4
48c07268f341 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 2
diff changeset
415 label="MSI data"
48c07268f341 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 2
diff changeset
416 help="Input file as imzML (composite upload), Analyze7.5 (composite upload) or Cardinal MSImageSet saved as RData (regular upload)"/>
48c07268f341 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 2
diff changeset
417 <param name="centroids" type="boolean" label="Centroided input" help="Choose Yes if peak detection has already been done." truevalue="TRUE" falsevalue="FALSE"/>
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
418 <conditional name="processed_cond">
4
48c07268f341 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
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parents: 2
diff changeset
419 <param name="processed_file" type="select" label="Processed imzML file" help="Choose no if your input is an Analyze7.5 or continuous imzML file">
48c07268f341 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 2
diff changeset
420 <option value="no_processed" selected="True">no</option>
48c07268f341 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 2
diff changeset
421 <option value="processed">yes</option>
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
422 </param>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
423 <when value="no_processed"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
424 <when value="processed">
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
425 <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"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
426 <param name="units" display="radio" type="select" label="Unit of the mass accuracy" help="either m/z or ppm">
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
427 <option value="mz" >mz</option>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
428 <option value="ppm" selected="True" >ppm</option>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
429 </param>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
430 </when>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
431 </conditional>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
432 <conditional name="annotation_cond">
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
433 <param name="annotation_tabular" type="select" label="Optional annotation of pixels with tabular files">
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
434 <option value="no_annotation" selected="True">no annotation</option>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
435 <option value="annotation">pixel annotations</option>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
436 </param>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
437 <when value="no_annotation"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
438 <when value="annotation">
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
439 <param name="annotation_files" type="data" multiple="true" format="tabular"
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
440 label="Pixel annotations tabular files"
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
441 help="Same number and order of files as input files. First column x values, second column y values. Up to 5 columns with pixel annotations"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
442 <param name="tabular_header" type="boolean" label="Tabular files contain a header line" truevalue="TRUE" falsevalue="FALSE"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
443 </when>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
444 </conditional>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
445 <conditional name="combine_conditional">
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
446 <param name="combine_method" type="select" label="Way of combining multiple files">
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
447 <option value="automatic_combine" selected="True" >automatic combination</option>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
448 <option value="xy_shifts">shift xy coordinates with a tabular file</option>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
449 </param>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
450 <when value="automatic_combine"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
451 <when value="xy_shifts">
2
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
452 <param name="coordinates_file" type="data" format="tabular" label="Datasetnames, x and y values to shift pixel coordinates before combining"
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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parents:
diff changeset
453 help="Tabular file with three columns: 1 for the filename, 1 for the x-coordinate shift and 1 for the y-coordinate shift. Pixels with the same coordinates after shifting will be deleted."/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
454 <param name="column_x" data_ref="coordinates_file" label="Column with values for shift in x direction" type="data_column"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
455 <param name="column_y" data_ref="coordinates_file" label="Column with values for shift in y direction" type="data_column"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
456 <param name="column_names" data_ref="coordinates_file" label="Column with dataset names" type="data_column"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
457 <param name="xy_header" type="boolean" label="Tabular files contain a header line" truevalue="TRUE" falsevalue="FALSE"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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parents:
diff changeset
458 </when>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
459 </conditional>
2
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
460 <param name="imzml_output" type="select" display = "radio" optional = "False"
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
461 label="Output format" help= "Choose the output format">
4
48c07268f341 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 2
diff changeset
462 <option value="imzml_format">imzML</option>
48c07268f341 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 2
diff changeset
463 <option value="rdata_format" selected="True" >RData</option>
2
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
464 </param>
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
465 </inputs>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
466 <outputs>
2
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
467 <data format="imzml" name="outfile_imzml" label="${tool.name} on ${on_string}: imzML">
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
468 <filter>imzml_output=='imzml_format'</filter>
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
469 </data>
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
470 <data format="rdata" name="outfile_rdata" label="${tool.name} on ${on_string}: RData">
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
471 <filter>imzml_output == 'rdata_format'</filter>
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
472 </data>
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
473 <data format="pdf" name="QC_overview" from_work_dir="Combined_qc.pdf" label = "${tool.name} on ${on_string}: QC"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
474 <data format="tabular" name="pixel_annotations" label="${tool.name} on ${on_string}: annotations"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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475 </outputs>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
476 <tests>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
477 <test>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
478 <param name="infiles" value="msidata_1.RData,msidata_2.RData,msidata_3.RData" ftype="rdata"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
479 <conditional name="annotation_cond">
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
480 <param name="annotation_tabular" value="annotation"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
481 <param name="annotation_files" value="annotations_file1.tabular,annotations_file2.tabular,annotations_file3.tabular" ftype="tabular"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
482 <param name="tabular_header" value="TRUE"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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483 </conditional>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
484 <param name="combine_method" value="xy_shifts"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
485 <param name="coordinates_file" ftype="tabular" value="xy_coordinates.tabular"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
486 <param name="column_x" value="1"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
487 <param name="column_y" value="2"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
488 <param name="column_names" value="3"/>
2
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
489 <param name="imzml_output" value="rdata_format"/>
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
490 <output name="pixel_annotations" file="123_annotation_output.tabular"/>
2
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
491 <output name="outfile_rdata" file="123_combined.RData" compare="sim_size" />
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
492 <output name="QC_overview" file="123_combined_QC.pdf" compare="sim_size"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
493 </test>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
494 <test>
2
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
495 <param name="infiles" value="msidata_1.RData,msidata_2.RData,msidata_3.RData" ftype="rdata"/>
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
496 <conditional name="annotation_cond">
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
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497 <param name="annotation_tabular" value="no_annotation"/>
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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diff changeset
498 </conditional>
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
499 <param name="combine_method" value="automatic_combine"/>
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
500 <param name="imzml_output" value="imzml_format"/>
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
501 <output name="QC_overview" file="123_combined_auto.pdf" compare="sim_size"/>
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
502 <output name="pixel_annotations" file="123_combined_auto.tabular"/>
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
503 <output name="outfile_imzml" ftype="imzml" file="123_combined_auto.imzml.txt" compare="sim_size">
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
504 <extra_files type="file" file="123_combined_auto.imzml" name="imzml" lines_diff="4"/>
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
505 <extra_files type="file" file="123_combined_auto.ibd" name="ibd" compare="sim_size"/>
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
506 </output>
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
507 </test>
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
508 <test>
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
509 <param name="infiles" value="msidata_1.RData,msidata_2.RData" ftype="rdata"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
510 <conditional name="annotation_cond">
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
511 <param name="annotation_tabular" value="annotation"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
512 <param name="annotation_files" value="annotations_file1.tabular,annotations_file2.tabular" ftype="tabular"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
513 <param name="tabular_header" value="TRUE"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
514 </conditional>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
515 <param name="combine_method" value="automatic_combine"/>
2
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
516 <param name="imzml_output" value="rdata_format"/>
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
517 <output name="pixel_annotations" file="12_annotation_output.tabular"/>
2
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
518 <output name="outfile_rdata" file="12_combined.RData" compare="sim_size" />
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
519 <output name="QC_overview" file="12_combined_QC.pdf" compare="sim_size"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
520 </test>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
521 <test>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
522 <param name="infiles" value="msidata_1.RData,123_combined.RData" ftype="rdata"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
523 <conditional name="annotation_cond">
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
524 <param name="annotation_tabular" value="annotation"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
525 <param name="annotation_files" value="annotations_file1.tabular,123_annotation.tabular" ftype="tabular"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
526 <param name="tabular_header" value="TRUE"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
527 </conditional>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
528 <param name="combine_method" value="automatic_combine"/>
2
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
529 <param name="imzml_output" value="imzml_format"/>
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
530 <output name="pixel_annotations" file="112_annotation_output.tabular"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
531 <output name="QC_overview" file="112_auto_combined_QC.pdf" compare="sim_size"/>
2
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
532 <output name="outfile_imzml" ftype="imzml" file="112_auto_combined.imzml.txt" compare="sim_size">
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
533 <extra_files type="file" file="112_auto_combined.imzml" name="imzml" lines_diff="4"/>
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
534 <extra_files type="file" file="112_auto_combined.ibd" name="ibd" compare="sim_size"/>
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
535 </output>
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
536 </test>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
537 <test>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
538 <param name="infiles" value="msidata_2.RData,123_combined.RData" ftype="rdata"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
539 <conditional name="annotation_cond">
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
540 <param name="annotation_tabular" value="no_annotation"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
541 </conditional>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
542 <param name="combine_method" value="automatic_combine"/>
2
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
543 <param name="imzml_output" value="rdata_format"/>
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
544 <output name="pixel_annotations" file="2123_annotation_output.tabular"/>
2
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
545 <output name="outfile_rdata" file="2123_auto_combined.RData" compare="sim_size" />
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
546 <output name="QC_overview" file="2123_auto_combined_QC.pdf" compare="sim_size"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
547 </test>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
548 </tests>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
549 <help>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
550 <![CDATA[
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
551
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
552 @CARDINAL_DESCRIPTION@
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
553
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
554 -----
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
555
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
556 This tool uses the Cardinal combine function to combine several mass spectrometry imaging data.
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
557
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
558 @MSIDATA_INPUT_DESCRIPTION@
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
559 - MSI data files must have the same m/z values (to obtain same m/z values for different files: filtering tool same m/z range and preprocessing tool same binning width)
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
560 - Coordinates stored as decimals rather than integers will be rounded to obtain a regular pixel grid. This might lead to duplicated coordinates which will be automatically removed before the tools analysis starts.
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
561 @SPECTRA_TABULAR_INPUT_DESCRIPTION@
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
562
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
563 - For xy shifts with tabular file: Tabular file with x and y coordinates shift and file name
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
564
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
565 - Each input file is shifted in x and y direction according to this tabular file. In the example the files have about the same pixel dimensions which is smaller than 510x260.
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
566 - The file can have any column names as header (in this case set "Tabular file contains a header line" to yes) or no header at all
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
567
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
568 ::
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
569
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
570 x_shift y_shift file name
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
571 0 0 file1
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
572 510 0 file2
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
573 0 260 file3
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
574 510 260 file4
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
575 ...
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
576 ...
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
577
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
578
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
579
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
580
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
581 **Options**
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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582
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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583 - "automatic combination": files are automatically arranged in a grid (duplicated pixels are allowed), subfiles are named according to the input file name
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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584 - "xy shifts": 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 as shown above). The xy shift option combines all datasets and removes all duplicated pixels (same x and y coordinates).
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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585
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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586 **Tips**
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587
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588 - The combine tools puts all samples into a common x-y-grid, therefore pixel coordinates will change. In case the pixels are already annotated, the annotations should be provided as tabular files and the tool will return an annotation file with the new pixel coordinates. This annotation file can then be used together with the combined MSI data for tools in which the annotation is required (e.g. 'MSI classification') or useful (e.g. 'MSI spectra plots').
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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589 - In case more annotations are required: The annotation input file should have an identifier column, for example the patient_ID. A second tabular file that contains more annotations and also one column with the identifier column (e.g. 'patient_ID') can be merged to the annotation output file of this tool with the tool 'join two files' and then set the 'Column to use' parameters for both files to the identifier column.
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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590
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591
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592
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593 **Output**
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594
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595 - MSI data as imzML file or .RData (can be read with the Cardinal package in R)
0
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596 - pdf that shows the pixel positions and annotations of the combined files
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597 - Tabular file with pixel annotations (x,y,column with input file names and up to five annotation columns)
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598
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599
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600 ]]>
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601 </help>
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602 <expand macro="citations"/>
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603 </tool>