Mercurial > repos > galaxyp > cardinal_combine

annotate combine.xml @ 9:11d9b3ebbabd draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
author galaxyp
date Tue, 03 Nov 2020 22:22:18 +0000
parents edb351764624
children d64858cd48c6
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9
11d9b3ebbabd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
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1 <tool id="cardinal_combine" name="MSI combine" version="@VERSION@.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">
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9 <requirement type="package" version="3.3.2">r-ggplot2</requirement>
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10 <requirement type="package" version="0.12">r-maldiquantforeign</requirement>
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11 <requirement type="package" version="1.19.3">r-maldiquant</requirement>
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12 </expand>
0
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13 <command detect_errors="exit_code">
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14 <![CDATA[
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15 #for $i, $infile in enumerate($infiles):
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16 #if $infile.ext == 'imzml'
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17 ln -s '${infile.extra_files_path}/imzml' infile_${i}.imzML &&
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18 ln -s '${infile.extra_files_path}/ibd' infile_${i}.ibd &&
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19 #elif $infile.ext == 'analyze75'
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20 ln -s '${infile.extra_files_path}/hdr' infile_${i}.hdr &&
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21 ln -s '${infile.extra_files_path}/img' infile_${i}.img &&
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22 ln -s '${infile.extra_files_path}/t2m' infile_${i}.t2m &&
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23 #else
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24 ln -s '$infile' infile_${i}.RData &&
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25 #end if
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26 #end for
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27 #if $annotation_cond.annotation_tabular == 'annotation'
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28 #for $i, $annotation_file in enumerate($annotation_cond.annotation_files):
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29 ln -s '$annotation_file' annotation_file_${i}.tabular &&
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30 #end for
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31 #end if
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32
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33 cat '${msi_combine}' &&
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34 Rscript '${msi_combine}' &&
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35 mkdir $outfile_imzml.files_path &&
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36 mv ./out.imzML "${os.path.join($outfile_imzml.files_path, 'imzml')}" | true &&
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37 mv ./out.ibd "${os.path.join($outfile_imzml.files_path, 'ibd')}" | true &&
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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
0
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46 #import re
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47
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48 ################ 1) load libraries and do 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 library(MALDIquantForeign)
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53 library(MALDIquant)
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54
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55
0
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56 ## read tabular file for xy_shift option
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57 #if str( $combine_conditional.combine_method ) == 'xy_shifts':
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58 input_list = read.delim("$combine_conditional.coordinates_file", header = $combine_conditional.xy_header,
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59 stringsAsFactors = FALSE)
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60 #end if
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61
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62 ## function to load RData and store with new variable name
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63 loadRData <- function(fileName){
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64 load(fileName)
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65 get(ls()[ls() != "fileName"])
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66 }
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67
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68 ## preparations for reading files one by one with for loop
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69 sample_names = numeric()
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70 x_shifts = 0
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71 y_shifts = 0
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72 max_y = numeric()
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73 valid_dataset = logical()
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74 coordinates_combined = data.frame(matrix(,ncol=2, nrow=0))
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75 msidata_combined = list()
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76 #set $msidata = []
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77 #set $pixelcoords = []
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78 #set $num_infiles = len($infiles)
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79 all_files = $num_infiles
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80
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81 ###################### 2) reading MSI files ####################################
0
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82
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83 #for $i, $infile in enumerate($infiles):
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84
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85 ## read and manipulate MSI data
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86
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87 #if $infile.ext == 'imzml'
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88 #if str($processed_cond.processed_file) == "processed":
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89 msidata_$i <- readImzML('infile_${i}', resolution=$processed_cond.accuracy, units = "$processed_cond.units", attach.only=TRUE)
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90 msidata_$i = collect(msidata_$i, as.matrix=TRUE) ##coercion to continuous
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91 centroided(msidata_$i) = $centroids
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92 #else
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93 msidata_$i <- readImzML('infile_${i}', attach.only=TRUE)
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94 centroided(msidata_$i) = $centroids
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95 #end if
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96 #elif $infile.ext == 'analyze75'
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97 msidata_$i = readAnalyze('infile_${i}', attach.only=TRUE)
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98 centroided(msidata_$i) = $centroids
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99 #else
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100 ## function to read RData files independent of filename
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101 loadRData <- function(fileName){
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102 load(fileName)
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103 get(ls()[ls() != "fileName"])
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104 }
0
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105 msidata_$i = loadRData('infile_${i}.RData')
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106 ## keep compatibility with old .RData files:
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107 msidata_$i\$column1 = NULL
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108 msidata_$i\$column2 = NULL
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109 msidata_$i\$column3 = NULL
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110 msidata_$i\$column4 = NULL
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111 msidata_$i\$column5 = NULL
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112 msidata_$i\$combined_sample = NULL
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113 msidata_$i <- as(msidata_$i, "MSImagingExperiment")
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114 #end if
0
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115
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116 ## remove duplicated coordinates, otherwise combine will fail
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117 print(paste0(sum(duplicated(coord(msidata_$i))), " duplicated coordinates were removed from input file"))
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118 msidata_${i} <- msidata_${i}[,!duplicated(coord(msidata_${i}))]
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119
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120 ## same name for MSI data files necessary to combine data into one single coordinate system
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121 run(msidata_$i) = "msidata"
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122
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123 ############ 3) Read and process annotation tabular files ######################
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124
0
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125 #if str($annotation_cond.annotation_tabular) == 'annotation'
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126 print("annotations")
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127
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128 ## read annotation tabular, set first two columns as x and y, merge with coordinates dataframe and order according to pixelorder in msidata
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129 input_annotation = read.delim("annotation_file_${i}.tabular", header = $annotation_cond.tabular_header, stringsAsFactors = FALSE)
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130 colnames(input_annotation)[1:2] = c("x", "y")
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131
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132 msidata_coordinates = cbind(coord(msidata_$i)[,1:2], 1:ncol(msidata_$i))
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133 colnames(msidata_coordinates)[3] = "pixel_index"
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134
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135 annotation_df = merge(msidata_coordinates, input_annotation, by=c("x", "y"), all.x=TRUE)
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136 annotation_df_sorted = annotation_df[order(annotation_df\$pixel_index),]## orders pixel according to msidata
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137 annotation_df_sorted\$pixel_index = NULL
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138
0
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139 ## extract columnnames from (last) annotation tabular (for QC plot names)
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140 annotation_colnames = colnames(input_annotation)
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141
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142 #end if
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143
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144 ############### 4) shift coordinates with xy shifts ############################
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145
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146 #if str( $combine_conditional.combine_method ) == 'xy_shifts':
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147
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148 ## optional: set all files to 1/1 and then add shift
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149 #if $combine_conditional.xy_origin:
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150 coord(msidata_$i)\$x = as.integer(coord(msidata_$i)\$x - min(coord(msidata_$i)\$x-1))
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151 coord(msidata_$i)\$y = as.integer(coord(msidata_$i)\$y - min(coord(msidata_$i)\$y-1))
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152 #end if
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153
0
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154 ## shift coordinates according to input tabular file and store file names
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155 coord(msidata_$i)\$x = as.integer(coord(msidata_$i)\$x + input_list[$i+1,$combine_conditional.column_x]) ## shifts x coordinates according to tabular file
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156 coord(msidata_$i)\$y = as.integer(coord(msidata_$i)\$y + input_list[$i+1,$combine_conditional.column_y]) ## shifts y coordinates according to tabular file
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157 sample_name = rep(paste(input_list[$i+1,$combine_conditional.column_names]),times=ncol(msidata_$i)) ## stores file name for each pixel
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158 sample_names = append(sample_names, sample_name)
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159
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160 ## store number of file to use later when removing duplicate coordinates
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161 pixelcoords_$i = cbind(coord(msidata_$i)[,1:2], rep($i+1,ncol(msidata_$i)))
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162 #silent $pixelcoords.append('pixelcoords_'+str($i))
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163 colnames(pixelcoords_$i)[3] = "file_number"
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164
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165 ##################### 5) shift coordinates automatically #######################
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166
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167 #elif str( $combine_conditional.combine_method ) == 'automatic_combine':
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168
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169 ## use name of Galaxy inputfile as sample annotation
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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170 sample_name = character()
0
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171 #set escaped_element_identifier = re.sub('[^\w\-\s\[/]]', '_', str($infile.element_identifier))
2
7b07fee610fc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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172
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173 if (ncol(msidata_$i)>0 & nrow(msidata_$i) >0)
0
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174 {
5
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175 sample_name = append(sample_name, rep(paste("$escaped_element_identifier"),ncol(msidata_$i)))
0
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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176 }
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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177
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178 ## Number of input files define grid which is row-wise filled with files
1
ac474da43605 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
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179 coord(msidata_$i)\$x = as.integer(coord(msidata_$i)\$x - (min(coord(msidata_$i)\$x-1)) + x_shifts)
ac474da43605 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
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180 coord(msidata_$i)\$y = as.integer(coord(msidata_$i)\$y - (min(coord(msidata_$i)\$y-1)) + y_shifts)
5
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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181
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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diff changeset
182 x_shifts = max(coord(msidata_$i)\$x) + $combine_conditional.shift_value
0
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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183 max_y = append(max_y, max(coord(msidata_$i)\$y))
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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184 all_files = $num_infiles
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185 new_row = ($i+1)/ceiling(sqrt(all_files))
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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186 new_row%%1==0
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187 if (new_row%%1==0)
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188 {x_shifts = 0 ### when row is filled: x values start again at zero
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189 y_shifts = max(max_y) + $combine_conditional.shift_value ### when row is filled: y value increases to start a new row
0
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190 max_y = numeric()}
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191
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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192 #end if
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193
5
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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194 ############################# 6) combination of files ##########################
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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195
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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196 ## combine shifted coordinates with sample name and annotations from input file
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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197
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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198 #if str($annotation_cond.annotation_tabular) == 'annotation'
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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199 cardinal_coordinates_$i = data.frame(as.matrix(Cardinal::coord(msidata_$i)[,1:2]), sample_name, annotation_df_sorted[,-c(1,2)])
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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200 #else
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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201 cardinal_coordinates_$i = data.frame(as.matrix(Cardinal::coord(msidata_$i)[,1:2]), sample_name)
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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202 #end if
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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diff changeset
203
0
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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204 ## store files to combine them later and for each file check if it is valid
5
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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205 #silent $msidata.append('msidata_'+str($i))
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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206 valid_dataset = append(valid_dataset, ncol(msidata_$i)>0 & nrow(msidata_$i)>0)
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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207
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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208
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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209 ######################### 6a) combination different mz axis ####################
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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210
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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211 ## combination for files with different mz axis via MALDIquant during for loop
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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212
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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213 #if $processed_true:
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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214 print("mz axis differ")
0
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215
5
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216 cardinal_mzs_$i = Cardinal::mz(msidata_$i)
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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217
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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218 for(number_spectra in 1:ncol(msidata_${i})){
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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219
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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220 if (centroided(msidata_$i) == FALSE){
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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221 ## create mass spectrum object
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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222 maldi_data_${i} = list()
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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223 for(number_spectra in 1:ncol(msidata_$i)){
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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224 maldi_data_${i}[[number_spectra]] = MALDIquant::createMassSpectrum(mass = cardinal_mzs_$i, intensity = Cardinal::iData(msidata_$i)[,number_spectra])}
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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225 }else{
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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226 maldi_data_${i} = list()
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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227 for (spectra in 1:ncol(msidata_$i))
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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228 {
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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229 single_peaks_${i} = createMassPeaks(cardinal_mzs_$i, Cardinal::spectra(msidata_$i)[,spectra], snr=as.numeric(rep("NA", nrow(msidata_$i))))
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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230 maldi_data_${i}[[spectra]] = single_peaks_${i}
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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231 }
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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232 }
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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233 }
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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234
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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235 msidata_combined = append(msidata_combined, maldi_data_$i)
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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236
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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diff changeset
237 #end if
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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238
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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diff changeset
239 coordinates_combined = rbind(coordinates_combined, cardinal_coordinates_$i)
0
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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240
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
241 #end for
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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242
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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243
6
1ccb0890a34a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
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diff changeset
244 ######################### 6b) combination same mz axis ###################
0
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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245
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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246 #if str( $combine_conditional.combine_method ) == 'automatic_combine':
5
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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247 print("automatic combine")
0
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248
5
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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249 #if not $processed_true:
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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250 ## combine only valid datasets
0
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251
5
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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252 valid_data = list(#echo ','.join($msidata)#)[valid_dataset]
9
11d9b3ebbabd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
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253 msidata = do.call(cbind, valid_data)
5
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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254 print("Valid datasets in order of input bottom to top:")
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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255 print(valid_dataset)
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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256 writeImzML(msidata, "out")
0
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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257
5
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258 #else
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259
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260 ## save msidata as imzML file MALDIquant
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261 MALDIquantForeign::exportImzMl(msidata_combined, file="out.imzML", processed=TRUE, coordinates=as.matrix(coordinates_combined[,1:2]))
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262
1
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263 #end if
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264
5
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265 ########################### xy shift combination ###############################
0
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266 ################################################################################
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267
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268 #elif str( $combine_conditional.combine_method ) == 'xy_shifts':
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269 print("xy_shifts")
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270
5
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271 #if not $processed_true:
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272
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273 duplicated_coordinates= duplicated(coordinates_combined[,1:2])| duplicated(coordinates_combined[,1:2], fromLast=TRUE)
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274 print(paste0("Number of removed duplicated coordinates after combination: ", sum(duplicated_coordinates)))
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275 coordinates_combined = coordinates_combined[!duplicated_coordinates,]
0
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276
5
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277 ## remove duplicated coordinates
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278 datasetlist = list()
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279 count = 1
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280 for (usable_dataset in list(#echo ','.join($msidata)#)){
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281
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282 pixelsofinterest = paste(coord(usable_dataset)\$x, coord(usable_dataset)\$y, sep="_") %in% paste(coordinates_combined\$x, coordinates_combined\$y, sep="_")
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283 filtered_dataset = usable_dataset[,pixelsofinterest]
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284 if (ncol(filtered_dataset) > 0 ){
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285 datasetlist[[count]] = filtered_dataset}
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286 count = count +1}
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287 msidata = do.call(cbind, datasetlist)
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288 writeImzML(msidata, "out")
0
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289
5
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290 #else
0
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291
5
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292 ## in case user made mistake with xy shifts: find duplicated coordinates
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293 duplicated_coordinates= duplicated(coordinates_combined[,1:2])| duplicated(coordinates_combined[,1:2], fromLast=TRUE)
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294 print(paste0("Number of removed duplicated coordinates after combination: ", sum(duplicated_coordinates)))
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295 unique_coordinates = data.frame(coordinates_combined)[!duplicated_coordinates,]
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296
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297 filtered_dataset = msidata_combined [!duplicated_coordinates]
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298 coordinates_matrix = as.matrix(unique_coordinates[,1:2])
4
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299
5
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300 ## save msidata as imzML file MALDIquant
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301 MALDIquantForeign::exportImzMl(filtered_dataset, file="out.imzML", processed=TRUE, coordinates=coordinates_matrix)
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302
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303 coordinates_combined = unique_coordinates
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304
2
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305 #end if
1
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306
0
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307 #end if
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308
5
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309 ################################## outputs #####################################
0
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310 ################################################################################
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311
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312 ########### QC with pixels and their annotations ################################
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313
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314 pdf("Combined_qc.pdf", width=15, height=15)
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315
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316 ## combined plot
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317 combine_plot = ggplot(coordinates_combined[,1:3], aes(x=x, y=y, fill=sample_name))+
0
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318 geom_tile() +
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319 coord_fixed()+
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320 ggtitle("Spatial orientation of combined data")+
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321 theme_bw()+
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322 theme(text=element_text(family="ArialMT", face="bold", size=15))+
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323 theme(legend.position="bottom",legend.direction="vertical")+
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324 guides(fill=guide_legend(ncol=4,byrow=TRUE))
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325 coord_labels = aggregate(cbind(x,y)~sample_name, data=coordinates_combined[,1:3], mean)
0
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326 coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$sample_name)
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327 print(combine_plot)
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328
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329 #if str($annotation_cond.annotation_tabular) == 'annotation'
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330 ## annotation plots
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331 for (inputcolumns in 4:ncol(coordinates_combined)){
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332 ## plot 1
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333 column1_df = coordinates_combined[,c(1,2,inputcolumns)]
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334 colnames(column1_df)[3] = "column1"
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335
5
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336 if (sum(is.na(column1_df[3])) < nrow(column1_df)){
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337 column1_plot = ggplot(column1_df, aes(x=x, y=y, fill=column1))+
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338 geom_tile() +
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339 coord_fixed()+
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340 ggtitle(paste0(annotation_colnames[inputcolumns-1]))+
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341 theme_bw()+
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342 theme(text=element_text(family="ArialMT", face="bold", size=15))+
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343 theme(legend.position="bottom",legend.direction="vertical")+
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344 guides(fill=guide_legend(ncol=4,byrow=TRUE, title=annotation_colnames[1]))
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345 print(column1_plot)}
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346 ##rename columnname for output tabular file
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diff changeset
347 colnames(column1_df)[3] = annotation_colnames[inputcolumns-1]
0
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348
5
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diff changeset
349 }
0
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diff changeset
350
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
351 #end if
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
352 dev.off()
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diff changeset
353
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
354 ##################### annotation tabular output ################################
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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355
5
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diff changeset
356 write.table(coordinates_combined, file="$pixel_annotations", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
1
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parents: 0
diff changeset
357
0
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
358 ]]></configfile>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
359 </configfiles>
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galaxyp
parents:
diff changeset
360 <inputs>
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galaxyp
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diff changeset
361 <param name="infiles" type="data" multiple="true" format="imzml,rdata,analyze75"
4
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parents: 2
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362 label="MSI data"
9
11d9b3ebbabd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents: 8
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363 help="Input file as imzML (composite upload), Analyze7.5 (composite upload) or Cardinal 'MSImageSet' or 'MSImagingExperiment' saved as RData (regular upload)"/>
4
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parents: 2
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364 <param name="centroids" type="boolean" label="Centroided input" help="Choose Yes if peak detection has already been done." truevalue="TRUE" falsevalue="FALSE"/>
0
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
365 <conditional name="processed_cond">
4
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parents: 2
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366 <param name="processed_file" type="select" label="Processed imzML file" help="Choose no if your input is an Analyze7.5 or continuous imzML file">
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367 <option value="no_processed" selected="True">no</option>
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parents: 2
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368 <option value="processed">yes</option>
0
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diff changeset
369 </param>
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galaxyp
parents:
diff changeset
370 <when value="no_processed"/>
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diff changeset
371 <when value="processed">
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372 <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"/>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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373 <param name="units" display="radio" type="select" label="Unit of the mass accuracy" help="either m/z or ppm">
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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374 <option value="mz" >mz</option>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
375 <option value="ppm" selected="True" >ppm</option>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
376 </param>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
377 </when>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
378 </conditional>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
379 <conditional name="annotation_cond">
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
380 <param name="annotation_tabular" type="select" label="Optional annotation of pixels with tabular files">
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
381 <option value="no_annotation" selected="True">no annotation</option>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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382 <option value="annotation">pixel annotations</option>
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diff changeset
383 </param>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
384 <when value="no_annotation"/>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
385 <when value="annotation">
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
386 <param name="annotation_files" type="data" multiple="true" format="tabular"
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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387 label="Pixel annotations tabular files"
5
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parents: 4
diff changeset
388 help="Same number and order of files as input files. First column x values, second column y values, further columns with annotations"/>
0
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
389 <param name="tabular_header" type="boolean" label="Tabular files contain a header line" truevalue="TRUE" falsevalue="FALSE"/>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
390 </when>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
391 </conditional>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
392 <conditional name="combine_conditional">
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
393 <param name="combine_method" type="select" label="Way of combining multiple files">
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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394 <option value="automatic_combine" selected="True" >automatic combination</option>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
395 <option value="xy_shifts">shift xy coordinates with a tabular file</option>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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396 </param>
5
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parents: 4
diff changeset
397 <when value="automatic_combine">
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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398 <param name="shift_value" type="integer" value="5" label="Number of empty pixels that should separate different datasets in x and y dimension"/>
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
399 </when>
0
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
400 <when value="xy_shifts">
2
7b07fee610fc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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parents: 1
diff changeset
401 <param name="coordinates_file" type="data" format="tabular" label="Datasetnames, x and y values to shift pixel coordinates before combining"
0
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
402 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."/>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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403 <param name="column_x" data_ref="coordinates_file" label="Column with values for shift in x direction" type="data_column"/>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
404 <param name="column_y" data_ref="coordinates_file" label="Column with values for shift in y direction" type="data_column"/>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
405 <param name="column_names" data_ref="coordinates_file" label="Column with dataset names" type="data_column"/>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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406 <param name="xy_header" type="boolean" label="Tabular files contain a header line" truevalue="TRUE" falsevalue="FALSE"/>
5
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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407 <param name="xy_origin" type="boolean" label="Set all file coordinates to 1/1 as origin" truevalue="TRUE" falsevalue="FALSE" help="Yes: all file coordinates are shifted in order to have at least one pixel with x = 1 and one with y = 1; then coordinates shifts are added. No: the coordinate shifts are added to the current coordinates of the file"/>
0
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
408 </when>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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409 </conditional>
5
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parents: 4
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410 <param name="processed_true" type="boolean" label="Do the files have different m/z axis?" help="If all m/z values of all files are exactly the same choose 'No'. If not sure choose 'Yes'." truevalue="TRUE" falsevalue="FALSE"/>
0
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
411 </inputs>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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412 <outputs>
5
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parents: 4
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413 <data format="imzml" name="outfile_imzml" label="${tool.name} on ${on_string}: imzML"/>
0
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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414 <data format="pdf" name="QC_overview" from_work_dir="Combined_qc.pdf" label = "${tool.name} on ${on_string}: QC"/>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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415 <data format="tabular" name="pixel_annotations" label="${tool.name} on ${on_string}: annotations"/>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
416 </outputs>
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diff changeset
417 <tests>
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galaxyp
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diff changeset
418 <test>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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419 <param name="infiles" value="msidata_1.RData,msidata_2.RData,msidata_3.RData" ftype="rdata"/>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
420 <conditional name="annotation_cond">
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
421 <param name="annotation_tabular" value="annotation"/>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
422 <param name="annotation_files" value="annotations_file1.tabular,annotations_file2.tabular,annotations_file3.tabular" ftype="tabular"/>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
423 <param name="tabular_header" value="TRUE"/>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
424 </conditional>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
425 <param name="combine_method" value="xy_shifts"/>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
426 <param name="coordinates_file" ftype="tabular" value="xy_coordinates.tabular"/>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
427 <param name="column_x" value="1"/>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
428 <param name="column_y" value="2"/>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
429 <param name="column_names" value="3"/>
5
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
430 <param name="processed_true" value="FALSE"/>
0
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
431 <output name="pixel_annotations" file="123_annotation_output.tabular"/>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
432 <output name="QC_overview" file="123_combined_QC.pdf" compare="sim_size"/>
5
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
433 <output name="outfile_imzml" ftype="imzml" file="123_combined.imzml.txt" compare="sim_size">
6
1ccb0890a34a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
434 <extra_files type="file" file="123_combined.imzml" name="imzml" lines_diff="12"/>
5
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
435 <extra_files type="file" file="123_combined.ibd" name="ibd" compare="sim_size"/>
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
436 </output>
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
437 </test>
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
438 <test>
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
439 <param name="infiles" value="123_combined_picked.rdata,123_combined_picked2.rdata" ftype="rdata"/>
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
440 <param name="centroids" value="TRUE"/>
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
441 <param name="combine_method" value="xy_shifts"/>
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
442 <param name="coordinates_file" ftype="tabular" value="xy_coordinates2.tabular"/>
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
443 <param name="column_x" value="1"/>
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
444 <param name="column_y" value="2"/>
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
445 <param name="column_names" value="3"/>
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
446 <param name="processed_true" value="TRUE"/>
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
447 <output name="pixel_annotations" file="picked.tabular"/>
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
448 <output name="QC_overview" file="picked_QC.pdf" compare="sim_size"/>
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
449 <output name="outfile_imzml" ftype="imzml" file="picked.imzml.txt" compare="sim_size">
6
1ccb0890a34a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
450 <extra_files type="file" file="picked.imzml" name="imzml" lines_diff="12"/>
5
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
451 <extra_files type="file" file="picked.ibd" name="ibd" compare="sim_size"/>
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
452 </output>
0
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
453 </test>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
454 <test>
2
7b07fee610fc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
455 <param name="infiles" value="msidata_1.RData,msidata_2.RData,msidata_3.RData" ftype="rdata"/>
7b07fee610fc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
456 <conditional name="annotation_cond">
7b07fee610fc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
457 <param name="annotation_tabular" value="no_annotation"/>
7b07fee610fc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
458 </conditional>
7b07fee610fc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
459 <param name="combine_method" value="automatic_combine"/>
5
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
460 <param name="processed_true" value="FALSE"/>
2
7b07fee610fc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
461 <output name="QC_overview" file="123_combined_auto.pdf" compare="sim_size"/>
7b07fee610fc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
462 <output name="pixel_annotations" file="123_combined_auto.tabular"/>
7b07fee610fc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
463 <output name="outfile_imzml" ftype="imzml" file="123_combined_auto.imzml.txt" compare="sim_size">
6
1ccb0890a34a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
464 <extra_files type="file" file="123_combined_auto.imzml" name="imzml" lines_diff="12"/>
2
7b07fee610fc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
465 <extra_files type="file" file="123_combined_auto.ibd" name="ibd" compare="sim_size"/>
7b07fee610fc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
466 </output>
7b07fee610fc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
467 </test>
7b07fee610fc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
468 <test>
0
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
469 <param name="infiles" value="msidata_1.RData,msidata_2.RData" ftype="rdata"/>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
470 <conditional name="annotation_cond">
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
471 <param name="annotation_tabular" value="annotation"/>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
472 <param name="annotation_files" value="annotations_file1.tabular,annotations_file2.tabular" ftype="tabular"/>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
473 <param name="tabular_header" value="TRUE"/>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
474 </conditional>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
475 <param name="combine_method" value="automatic_combine"/>
5
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
476 <param name="processed_true" value="FALSE"/>
0
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
477 <output name="pixel_annotations" file="12_annotation_output.tabular"/>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
478 <output name="QC_overview" file="12_combined_QC.pdf" compare="sim_size"/>
5
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
479 <output name="outfile_imzml" ftype="imzml" file="12_combined.imzml.txt" compare="sim_size">
6
1ccb0890a34a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
480 <extra_files type="file" file="12_combined.imzml" name="imzml" lines_diff="12"/>
5
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
481 <extra_files type="file" file="12_combined.ibd" name="ibd" compare="sim_size"/>
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
482 </output>
0
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
483 </test>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
484 <test>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
485 <param name="infiles" value="msidata_1.RData,123_combined.RData" ftype="rdata"/>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
486 <conditional name="annotation_cond">
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
487 <param name="annotation_tabular" value="annotation"/>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
488 <param name="annotation_files" value="annotations_file1.tabular,123_annotation.tabular" ftype="tabular"/>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
489 <param name="tabular_header" value="TRUE"/>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
490 </conditional>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
491 <param name="combine_method" value="automatic_combine"/>
5
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
492 <param name="processed_true" value="FALSE"/>
0
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
493 <output name="pixel_annotations" file="112_annotation_output.tabular"/>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
494 <output name="QC_overview" file="112_auto_combined_QC.pdf" compare="sim_size"/>
2
7b07fee610fc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
495 <output name="outfile_imzml" ftype="imzml" file="112_auto_combined.imzml.txt" compare="sim_size">
6
1ccb0890a34a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
496 <extra_files type="file" file="112_auto_combined.imzml" name="imzml" lines_diff="12"/>
2
7b07fee610fc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
497 <extra_files type="file" file="112_auto_combined.ibd" name="ibd" compare="sim_size"/>
7b07fee610fc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
498 </output>
0
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
499 </test>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
500 <test>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
501 <param name="infiles" value="msidata_2.RData,123_combined.RData" ftype="rdata"/>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
502 <conditional name="annotation_cond">
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
503 <param name="annotation_tabular" value="no_annotation"/>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
504 </conditional>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
505 <param name="combine_method" value="automatic_combine"/>
5
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
506 <param name="processed_true" value="FALSE"/>
0
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
507 <output name="pixel_annotations" file="2123_annotation_output.tabular"/>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
508 <output name="QC_overview" file="2123_auto_combined_QC.pdf" compare="sim_size"/>
5
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
509 <output name="outfile_imzml" ftype="imzml" file="2123_auto_combined.imzml.txt" compare="sim_size">
6
1ccb0890a34a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
510 <extra_files type="file" file="2123_auto_combined.imzml" name="imzml" lines_diff="12"/>
5
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
511 <extra_files type="file" file="2123_auto_combined.ibd" name="ibd" compare="sim_size"/>
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
512 </output>
0
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
513 </test>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
514 </tests>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
515 <help>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
516 <![CDATA[
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
517
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
518 @CARDINAL_DESCRIPTION@
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
519
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
520 -----
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
521
5
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
522 This tool combines several mass spectrometry imaging data files.
0
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
523
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
524 @MSIDATA_INPUT_DESCRIPTION@
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
525 - 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.
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
526 @SPECTRA_TABULAR_INPUT_DESCRIPTION@
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
527
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
528 - For xy shifts with tabular file: Tabular file with x and y coordinates shift and file name
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
529
5
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
530 - Each input file is renamed and 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.
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
531 - 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 (set "Tabular file contains a header line" to "No").
0
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
532
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
533 ::
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
534
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
535 x_shift y_shift file name
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
536 0 0 file1
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
537 510 0 file2
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
538 0 260 file3
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
539 510 260 file4
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
540 ...
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
541 ...
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
542
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
543
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
544
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
545
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
546 **Options**
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
547
5
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
548 - "automatic combination": files are automatically arranged in a grid, subfiles are named according to the input file name
0
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
549 - "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).
5
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
550 - "Set all file coordinates to 1/1 as origin" can be choosen to override current pixel coordinates of the input file and set their minimal x and minimal y values to 1. Then the shifts from the xy shift tabular files are used to move the pixels of each dataset.
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
551 - In case the input files have not exactly the same m/z values set "Do the files have different m/z axis?" to "Yes". Then functionalities of the "MALDIquant" package are used to combine the datasets.
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
552
0
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
553
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
554 **Tips**
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
555
5
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
556 - The combine tool 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').
0
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
557
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
558
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
559 **Output**
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
560
6
1ccb0890a34a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
561 - MSI data as imzML file (in continuous format when m/z axis were the same; in processed format when m/z axis were different)
5
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
562 - Pdf with pixel positions and annotations of the combined files
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
563 - Tabular file with pixel annotations (x,y,column with input file names and annotation columns)
0
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
564
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
565
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
566 ]]>
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
567 </help>
5
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
568 <citations>
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
569 <citation type="doi">10.1093/bioinformatics/btv146</citation>
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
570 <citation type="doi">10.1007/978-3-319-45809-0_6</citation>
7
a93991a9db04 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 6
diff changeset
571 <citation type="doi">10.1093/gigascience/giz143</citation>
5
8563ef53288b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
572 </citations>
0
b414378b969f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
573 </tool>