Mercurial > repos > galaxyp > cardinal_combine

annotate combine.xml @ 14:5f066029763e draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7-dirty"
author galaxyp
date Fri, 19 Feb 2021 18:54:56 +0000
parents 7e18fcb92a6a
children aad328eb6c0f
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1 <tool id="cardinal_combine" name="MSI combine" version="@VERSION@.1">
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2 <description>
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3 combine several mass spectrometry imaging datasets into one
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4 </description>
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
7
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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
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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 ####################################
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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_$i, "MSImagingExperiment")
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114 #end if
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115
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116 ## remove duplicated coordinates, otherwise combine will fail
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117 print(paste0(sum(duplicated(coord(msidata_$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 ## remove z dimension and 3D information in pixelData to allow combining datasets with and without z dimension
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124 coord(msidata_${i})\$z <- NULL
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125 pData(msidata_${i})\$'3DPositionX' <- NULL
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126 pData(msidata_${i})\$'3DPositionY' <- NULL
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127
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128 ############ 3) Read and process annotation tabular files ######################
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129
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130 #if str($annotation_cond.annotation_tabular) == 'annotation'
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131 print("annotations")
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132
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133 ## 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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134 input_annotation = read.delim("annotation_file_${i}.tabular", header = $annotation_cond.tabular_header, stringsAsFactors = FALSE)
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135 colnames(input_annotation)[1:2] = c("x", "y")
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136
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137 msidata_coordinates = cbind(coord(msidata_$i)[,1:2], 1:ncol(msidata_$i))
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138 colnames(msidata_coordinates)[3] = "pixel_index"
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139
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140 annotation_df = merge(msidata_coordinates, input_annotation, by=c("x", "y"), all.x=TRUE)
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141 annotation_df_sorted = annotation_df[order(annotation_df\$pixel_index),]## orders pixel according to msidata
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142 annotation_df_sorted\$pixel_index = NULL
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143
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144 ## extract columnnames from (last) annotation tabular (for QC plot names)
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145 annotation_colnames = colnames(input_annotation)
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146
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147 #end if
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148
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149 ############### 4) shift coordinates with xy shifts ############################
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150
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151 #if str( $combine_conditional.combine_method ) == 'xy_shifts':
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152
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153 ## optional: set all files to 1/1 and then add shift
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154 #if $combine_conditional.xy_origin:
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155 coord(msidata_$i)\$x = as.integer(coord(msidata_$i)\$x - min(coord(msidata_$i)\$x-1))
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156 coord(msidata_$i)\$y = as.integer(coord(msidata_$i)\$y - min(coord(msidata_$i)\$y-1))
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157 #end if
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158
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159 ## shift coordinates according to input tabular file and store file names
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160 coord(msidata_$i)\$x = as.integer(coord(msidata_$i)\$x + input_list[$i+1,$combine_conditional.column_x]) ## shifts x coordinates according to tabular file
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161 coord(msidata_$i)\$y = as.integer(coord(msidata_$i)\$y + input_list[$i+1,$combine_conditional.column_y]) ## shifts y coordinates according to tabular file
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162 sample_name = rep(paste(input_list[$i+1,$combine_conditional.column_names]),times=ncol(msidata_$i)) ## stores file name for each pixel
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163 sample_names = append(sample_names, sample_name)
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164
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165 ## store number of file to use later when removing duplicate coordinates
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166 pixelcoords_$i = cbind(coord(msidata_$i)[,1:2], rep($i+1,ncol(msidata_$i)))
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167 #silent $pixelcoords.append('pixelcoords_'+str($i))
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168 colnames(pixelcoords_$i)[3] = "file_number"
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169
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170 ##################### 5) shift coordinates automatically #######################
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171
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172 #elif str( $combine_conditional.combine_method ) == 'automatic_combine':
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173
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174 ## use name of Galaxy inputfile as sample annotation
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175 sample_name = character()
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176 #set escaped_element_identifier = re.sub('[^\w\-\s\[/]]', '_', str($infile.element_identifier))
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177
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178 if (ncol(msidata_$i)>0 & nrow(msidata_$i) >0)
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179 {
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180 sample_name = append(sample_name, rep(paste("$escaped_element_identifier"),ncol(msidata_$i)))
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181 }
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182
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183 ## Number of input files define grid which is row-wise filled with files
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184 coord(msidata_$i)\$x = as.integer(coord(msidata_$i)\$x - (min(coord(msidata_$i)\$x-1)) + x_shifts)
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185 coord(msidata_$i)\$y = as.integer(coord(msidata_$i)\$y - (min(coord(msidata_$i)\$y-1)) + y_shifts)
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186
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187 x_shifts = max(coord(msidata_$i)\$x) + $combine_conditional.shift_value
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188 max_y = append(max_y, max(coord(msidata_$i)\$y))
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189 all_files = $num_infiles
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190 new_row = ($i+1)/ceiling(sqrt(all_files))
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191 new_row%%1==0
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192 if (new_row%%1==0)
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193 {x_shifts = 0 ### when row is filled: x values start again at zero
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194 y_shifts = max(max_y) + $combine_conditional.shift_value ### when row is filled: y value increases to start a new row
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195 max_y = numeric()}
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196
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197 #end if
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198
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199 ############################# 6) combination of files ##########################
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200
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201 ## combine shifted coordinates with sample name and annotations from input file
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202
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203 #if str($annotation_cond.annotation_tabular) == 'annotation'
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204 cardinal_coordinates_$i = data.frame(as.matrix(Cardinal::coord(msidata_$i)[,1:2]), sample_name, annotation_df_sorted[,-c(1,2)])
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205 #else
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206 cardinal_coordinates_$i = data.frame(as.matrix(Cardinal::coord(msidata_$i)[,1:2]), sample_name)
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207 #end if
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208
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209 ## store files to combine them later and for each file check if it is valid
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210 #silent $msidata.append('msidata_'+str($i))
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211 valid_dataset = append(valid_dataset, ncol(msidata_$i)>0 & nrow(msidata_$i)>0)
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212
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213
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214 ######################### 6a) combination different mz axis ####################
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215
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216 ## combination for files with different mz axis via MALDIquant during for loop
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217
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218 #if $processed_true:
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219 print("mz axis differ")
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220
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221 cardinal_mzs_$i = Cardinal::mz(msidata_$i)
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222
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223 for(number_spectra in 1:ncol(msidata_${i})){
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224
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225 if (centroided(msidata_$i) == FALSE){
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226 ## create mass spectrum object
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227 maldi_data_${i} = list()
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228 for(number_spectra in 1:ncol(msidata_$i)){
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229 maldi_data_${i}[[number_spectra]] = MALDIquant::createMassSpectrum(mass = cardinal_mzs_$i, intensity = Cardinal::iData(msidata_$i)[,number_spectra])}
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230 }else{
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231 maldi_data_${i} = list()
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232 for (spectra in 1:ncol(msidata_$i))
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233 {
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234 single_peaks_${i} = createMassPeaks(cardinal_mzs_$i, Cardinal::spectra(msidata_$i)[,spectra], snr=as.numeric(rep("NA", nrow(msidata_$i))))
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235 maldi_data_${i}[[spectra]] = single_peaks_${i}
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236 }
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237 }
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238 }
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239
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240 msidata_combined = append(msidata_combined, maldi_data_$i)
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241
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242 #end if
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243
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244 coordinates_combined = rbind(coordinates_combined, cardinal_coordinates_$i)
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245
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246 #end for
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247
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248
6
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249 ######################### 6b) combination same mz axis ###################
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250
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251 #if str( $combine_conditional.combine_method ) == 'automatic_combine':
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252 print("automatic combine")
0
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253
5
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254 #if not $processed_true:
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255 ## combine only valid datasets
0
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256
5
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257 valid_data = list(#echo ','.join($msidata)#)[valid_dataset]
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258 msidata = do.call(cbind, valid_data)
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259 print("Valid datasets in order of input bottom to top:")
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260 print(valid_dataset)
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261 writeImzML(msidata, "out")
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262
5
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263 #else
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264
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265 ## save msidata as imzML file MALDIquant
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266 MALDIquantForeign::exportImzMl(msidata_combined, file="out.imzML", processed=TRUE, coordinates=as.matrix(coordinates_combined[,1:2]))
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267
1
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268 #end if
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269
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270 ########################### xy shift combination ###############################
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271 ################################################################################
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272
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273 #elif str( $combine_conditional.combine_method ) == 'xy_shifts':
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274 print("xy_shifts")
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275
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276 #if not $processed_true:
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277
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278 duplicated_coordinates= duplicated(coordinates_combined[,1:2])| duplicated(coordinates_combined[,1:2], fromLast=TRUE)
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279 print(paste0("Number of removed duplicated coordinates after combination: ", sum(duplicated_coordinates)))
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280 coordinates_combined = coordinates_combined[!duplicated_coordinates,]
0
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281
5
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282 ## remove duplicated coordinates
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283 datasetlist = list()
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284 count = 1
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285 for (usable_dataset in list(#echo ','.join($msidata)#)){
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286
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287 pixelsofinterest = paste(coord(usable_dataset)\$x, coord(usable_dataset)\$y, sep="_") %in% paste(coordinates_combined\$x, coordinates_combined\$y, sep="_")
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288 filtered_dataset = usable_dataset[,pixelsofinterest]
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289 if (ncol(filtered_dataset) > 0 ){
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290 datasetlist[[count]] = filtered_dataset}
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291 count = count +1}
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292 msidata = do.call(cbind, datasetlist)
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293 writeImzML(msidata, "out")
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294
5
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295 #else
0
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296
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297 ## in case user made mistake with xy shifts: find duplicated coordinates
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298 duplicated_coordinates= duplicated(coordinates_combined[,1:2])| duplicated(coordinates_combined[,1:2], fromLast=TRUE)
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299 print(paste0("Number of removed duplicated coordinates after combination: ", sum(duplicated_coordinates)))
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300 unique_coordinates = data.frame(coordinates_combined)[!duplicated_coordinates,]
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301
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302 filtered_dataset = msidata_combined [!duplicated_coordinates]
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303 coordinates_matrix = as.matrix(unique_coordinates[,1:2])
4
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304
5
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305 ## save msidata as imzML file MALDIquant
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306 MALDIquantForeign::exportImzMl(filtered_dataset, file="out.imzML", processed=TRUE, coordinates=coordinates_matrix)
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307
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308 coordinates_combined = unique_coordinates
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309
2
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310 #end if
1
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311
0
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312 #end if
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313
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314 ################################## outputs #####################################
0
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315 ################################################################################
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316
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317 ########### QC with pixels and their annotations ################################
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318
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319 pdf("Combined_qc.pdf", width=15, height=15)
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320
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321 ## combined plot
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322 combine_plot = ggplot(coordinates_combined[,1:3], aes(x=x, y=y, fill=sample_name))+
0
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323 geom_tile() +
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324 coord_fixed()+
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325 ggtitle("Spatial orientation of combined data")+
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326 theme_bw()+
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327 theme(text=element_text(family="ArialMT", face="bold", size=15))+
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328 theme(legend.position="bottom",legend.direction="vertical")+
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329 guides(fill=guide_legend(ncol=4,byrow=TRUE))
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330 coord_labels = aggregate(cbind(x,y)~sample_name, data=coordinates_combined[,1:3], mean)
0
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331 coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$sample_name)
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332 print(combine_plot)
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333
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334 #if str($annotation_cond.annotation_tabular) == 'annotation'
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335 ## annotation plots
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336 for (inputcolumns in 4:ncol(coordinates_combined)){
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337 ## plot 1
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338 column1_df = coordinates_combined[,c(1,2,inputcolumns)]
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339 colnames(column1_df)[3] = "column1"
0
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340
5
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341 if (sum(is.na(column1_df[3])) < nrow(column1_df)){
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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342 column1_plot = ggplot(column1_df, aes(x=x, y=y, fill=column1))+
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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343 geom_tile() +
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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344 coord_fixed()+
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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345 ggtitle(paste0(annotation_colnames[inputcolumns-1]))+
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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346 theme_bw()+
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347 theme(text=element_text(family="ArialMT", face="bold", size=15))+
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348 theme(legend.position="bottom",legend.direction="vertical")+
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349 guides(fill=guide_legend(ncol=4,byrow=TRUE, title=annotation_colnames[1]))
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350 print(column1_plot)}
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diff changeset
351 ##rename columnname for output tabular file
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352 colnames(column1_df)[3] = annotation_colnames[inputcolumns-1]
0
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353
5
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diff changeset
354 }
0
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diff changeset
355
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
356 #end if
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
357 dev.off()
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diff changeset
358
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
359 ##################### annotation tabular output ################################
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
360
5
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diff changeset
361 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
362
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
363 ]]></configfile>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
364 </configfiles>
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parents:
diff changeset
365 <inputs>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
366 <param name="infiles" type="data" multiple="true" format="imzml,rdata,analyze75"
4
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parents: 2
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367 label="MSI data"
9
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parents: 8
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368 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
diff changeset
369 <param name="centroids" type="boolean" label="Centroided input" help="Choose Yes if peak detection has already been done." truevalue="TRUE" falsevalue="FALSE"/>
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
370 <conditional name="processed_cond">
4
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parents: 2
diff changeset
371 <param name="processed_file" type="select" label="Processed imzML file" help="Choose no if your input is an Analyze7.5 or continuous imzML file">
48c07268f341 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
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parents: 2
diff changeset
372 <option value="no_processed" selected="True">no</option>
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parents: 2
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373 <option value="processed">yes</option>
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
374 </param>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
375 <when value="no_processed"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
376 <when value="processed">
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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377 <param name="accuracy" type="float" value="50" label="Mass accuracy to which the m/z values will be binned" help="This should be set to the native accuracy of the mass spectrometer, if known"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
378 <param name="units" display="radio" type="select" label="Unit of the mass accuracy" help="either m/z or ppm">
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
379 <option value="mz" >mz</option>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
380 <option value="ppm" selected="True" >ppm</option>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
381 </param>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
382 </when>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
383 </conditional>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
384 <conditional name="annotation_cond">
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
385 <param name="annotation_tabular" type="select" label="Optional annotation of pixels with tabular files">
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
386 <option value="no_annotation" selected="True">no annotation</option>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
387 <option value="annotation">pixel annotations</option>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
388 </param>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
389 <when value="no_annotation"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
390 <when value="annotation">
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
391 <param name="annotation_files" type="data" multiple="true" format="tabular"
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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392 label="Pixel annotations tabular files"
5
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parents: 4
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393 help="Same number and order of files as input files. First column x values, second column y values, further columns with annotations"/>
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
394 <param name="tabular_header" type="boolean" label="Tabular files contain a header line" truevalue="TRUE" falsevalue="FALSE"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
395 </when>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
396 </conditional>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
397 <conditional name="combine_conditional">
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
398 <param name="combine_method" type="select" label="Way of combining multiple files">
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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399 <option value="automatic_combine" selected="True" >automatic combination</option>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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400 <option value="xy_shifts">shift xy coordinates with a tabular file</option>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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401 </param>
5
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402 <when value="automatic_combine">
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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403 <param name="shift_value" type="integer" value="5" label="Number of empty pixels that should separate different datasets in x and y dimension"/>
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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parents: 4
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404 </when>
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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405 <when value="xy_shifts">
2
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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parents: 1
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406 <param name="coordinates_file" type="data" format="tabular" label="Datasetnames, x and y values to shift pixel coordinates before combining"
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
407 help="Tabular file with three columns: 1 for the filename, 1 for the x-coordinate shift and 1 for the y-coordinate shift. Pixels with the same coordinates after shifting will be deleted."/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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408 <param name="column_x" data_ref="coordinates_file" label="Column with values for shift in x direction" type="data_column"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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409 <param name="column_y" data_ref="coordinates_file" label="Column with values for shift in y direction" type="data_column"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
410 <param name="column_names" data_ref="coordinates_file" label="Column with dataset names" type="data_column"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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411 <param name="xy_header" type="boolean" label="Tabular files contain a header line" truevalue="TRUE" falsevalue="FALSE"/>
5
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412 <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
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
413 </when>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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414 </conditional>
5
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parents: 4
diff changeset
415 <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
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
416 </inputs>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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417 <outputs>
5
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418 <data format="imzml" name="outfile_imzml" label="${tool.name} on ${on_string}: imzML"/>
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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parents:
diff changeset
419 <data format="pdf" name="QC_overview" from_work_dir="Combined_qc.pdf" label = "${tool.name} on ${on_string}: QC"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
420 <data format="tabular" name="pixel_annotations" label="${tool.name} on ${on_string}: annotations"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
421 </outputs>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
422 <tests>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
423 <test>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
424 <param name="infiles" value="msidata_1.RData,msidata_2.RData,msidata_3.RData" ftype="rdata"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
425 <conditional name="annotation_cond">
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
426 <param name="annotation_tabular" value="annotation"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
427 <param name="annotation_files" value="annotations_file1.tabular,annotations_file2.tabular,annotations_file3.tabular" ftype="tabular"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
428 <param name="tabular_header" value="TRUE"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
429 </conditional>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
430 <param name="combine_method" value="xy_shifts"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
431 <param name="coordinates_file" ftype="tabular" value="xy_coordinates.tabular"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
432 <param name="column_x" value="1"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
433 <param name="column_y" value="2"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
434 <param name="column_names" value="3"/>
5
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
435 <param name="processed_true" value="FALSE"/>
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
436 <output name="pixel_annotations" file="123_annotation_output.tabular"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
437 <output name="QC_overview" file="123_combined_QC.pdf" compare="sim_size"/>
5
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
438 <output name="outfile_imzml" ftype="imzml" file="123_combined.imzml.txt" compare="sim_size">
6
bb1ac6b47a6c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
439 <extra_files type="file" file="123_combined.imzml" name="imzml" lines_diff="12"/>
5
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
440 <extra_files type="file" file="123_combined.ibd" name="ibd" compare="sim_size"/>
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
441 </output>
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
442 </test>
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
443 <test>
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
444 <param name="infiles" value="123_combined_picked.rdata,123_combined_picked2.rdata" ftype="rdata"/>
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
445 <param name="centroids" value="TRUE"/>
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
446 <param name="combine_method" value="xy_shifts"/>
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
447 <param name="coordinates_file" ftype="tabular" value="xy_coordinates2.tabular"/>
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
448 <param name="column_x" value="1"/>
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
449 <param name="column_y" value="2"/>
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
450 <param name="column_names" value="3"/>
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
451 <param name="processed_true" value="TRUE"/>
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
452 <output name="pixel_annotations" file="picked.tabular"/>
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
453 <output name="QC_overview" file="picked_QC.pdf" compare="sim_size"/>
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
454 <output name="outfile_imzml" ftype="imzml" file="picked.imzml.txt" compare="sim_size">
6
bb1ac6b47a6c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
455 <extra_files type="file" file="picked.imzml" name="imzml" lines_diff="12"/>
5
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
456 <extra_files type="file" file="picked.ibd" name="ibd" compare="sim_size"/>
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
457 </output>
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
458 </test>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
459 <test>
2
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
460 <param name="infiles" value="msidata_1.RData,msidata_2.RData,msidata_3.RData" ftype="rdata"/>
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
461 <conditional name="annotation_cond">
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
462 <param name="annotation_tabular" value="no_annotation"/>
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
463 </conditional>
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
464 <param name="combine_method" value="automatic_combine"/>
5
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
465 <param name="processed_true" value="FALSE"/>
2
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
466 <output name="QC_overview" file="123_combined_auto.pdf" compare="sim_size"/>
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
467 <output name="pixel_annotations" file="123_combined_auto.tabular"/>
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
468 <output name="outfile_imzml" ftype="imzml" file="123_combined_auto.imzml.txt" compare="sim_size">
6
bb1ac6b47a6c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
469 <extra_files type="file" file="123_combined_auto.imzml" name="imzml" lines_diff="12"/>
2
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
470 <extra_files type="file" file="123_combined_auto.ibd" name="ibd" compare="sim_size"/>
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
471 </output>
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
472 </test>
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
473 <test>
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
474 <param name="infiles" value="msidata_1.RData,msidata_2.RData" ftype="rdata"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
475 <conditional name="annotation_cond">
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
476 <param name="annotation_tabular" value="annotation"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
477 <param name="annotation_files" value="annotations_file1.tabular,annotations_file2.tabular" ftype="tabular"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
478 <param name="tabular_header" value="TRUE"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
479 </conditional>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
480 <param name="combine_method" value="automatic_combine"/>
5
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
481 <param name="processed_true" value="FALSE"/>
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
482 <output name="pixel_annotations" file="12_annotation_output.tabular"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
483 <output name="QC_overview" file="12_combined_QC.pdf" compare="sim_size"/>
5
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
484 <output name="outfile_imzml" ftype="imzml" file="12_combined.imzml.txt" compare="sim_size">
6
bb1ac6b47a6c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
485 <extra_files type="file" file="12_combined.imzml" name="imzml" lines_diff="12"/>
5
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
486 <extra_files type="file" file="12_combined.ibd" name="ibd" compare="sim_size"/>
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
487 </output>
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
488 </test>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
489 <test>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
490 <param name="infiles" value="msidata_1.RData,123_combined.RData" ftype="rdata"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
491 <conditional name="annotation_cond">
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
492 <param name="annotation_tabular" value="annotation"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
493 <param name="annotation_files" value="annotations_file1.tabular,123_annotation.tabular" ftype="tabular"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
494 <param name="tabular_header" value="TRUE"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
495 </conditional>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
496 <param name="combine_method" value="automatic_combine"/>
5
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
497 <param name="processed_true" value="FALSE"/>
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
498 <output name="pixel_annotations" file="112_annotation_output.tabular"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
499 <output name="QC_overview" file="112_auto_combined_QC.pdf" compare="sim_size"/>
2
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
500 <output name="outfile_imzml" ftype="imzml" file="112_auto_combined.imzml.txt" compare="sim_size">
6
bb1ac6b47a6c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
501 <extra_files type="file" file="112_auto_combined.imzml" name="imzml" lines_diff="12"/>
2
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
502 <extra_files type="file" file="112_auto_combined.ibd" name="ibd" compare="sim_size"/>
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
503 </output>
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
504 </test>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
505 <test>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
506 <param name="infiles" value="msidata_2.RData,123_combined.RData" ftype="rdata"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
507 <conditional name="annotation_cond">
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
508 <param name="annotation_tabular" value="no_annotation"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
509 </conditional>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
510 <param name="combine_method" value="automatic_combine"/>
5
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
511 <param name="processed_true" value="FALSE"/>
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
512 <output name="pixel_annotations" file="2123_annotation_output.tabular"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
513 <output name="QC_overview" file="2123_auto_combined_QC.pdf" compare="sim_size"/>
5
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
514 <output name="outfile_imzml" ftype="imzml" file="2123_auto_combined.imzml.txt" compare="sim_size">
6
bb1ac6b47a6c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
515 <extra_files type="file" file="2123_auto_combined.imzml" name="imzml" lines_diff="12"/>
5
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
516 <extra_files type="file" file="2123_auto_combined.ibd" name="ibd" compare="sim_size"/>
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
517 </output>
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
518 </test>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
519 </tests>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
520 <help>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
521 <![CDATA[
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
522
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
523 @CARDINAL_DESCRIPTION@
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
524
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
525 -----
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
526
5
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
527 This tool combines several mass spectrometry imaging data files.
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
528
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
529 @MSIDATA_INPUT_DESCRIPTION@
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
530 - Coordinates stored as decimals rather than integers will be rounded to obtain a regular pixel grid. This might lead to duplicated coordinates which will be automatically removed before the tools analysis starts.
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
531 @SPECTRA_TABULAR_INPUT_DESCRIPTION@
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
532
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
533 - For xy shifts with tabular file: Tabular file with x and y coordinates shift and file name
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
534
5
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
535 - 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.
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
536 - 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
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
537
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
538 ::
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
539
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
540 x_shift y_shift file name
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
541 0 0 file1
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
542 510 0 file2
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
543 0 260 file3
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
544 510 260 file4
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
545 ...
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
546 ...
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
547
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
548
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
549
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
550
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
551 **Options**
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
552
5
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
553 - "automatic combination": files are automatically arranged in a grid, subfiles are named according to the input file name
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
554 - "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
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
555 - "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.
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
556 - 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.
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
557
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
558
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
559 **Tips**
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
560
5
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
561 - 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
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
562
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
563
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
564 **Output**
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
565
6
bb1ac6b47a6c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
galaxyp
parents: 5
diff changeset
566 - 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
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
567 - Pdf with pixel positions and annotations of the combined files
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
568 - Tabular file with pixel annotations (x,y,column with input file names and annotation columns)
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
569
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
570
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
571 ]]>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
572 </help>
5
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
573 <citations>
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
574 <citation type="doi">10.1093/bioinformatics/btv146</citation>
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
575 <citation type="doi">10.1007/978-3-319-45809-0_6</citation>
7
392b2dfd261d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
galaxyp
parents: 6
diff changeset
576 <citation type="doi">10.1093/gigascience/giz143</citation>
5
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
577 </citations>
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
578 </tool>