Mercurial > repos > galaxyp > cardinal_combine

annotate combine.xml @ 5:b41107d8fe89 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
author galaxyp
date Fri, 13 Dec 2019 13:54:23 -0500
parents 48c07268f341
children bb1ac6b47a6c
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b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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1 <tool id="cardinal_combine" name="MSI combine" version="2.2.6.0">
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2 <description>
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3 combine several mass spectrometry imaging datasets into one
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4 </description>
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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8 <requirements>
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9 <requirement type="package" version="2.2.6">bioconductor-cardinal</requirement>
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10 <requirement type="package" version="3.6.1">r-base</requirement>
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11 <requirement type="package" version="3.2.1">r-ggplot2</requirement>
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12 <requirement type="package" version="0.12">r-maldiquantforeign</requirement>
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13 <requirement type="package" version="1.19.3">r-maldiquant</requirement>
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14 </requirements>
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15 <command detect_errors="exit_code">
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16 <![CDATA[
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17 #for $i, $infile in enumerate($infiles):
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18 #if $infile.ext == 'imzml'
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19 ln -s '${infile.extra_files_path}/imzml' infile_${i}.imzML &&
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20 ln -s '${infile.extra_files_path}/ibd' infile_${i}.ibd &&
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21 #elif $infile.ext == 'analyze75'
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22 ln -s '${infile.extra_files_path}/hdr' infile_${i}.hdr &&
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23 ln -s '${infile.extra_files_path}/img' infile_${i}.img &&
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24 ln -s '${infile.extra_files_path}/t2m' infile_${i}.t2m &&
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25 #else
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26 ln -s '$infile' infile_${i}.RData &&
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27 #end if
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28 #end for
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29 #if $annotation_cond.annotation_tabular == 'annotation'
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30 #for $i, $annotation_file in enumerate($annotation_cond.annotation_files):
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31 ln -s '$annotation_file' annotation_file_${i}.tabular &&
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32 #end for
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33 #end if
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34
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35 cat '${msi_combine}' &&
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36 Rscript '${msi_combine}' &&
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37 mkdir $outfile_imzml.files_path &&
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38 mv ./out.imzML "${os.path.join($outfile_imzml.files_path, 'imzml')}" | true &&
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39 mv ./out.ibd "${os.path.join($outfile_imzml.files_path, 'ibd')}" | true &&
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40 echo "imzML file:" > $outfile_imzml &&
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41 ls -l "$outfile_imzml.files_path" >> $outfile_imzml
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42
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43 ]]>
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44 </command>
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45 <configfiles>
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46 <configfile name="msi_combine"><![CDATA[
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47 #import re
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48
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49 ################ 1) load libraries and do preparations #################
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50
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51 library(Cardinal)
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52 library(ggplot2)
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53 library(MALDIquantForeign)
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54 library(MALDIquant)
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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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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}', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units", attach.only=TRUE, as = c("MSImageSet"))
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90 centroided(msidata_$i) = $centroids
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91 #else
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92 msidata_$i <- readImzML('infile_${i}', attach.only=TRUE, as = c("MSImageSet"))
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93 centroided(msidata_$i) = $centroids
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94 #end if
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95 #elif $infile.ext == 'analyze75'
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96 msidata_$i <- readAnalyze('infile_${i}', attach.only=TRUE, as = c("MSImageSet"))
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97 centroided(msidata_$i) = $centroids
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98 #else
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99 msidata_$i = loadRData('infile_${i}.RData')
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100 ## keep compatibility with old .RData files:
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101 msidata_$i\$column1 = NULL
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102 msidata_$i\$column2 = NULL
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103 msidata_$i\$column3 = NULL
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104 msidata_$i\$column4 = NULL
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105 msidata_$i\$column5 = NULL
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106 msidata_$i\$combined_sample = NULL
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107
0
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108 #end if
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109
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110 ## remove duplicated coordinates, otherwise combine will fail
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111 print(paste0(sum(duplicated(coord(msidata_$i))), " duplicated coordinates were removed from input file"))
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112 msidata_${i} <- msidata_${i}[,!duplicated(coord(msidata_${i}))]
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113
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114 ## same name for MSI data files necessary to combine data into one single coordinate system
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115 sampleNames(msidata_$i) = "msidata"
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116
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117 ############ 3) Read and process annotation tabular files ######################
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118
0
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119 #if str($annotation_cond.annotation_tabular) == 'annotation'
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120 print("annotations")
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121
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122 ## read annotation tabular, set first two columns as x and y, merge with coordinates dataframe and order according to pixelorder in msidata
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123 input_annotation = read.delim("annotation_file_${i}.tabular", header = $annotation_cond.tabular_header, stringsAsFactors = FALSE)
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124 colnames(input_annotation)[1:2] = c("x", "y")
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125
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126 msidata_coordinates = cbind(coord(msidata_$i)[,1:2], 1:ncol(msidata_$i))
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127 colnames(msidata_coordinates)[3] = "pixel_index"
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128
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129 annotation_df = merge(msidata_coordinates, input_annotation, by=c("x", "y"), all.x=TRUE)
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130 annotation_df_sorted = annotation_df[order(annotation_df\$pixel_index),]## orders pixel according to msidata
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131 annotation_df_sorted\$pixel_index = NULL
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132
0
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133 ## extract columnnames from (last) annotation tabular (for QC plot names)
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134 annotation_colnames = colnames(input_annotation)
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135
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136 #end if
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137
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138 ############### 4) shift coordinates with xy shifts ############################
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139
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140 #if str( $combine_conditional.combine_method ) == 'xy_shifts':
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141
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142 ## optional: set all files to 1/1 and then add shift
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143 #if $combine_conditional.xy_origin:
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144 coord(msidata_$i)\$x = as.integer(coord(msidata_$i)\$x - min(coord(msidata_$i)\$x-1))
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145 coord(msidata_$i)\$y = as.integer(coord(msidata_$i)\$y - min(coord(msidata_$i)\$y-1))
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146 #end if
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147
0
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148 ## shift coordinates according to input tabular file and store file names
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149 coord(msidata_$i)\$x = as.integer(coord(msidata_$i)\$x + input_list[$i+1,$combine_conditional.column_x]) ## shifts x coordinates according to tabular file
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150 coord(msidata_$i)\$y = as.integer(coord(msidata_$i)\$y + input_list[$i+1,$combine_conditional.column_y]) ## shifts y coordinates according to tabular file
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151 sample_name = rep(paste(input_list[$i+1,$combine_conditional.column_names]),times=ncol(msidata_$i)) ## stores file name for each pixel
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152 sample_names = append(sample_names, sample_name)
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153
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154 ## store number of file to use later when removing duplicate coordinates
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155 pixelcoords_$i = cbind(coord(msidata_$i)[,1:2], rep($i+1,ncol(msidata_$i)))
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156 #silent $pixelcoords.append('pixelcoords_'+str($i))
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157 colnames(pixelcoords_$i)[3] = "file_number"
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158
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159 ##################### 5) shift coordinates automatically #######################
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160
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161 #elif str( $combine_conditional.combine_method ) == 'automatic_combine':
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162
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163 ## use name of Galaxy inputfile as sample annotation
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164 sample_name = character()
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165 #set escaped_element_identifier = re.sub('[^\w\-\s\[/]]', '_', str($infile.element_identifier))
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166
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167 if (ncol(msidata_$i)>0 & nrow(msidata_$i) >0)
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168 {
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169 sample_name = append(sample_name, rep(paste("$escaped_element_identifier"),ncol(msidata_$i)))
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170 }
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171
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172 ## Number of input files define grid which is row-wise filled with files
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173 coord(msidata_$i)\$x = as.integer(coord(msidata_$i)\$x - (min(coord(msidata_$i)\$x-1)) + x_shifts)
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174 coord(msidata_$i)\$y = as.integer(coord(msidata_$i)\$y - (min(coord(msidata_$i)\$y-1)) + y_shifts)
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175
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176 x_shifts = max(coord(msidata_$i)\$x) + $combine_conditional.shift_value
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177 max_y = append(max_y, max(coord(msidata_$i)\$y))
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178 all_files = $num_infiles
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179 new_row = ($i+1)/ceiling(sqrt(all_files))
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180 new_row%%1==0
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181 if (new_row%%1==0)
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182 {x_shifts = 0 ### when row is filled: x values start again at zero
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183 y_shifts = max(max_y) + $combine_conditional.shift_value ### when row is filled: y value increases to start a new row
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184 max_y = numeric()}
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185
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186 #end if
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187
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188 ############################# 6) combination of files ##########################
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189
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190 ## combine shifted coordinates with sample name and annotations from input file
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191
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192 #if str($annotation_cond.annotation_tabular) == 'annotation'
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193 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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194 #else
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195 cardinal_coordinates_$i = data.frame(as.matrix(Cardinal::coord(msidata_$i)[,1:2]), sample_name)
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196 #end if
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197
0
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198 ## store files to combine them later and for each file check if it is valid
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199 #silent $msidata.append('msidata_'+str($i))
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200 valid_dataset = append(valid_dataset, ncol(msidata_$i)>0 & nrow(msidata_$i)>0)
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201
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202
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203 ######################### 6a) combination different mz axis ####################
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204
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205 ## combination for files with different mz axis via MALDIquant during for loop
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206
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207 #if $processed_true:
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208 print("mz axis differ")
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209
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210 cardinal_mzs_$i = Cardinal::mz(msidata_$i)
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211
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212 for(number_spectra in 1:ncol(msidata_${i})){
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213
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214 if (centroided(msidata_$i) == FALSE){
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215 ## create mass spectrum object
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216 maldi_data_${i} = list()
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217 for(number_spectra in 1:ncol(msidata_$i)){
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218 maldi_data_${i}[[number_spectra]] = MALDIquant::createMassSpectrum(mass = cardinal_mzs_$i, intensity = Cardinal::iData(msidata_$i)[,number_spectra])}
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219 }else{
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220 maldi_data_${i} = list()
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221 for (spectra in 1:ncol(msidata_$i))
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222 {
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223 single_peaks_${i} = createMassPeaks(cardinal_mzs_$i, Cardinal::spectra(msidata_$i)[,spectra], snr=as.numeric(rep("NA", nrow(msidata_$i))))
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224 maldi_data_${i}[[spectra]] = single_peaks_${i}
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225 }
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226 }
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227 }
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228
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229 msidata_combined = append(msidata_combined, maldi_data_$i)
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230
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231 #end if
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232
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233 coordinates_combined = rbind(coordinates_combined, cardinal_coordinates_$i)
0
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234
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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235 #end for
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236
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237
5
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238 ######################### 6a) combination same mz axis ###################
0
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239
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240 #if str( $combine_conditional.combine_method ) == 'automatic_combine':
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241 print("automatic combine")
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242
5
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243 #if not $processed_true:
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244 ## combine only valid datasets
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245
5
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246 valid_data = list(#echo ','.join($msidata)#)[valid_dataset]
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247 msidata = do.call(combine, valid_data)
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248 print("Valid datasets in order of input bottom to top:")
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249 print(valid_dataset)
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250 writeImzML(msidata, "out")
0
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251
5
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252 #else
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253
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254 ## save msidata as imzML file MALDIquant
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255 MALDIquantForeign::exportImzMl(msidata_combined, file="out.imzML", processed=TRUE, coordinates=as.matrix(coordinates_combined[,1:2]))
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256
1
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257 #end if
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258
5
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259 ########################### xy shift combination ###############################
0
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260 ################################################################################
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261
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262 #elif str( $combine_conditional.combine_method ) == 'xy_shifts':
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263 print("xy_shifts")
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264
5
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265 #if not $processed_true:
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266
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267 duplicated_coordinates= duplicated(coordinates_combined[,1:2])| duplicated(coordinates_combined[,1:2], fromLast=TRUE)
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268 print(paste0("Number of removed duplicated coordinates after combination: ", sum(duplicated_coordinates)))
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269 coordinates_combined = coordinates_combined[!duplicated_coordinates,]
0
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270
5
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271 ## remove duplicated coordinates
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272 datasetlist = list()
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273 count = 1
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274 for (usable_dataset in list(#echo ','.join($msidata)#)){
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275 pixelsofinterest = pixels(usable_dataset)[names(pixels(usable_dataset)) %in% rownames(coordinates_combined)]
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276 filtered_dataset = usable_dataset[,pixelsofinterest]
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277 if (ncol(filtered_dataset) > 0 ){
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278 datasetlist[[count]] = filtered_dataset}
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279 count = count +1}
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280
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281 msidata = do.call(combine, datasetlist)
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282 writeImzML(msidata, "out")
0
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283
5
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284 #else
0
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285
5
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286 ## in case user made mistake with xy shifts: find duplicated coordinates
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287 duplicated_coordinates= duplicated(coordinates_combined[,1:2])| duplicated(coordinates_combined[,1:2], fromLast=TRUE)
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288 print(paste0("Number of removed duplicated coordinates after combination: ", sum(duplicated_coordinates)))
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289 unique_coordinates = data.frame(coordinates_combined)[!duplicated_coordinates,]
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290
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291 filtered_dataset = msidata_combined [!duplicated_coordinates]
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292 coordinates_matrix = as.matrix(unique_coordinates[,1:2])
4
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293
5
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294 ## save msidata as imzML file MALDIquant
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295 MALDIquantForeign::exportImzMl(filtered_dataset, file="out.imzML", processed=TRUE, coordinates=coordinates_matrix)
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296
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297 ## create x,y,sample_name dataframe for QC pdf
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298 ## position_df = unique_coordinates ### ! anders
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299 ## colnames(position_df)[3] = "sample_name"
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300 ##coordinates_combined = coordinates_combined[pixelsofinterest,] ###! anders
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301 coordinates_combined = unique_coordinates
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302 ##TODO: hier aufräumen kann alles weg?!
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303
2
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304 #end if
1
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305
0
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306 #end if
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307
5
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308 ################################## outputs #####################################
0
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309 ################################################################################
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310
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311 ########### QC with pixels and their annotations ################################
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312
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313 pdf("Combined_qc.pdf", width=15, height=15)
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314
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315 ## combined plot
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316 combine_plot = ggplot(coordinates_combined[,1:3], aes(x=x, y=y, fill=sample_name))+
0
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317 geom_tile() +
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318 coord_fixed()+
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319 ggtitle("Spatial orientation of combined data")+
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320 theme_bw()+
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321 theme(text=element_text(family="ArialMT", face="bold", size=15))+
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322 theme(legend.position="bottom",legend.direction="vertical")+
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323 guides(fill=guide_legend(ncol=4,byrow=TRUE))
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324 coord_labels = aggregate(cbind(x,y)~sample_name, data=coordinates_combined[,1:3], mean)
0
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325 coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$sample_name)
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326
0
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327 print(combine_plot)
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328
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329 #if str($annotation_cond.annotation_tabular) == 'annotation'
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330 ## annotation plots
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331 for (inputcolumns in 4:ncol(coordinates_combined)){
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332 ## plot 1
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333 column1_df = coordinates_combined[,c(1,2,inputcolumns)]
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334 colnames(column1_df)[3] = "column1"
0
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335
5
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336 if (sum(is.na(column1_df[3])) < nrow(column1_df)){
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337 column1_plot = ggplot(column1_df, aes(x=x, y=y, fill=column1))+
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338 geom_tile() +
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339 coord_fixed()+
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340 ggtitle(paste0(annotation_colnames[inputcolumns-1]))+
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341 theme_bw()+
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342 theme(text=element_text(family="ArialMT", face="bold", size=15))+
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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343 theme(legend.position="bottom",legend.direction="vertical")+
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344 guides(fill=guide_legend(ncol=4,byrow=TRUE, title=annotation_colnames[1]))
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345 print(column1_plot)}
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346 ##rename columnname for output tabular file
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347 colnames(column1_df)[3] = annotation_colnames[inputcolumns-1]
0
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348
5
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349 }
0
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diff changeset
350
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
351 #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
352 dev.off()
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diff changeset
353
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
354 ##################### annotation tabular output ################################
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355
5
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356 write.table(coordinates_combined, file="$pixel_annotations", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
1
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357
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
358 ]]></configfile>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
359 </configfiles>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
360 <inputs>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
361 <param name="infiles" type="data" multiple="true" format="imzml,rdata,analyze75"
4
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parents: 2
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362 label="MSI data"
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parents: 2
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363 help="Input file as imzML (composite upload), Analyze7.5 (composite upload) or Cardinal MSImageSet saved as RData (regular upload)"/>
48c07268f341 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
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364 <param name="centroids" type="boolean" label="Centroided input" help="Choose Yes if peak detection has already been done." truevalue="TRUE" falsevalue="FALSE"/>
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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365 <conditional name="processed_cond">
4
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366 <param name="processed_file" type="select" label="Processed imzML file" help="Choose no if your input is an Analyze7.5 or continuous imzML file">
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367 <option value="no_processed" selected="True">no</option>
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368 <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
369 </param>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
370 <when value="no_processed"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
371 <when value="processed">
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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372 <param name="accuracy" type="float" value="50" label="Mass accuracy to which the m/z values will be binned" help="This should be set to the native accuracy of the mass spectrometer, if known"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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373 <param name="units" display="radio" type="select" label="Unit of the mass accuracy" help="either m/z or ppm">
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
374 <option value="mz" >mz</option>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
375 <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
376 </param>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
377 </when>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
378 </conditional>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
379 <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
380 <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
381 <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
382 <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
383 </param>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
384 <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
385 <when value="annotation">
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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386 <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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387 label="Pixel annotations tabular files"
5
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388 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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389 <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
390 </when>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
391 </conditional>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
392 <conditional name="combine_conditional">
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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393 <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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394 <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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395 <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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396 </param>
5
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397 <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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398 <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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399 </when>
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
400 <when value="xy_shifts">
2
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parents: 1
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401 <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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402 help="Tabular file with three columns: 1 for the filename, 1 for the x-coordinate shift and 1 for the y-coordinate shift. Pixels with the same coordinates after shifting will be deleted."/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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403 <param name="column_x" data_ref="coordinates_file" label="Column with values for shift in x direction" type="data_column"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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404 <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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405 <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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406 <param name="xy_header" type="boolean" label="Tabular files contain a header line" truevalue="TRUE" falsevalue="FALSE"/>
5
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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407 <param name="xy_origin" type="boolean" label="Set all file coordinates to 1/1 as origin" truevalue="TRUE" falsevalue="FALSE" help="Yes: all file coordinates are shifted in order to have at least one pixel with x = 1 and one with y = 1; then coordinates shifts are added. No: the coordinate shifts are added to the current coordinates of the file"/>
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
408 </when>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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409 </conditional>
5
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410 <param name="processed_true" type="boolean" label="Do the files have different m/z axis?" help="If all m/z values of all files are exactly the same choose 'No'. If not sure choose 'Yes'." truevalue="TRUE" falsevalue="FALSE"/>
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
411 </inputs>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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412 <outputs>
5
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413 <data format="imzml" name="outfile_imzml" label="${tool.name} on ${on_string}: imzML"/>
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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414 <data format="pdf" name="QC_overview" from_work_dir="Combined_qc.pdf" label = "${tool.name} on ${on_string}: QC"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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415 <data format="tabular" name="pixel_annotations" label="${tool.name} on ${on_string}: annotations"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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416 </outputs>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
417 <tests>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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418 <test>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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419 <param name="infiles" value="msidata_1.RData,msidata_2.RData,msidata_3.RData" ftype="rdata"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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diff changeset
420 <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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421 <param name="annotation_tabular" value="annotation"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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parents:
diff changeset
422 <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
423 <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
424 </conditional>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
425 <param name="combine_method" value="xy_shifts"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
426 <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
427 <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
428 <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
429 <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
430 <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
431 <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
432 <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
433 <output name="outfile_imzml" ftype="imzml" file="123_combined.imzml.txt" 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
434 <extra_files type="file" file="123_combined.imzml" name="imzml" lines_diff="4"/>
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
435 <extra_files type="file" file="123_combined.ibd" name="ibd" compare="sim_size"/>
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
436 </output>
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
437 </test>
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
438 <test>
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
439 <param name="infiles" value="123_combined_picked.rdata,123_combined_picked2.rdata" ftype="rdata"/>
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
440 <param name="centroids" value="TRUE"/>
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
441 <param name="combine_method" value="xy_shifts"/>
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
442 <param name="coordinates_file" ftype="tabular" value="xy_coordinates2.tabular"/>
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
443 <param name="column_x" value="1"/>
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="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
445 <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
446 <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
447 <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
448 <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
449 <output name="outfile_imzml" ftype="imzml" file="picked.imzml.txt" 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
450 <extra_files type="file" file="picked.imzml" name="imzml" lines_diff="6"/>
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
451 <extra_files type="file" file="picked.ibd" name="ibd" compare="sim_size"/>
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
452 </output>
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
453 </test>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
454 <test>
2
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
455 <param name="infiles" value="msidata_1.RData,msidata_2.RData,msidata_3.RData" ftype="rdata"/>
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
456 <conditional name="annotation_cond">
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
457 <param name="annotation_tabular" value="no_annotation"/>
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
458 </conditional>
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
459 <param name="combine_method" value="automatic_combine"/>
5
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
460 <param name="processed_true" value="FALSE"/>
2
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
461 <output name="QC_overview" file="123_combined_auto.pdf" compare="sim_size"/>
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
462 <output name="pixel_annotations" file="123_combined_auto.tabular"/>
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
463 <output name="outfile_imzml" ftype="imzml" file="123_combined_auto.imzml.txt" compare="sim_size">
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
464 <extra_files type="file" file="123_combined_auto.imzml" name="imzml" lines_diff="4"/>
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
465 <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
466 </output>
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
467 </test>
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
468 <test>
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
469 <param name="infiles" value="msidata_1.RData,msidata_2.RData" ftype="rdata"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
470 <conditional name="annotation_cond">
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
471 <param name="annotation_tabular" value="annotation"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
472 <param name="annotation_files" value="annotations_file1.tabular,annotations_file2.tabular" ftype="tabular"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
473 <param name="tabular_header" value="TRUE"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
474 </conditional>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
475 <param name="combine_method" value="automatic_combine"/>
5
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
476 <param name="processed_true" value="FALSE"/>
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
477 <output name="pixel_annotations" file="12_annotation_output.tabular"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
478 <output name="QC_overview" file="12_combined_QC.pdf" compare="sim_size"/>
5
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
479 <output name="outfile_imzml" ftype="imzml" file="12_combined.imzml.txt" compare="sim_size">
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
480 <extra_files type="file" file="12_combined.imzml" name="imzml" lines_diff="4"/>
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
481 <extra_files type="file" file="12_combined.ibd" name="ibd" compare="sim_size"/>
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
482 </output>
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
483 </test>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
484 <test>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
485 <param name="infiles" value="msidata_1.RData,123_combined.RData" ftype="rdata"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
486 <conditional name="annotation_cond">
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
487 <param name="annotation_tabular" value="annotation"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
488 <param name="annotation_files" value="annotations_file1.tabular,123_annotation.tabular" ftype="tabular"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
489 <param name="tabular_header" value="TRUE"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
490 </conditional>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
491 <param name="combine_method" value="automatic_combine"/>
5
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
492 <param name="processed_true" value="FALSE"/>
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
493 <output name="pixel_annotations" file="112_annotation_output.tabular"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
494 <output name="QC_overview" file="112_auto_combined_QC.pdf" compare="sim_size"/>
2
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
495 <output name="outfile_imzml" ftype="imzml" file="112_auto_combined.imzml.txt" compare="sim_size">
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
496 <extra_files type="file" file="112_auto_combined.imzml" name="imzml" lines_diff="4"/>
129cddd02600 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
497 <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
498 </output>
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
499 </test>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
500 <test>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
501 <param name="infiles" value="msidata_2.RData,123_combined.RData" ftype="rdata"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
502 <conditional name="annotation_cond">
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
503 <param name="annotation_tabular" value="no_annotation"/>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
504 </conditional>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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505 <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
506 <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
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diff changeset
507 <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
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diff changeset
508 <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
509 <output name="outfile_imzml" ftype="imzml" file="2123_auto_combined.imzml.txt" 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
510 <extra_files type="file" file="2123_auto_combined.imzml" name="imzml" lines_diff="4"/>
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
511 <extra_files type="file" file="2123_auto_combined.ibd" name="ibd" compare="sim_size"/>
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
512 </output>
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
513 </test>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
514 </tests>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
515 <help>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
516 <![CDATA[
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
517
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
518 @CARDINAL_DESCRIPTION@
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
519
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
520 -----
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
521
5
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
522 This tool combines several mass spectrometry imaging data files.
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
523
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
524 @MSIDATA_INPUT_DESCRIPTION@
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
525 - Coordinates stored as decimals rather than integers will be rounded to obtain a regular pixel grid. This might lead to duplicated coordinates which will be automatically removed before the tools analysis starts.
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
526 @SPECTRA_TABULAR_INPUT_DESCRIPTION@
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
527
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
528 - For xy shifts with tabular file: Tabular file with x and y coordinates shift and file name
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
529
5
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
530 - Each input file is renamed and shifted in x and y direction according to this tabular file. In the example the files have about the same pixel dimensions which is smaller than 510x260.
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
531 - The file can have any column names as header (in this case set "Tabular file contains a header line" to "Yes") or no header at all (set "Tabular file contains a header line" to "No").
0
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 ::
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
534
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
535 x_shift y_shift file name
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
536 0 0 file1
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
537 510 0 file2
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
538 0 260 file3
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
539 510 260 file4
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
540 ...
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
541 ...
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
542
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
543
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
544
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
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diff changeset
546 **Options**
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
547
5
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
548 - "automatic combination": files are automatically arranged in a grid, subfiles are named according to the input file name
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
549 - "xy shifts": each file can be moved in x and y direction according to the users need (define one tabular file in the order in which the files are loaded in the history (bottom to top) and define for each file the x and y coordinates shifts in separate columns and the file name in a third column as shown above). The xy shift option combines all datasets and removes all duplicated pixels (same x and y coordinates).
5
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
550 - "Set all file coordinates to 1/1 as origin" can be choosen to override current pixel coordinates of the input file and set their minimal x and minimal y values to 1. Then the shifts from the xy shift tabular files are used to move the pixels of each dataset.
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
551 - In case the input files have not exactly the same m/z values set "Do the files have different m/z axis?" to "Yes". Then functionalities of the "MALDIquant" package are used to combine the datasets.
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
552
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
553
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
554 **Tips**
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
555
5
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
556 - The combine tool puts all samples into a common x-y-grid, therefore pixel coordinates will change. In case the pixels are already annotated, the annotations should be provided as tabular files and the tool will return an annotation file with the new pixel coordinates. This annotation file can then be used together with the combined MSI data for tools in which the annotation is required (e.g. 'MSI classification') or useful (e.g. 'MSI spectra plots').
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
557
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
558
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
559 **Output**
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 - MSI data as imzML file (in continous format when m/z axis were the same; in processed format when m/z axis were different)
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
562 - Pdf with pixel positions and annotations of the combined files
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
563 - Tabular file with pixel annotations (x,y,column with input file names and annotation columns)
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
564
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
565
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
566 ]]>
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
567 </help>
5
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
568 <citations>
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
569 <citation type="doi">10.1093/bioinformatics/btv146</citation>
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
570 <citation type="doi">10.1007/978-3-319-45809-0_6</citation>
b41107d8fe89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
galaxyp
parents: 4
diff changeset
571 </citations>
0
93be1d20b5c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
572 </tool>