Mercurial > repos > galaxyp > cardinal_segmentations

annotate macros.xml @ 3:09b638ceee45 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2
author galaxyp
date Thu, 28 Feb 2019 09:23:26 -0500
parents 034885df9b09
children 9f7d1ec01767
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e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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1 <macros>
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2 <token name="@VERSION@">1.12.1</token>
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4 <xml name="requirements">
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5 <requirements>
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6 <requirement type="package" version="@VERSION@">bioconductor-cardinal</requirement>
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7 <requirement type="package" version="3.5.1">r-base</requirement>
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8 <yield/>
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9 </requirements>
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10 </xml>
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11
1
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12 <xml name="print_version">
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13 <version_command><![CDATA[
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14 echo $(R --version | grep version | grep -v GNU)", Cardinal version" $(R --vanilla --slave -e "library(Cardinal); cat(sessionInfo()\$otherPkgs\$Cardinal\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
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15 ]]></version_command>
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16 </xml>
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17
0
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18 <token name="@INPUT_LINKING@"><![CDATA[
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19 #if $infile.ext == 'imzml'
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20 ln -s '${infile.extra_files_path}/imzml' infile.imzML &&
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21 ln -s '${infile.extra_files_path}/ibd' infile.ibd &&
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22 #elif $infile.ext == 'analyze75'
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23 ln -s '${infile.extra_files_path}/hdr' infile.hdr &&
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24 ln -s '${infile.extra_files_path}/img' infile.img &&
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25 ln -s '${infile.extra_files_path}/t2m' infile.t2m &&
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26 #else
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27 ln -s $infile infile.RData &&
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28 #end if
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29 ]]></token>
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32 <token name="@READING_MSIDATA@"><![CDATA[
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33 ## importing MSI data files
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34
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35 ## function to read RData files independent of filename
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36 loadRData <- function(fileName){
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37 load(fileName)
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38 get(ls()[ls() != "fileName"])
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39 }
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40
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41 #if $infile.ext == 'imzml'
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42 #if str($processed_cond.processed_file) == "processed":
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43 msidata <- readImzML('infile', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units", attach.only=TRUE)
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44 centroided(msidata) = $centroids
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45 #else
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46 msidata <- readImzML('infile', attach.only=TRUE)
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47 centroided(msidata) = $centroids
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48 #end if
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49 #elif $infile.ext == 'analyze75'
1
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50 msidata = readAnalyze('infile', attach.only=TRUE)
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51 centroided(msidata) = $centroids
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52 #else
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53 msidata = loadRData('infile.RData')
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54 #end if
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55
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56 ]]></token>
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57
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58 <token name="@DATA_PROPERTIES@"><![CDATA[
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59 ## Number of features (mz)
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60 maxfeatures = length(features(msidata))
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61 ## Range mz
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62 minmz = round(min(mz(msidata)), digits=2)
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63 maxmz = round(max(mz(msidata)), digits=2)
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64 ## Number of spectra (pixels)
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65 pixelcount = length(pixels(msidata))
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66 ## Range x coordinates
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67 minimumx = min(coord(msidata)[,1])
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68 maximumx = max(coord(msidata)[,1])
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69 ## Range y coordinates
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70 minimumy = min(coord(msidata)[,2])
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71 maximumy = max(coord(msidata)[,2])
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72
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73
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74 properties = c("Number of m/z features",
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75 "Range of m/z values",
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76 "Number of pixels",
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77 "Range of x coordinates",
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78 "Range of y coordinates")
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79
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80 values = c(paste0(maxfeatures),
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81 paste0(minmz, " - ", maxmz),
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82 paste0(pixelcount),
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83 paste0(minimumx, " - ", maximumx),
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84 paste0(minimumy, " - ", maximumy))
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85
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86 property_df = data.frame(properties, values)
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87 ]]></token>
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88
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89 <token name="@READING_MSIDATA_INRAM@"><![CDATA[
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90 ## importing MSI data files
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91
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92 ## function to read RData files independent of filename
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93 loadRData <- function(fileName){
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94 load(fileName)
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95 get(ls()[ls() != "fileName"])
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96 }
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97
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98 #if $infile.ext == 'imzml'
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99 #if str($processed_cond.processed_file) == "processed":
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100 msidata <- readImzML('infile', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units")
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101 centroided(msidata) = $centroids
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102 #else
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103 msidata <- readImzML('infile')
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104 centroided(msidata) = $centroids
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105 #end if
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106 #elif $infile.ext == 'analyze75'
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107 msidata = readAnalyze('infile')
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108 centroided(msidata) = $centroids
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109 #else
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110 msidata = loadRData('infile.RData')
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111 #end if
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112
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113 ]]></token>
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114
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115 <token name="@DATA_PROPERTIES_INRAM@"><![CDATA[
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116 ########################### QC numbers ########################
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117 ## including intensity calculations which need data in RAM
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118 ## Number of features (mz)
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119 maxfeatures = length(features(msidata))
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120 ## Range mz
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121 minmz = round(min(mz(msidata)), digits=2)
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122 maxmz = round(max(mz(msidata)), digits=2)
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123 ## Number of spectra (pixels)
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124 pixelcount = length(pixels(msidata))
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125 ## Range x coordinates
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126 minimumx = min(coord(msidata)[,1])
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127 maximumx = max(coord(msidata)[,1])
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128 ## Range y coordinates
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129 minimumy = min(coord(msidata)[,2])
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130 maximumy = max(coord(msidata)[,2])
0
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131 ## Range of intensities
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132 minint = round(min(spectra(msidata)[], na.rm=TRUE), digits=2)
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133 maxint = round(max(spectra(msidata)[], na.rm=TRUE), digits=2)
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134 ## Number of intensities > 0, for if conditions
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135 npeaks= sum(spectra(msidata)[]>0, na.rm=TRUE)
2
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136 ## Number of NA in spectra matrix
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137 NAcount = sum(is.na(spectra(msidata)[]))
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138 ## Number of NA in spectra matrix
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139 infcount = sum(is.infinite(spectra(msidata)[]))
0
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140
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141 properties = c("Number of m/z features",
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142 "Range of m/z values",
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143 "Number of pixels",
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144 "Range of x coordinates",
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145 "Range of y coordinates",
2
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146 "Range of intensities",
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147 "Number of NA intensities",
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148 "Number of Inf intensities")
0
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149
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150 values = c(paste0(maxfeatures),
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151 paste0(minmz, " - ", maxmz),
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152 paste0(pixelcount),
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153 paste0(minimumx, " - ", maximumx),
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154 paste0(minimumy, " - ", maximumy),
2
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155 paste0(minint, " - ", maxint),
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156 paste0(NAcount),
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157 paste0(infcount))
0
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158
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159 property_df = data.frame(properties, values)
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160 ]]></token>
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161
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162 <token name="@CARDINAL_DESCRIPTION@"><![CDATA[
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163 Cardinal is an R package that implements statistical & computational tools for analyzing mass spectrometry imaging datasets.
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164 `More information on Cardinal <http://cardinalmsi.org/>`_
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165 ]]></token>
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166 <token name="@MSIDATA_INPUT_DESCRIPTION@"><![CDATA[
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167 **Input data**
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168
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169 - MSI data: 3 types of input data can be used:
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170
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171 - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/wp/imzml/>`_
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172 - Analyze7.5 (upload hdr, img and t2m file via the "composite" function)
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173 - Cardinal "MSImageSet" data saved as .RData
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174 ]]></token>
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175 <token name="@MZ_TABULAR_INPUT_DESCRIPTION@"><![CDATA[
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176 - Optional tabular file with m/z values:
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177
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178 - One column with numeric m/z values (without empty fields or letters)
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179 - The file is allowed to have any column names as header (in this case set "Tabular file contains a header line" to yes)
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180 - m/z features outside the m/z range of the input file are ignored
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181
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182
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183 ::
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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184
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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185 m/z
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186 100.0
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187 100.01
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188 100.02
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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189 ...
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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190 ...
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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191
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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192 ]]></token>
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193 <token name="@MZ_2COLS_TABULAR_INPUT_DESCRIPTION@"><![CDATA[
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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194 - Tabular file with m/z values:
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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195
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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196 - One column with numeric m/z values (without empty fields or letters), another column with names for the m/z (m/z column can also be used as name)
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197 - The file is allowed to have any column names as header (in this case set "Tabular file contains a header line" to yes)
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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198 - m/z features outside the m/z range of the input file are ignored
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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199
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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200
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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201 ::
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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202
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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203 m/z name
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204 100.0 analyte1
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205 100.01 analyte2
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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206 100.02 analyte3
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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207 ...
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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208 ...
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209
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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210 ]]></token>
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211 <token name="@SPECTRA_TABULAR_INPUT_DESCRIPTION@"><![CDATA[
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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212 - Optional file with pixel coordinates and annotation:
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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213
2
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galaxyp
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214 - Tabular file: One column with x values, one column with y values and one column with annotations
0
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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215 - The file is allowed to have any column names as header (in this case set "Tabular file contains a header line" to yes)
2
034885df9b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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216 - Pixel with coordinates outside the coordinates of the input file are ignored
0
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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217
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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218 ::
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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219
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220 x_coord y_coord annotation
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221 1 1 healthy
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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222 2 1 healthy
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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223 3 1 disease
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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224 ...
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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225 ...
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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226
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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227 ]]></token>
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228
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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229 <xml name="reading_msidata">
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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230 <param name="infile" type="data" format="imzml,rdata,analyze75"
2
034885df9b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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231 label="MSI data"
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232 help="Input file as imzML (composite upload), or Cardinal MSImageSet saved as RData (regular upload)"/>
034885df9b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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233 <param name="centroids" type="boolean" label="Centroided input" help="Choose Yes if peak detection has already been done." truevalue="TRUE" falsevalue="FALSE"/>
0
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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234 <conditional name="processed_cond">
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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235 <param name="processed_file" type="select" label="Processed imzML file" help="Choose no if your input is an Analyze7.5 or continuous imzML file">
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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236 <option value="no_processed" selected="True">no</option>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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237 <option value="processed">yes</option>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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238 </param>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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239 <when value="no_processed"/>
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240 <when value="processed">
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241 <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"/>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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242 <param name="units" display="radio" type="select" label="Unit of the mass accuracy" help="either m/z or ppm">
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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243 <option value="mz" >mz</option>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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244 <option value="ppm" selected="True" >ppm</option>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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245 </param>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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246 </when>
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247 </conditional>
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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248 </xml>
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249
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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250 <xml name="pdf_filename">
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251 <param name="filename" type="text" value="" label="Title" help="Will appear in the pdf output, if nothing given it will take the dataset name">
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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252 <sanitizer invalid_char="">
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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253 <valid initial="string.ascii_letters,string.digits">
1
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diff changeset
254 <add value="_"/>
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255 <add value=" "/>
0
e56a955cd1c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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256 </valid>
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257 </sanitizer>
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258 </param>
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259 </xml>
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260
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261 <xml name="sanitizer_multiple_digits">
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262 <sanitizer invalid_char="">
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263 <valid initial="string.digits">
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264 <add value=":" />
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265 <add value="," />
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266 </valid>
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267 </sanitizer>
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268 </xml>
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269
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270 <xml name="reading_1_column_mz_tabular" token_label="Tabular file with m/z features">
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271 <param name="mz_tabular" type="data" format="tabular" label="@LABEL@" help="Only numeric m/z values are allowed"/>
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272 <param name="feature_column" data_ref="mz_tabular" label="Column with features" type="data_column"/>
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273 <param name="feature_header" type="boolean" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/>
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274 </xml>
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275
1
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276 <xml name="reading_2_column_mz_tabular" token_optional="false">
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277 <param name="calibrant_file" type="data" optional="@OPTIONAL@" format="tabular"
0
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278 label="m/z of interest (e.g. internal Calibrants)" help="one column with m/z values, optional second column with names (m/z values can also be selected as name)"/>
1
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279 <param name="mz_column" data_ref="calibrant_file" optional="@OPTIONAL@" label="Column with m/z values" type="data_column"/>
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280 <param name="name_column" data_ref="calibrant_file" optional="@OPTIONAL@" label="Column with name of m/z values" type="data_column"/>
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281 <param name="calibrant_header" type="boolean" optional="@OPTIONAL@" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/>
0
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282 </xml>
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283
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284 <xml name="reading_pixel_annotations">
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285 <param name="annotation_file" type="data" format="tabular" label="Tabular file with pixel coordinates and annotation"
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286 help="Tabular file with three columns: x values, y values and pixel annotations"/>
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287 <param name="column_x" data_ref="annotation_file" label="Column with x values" type="data_column"/>
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288 <param name="column_y" data_ref="annotation_file" label="Column with y values" type="data_column"/>
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289 <param name="column_names" data_ref="annotation_file" label="Column with pixel annotations" type="data_column"/>
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290 <param name="tabular_header" type="boolean" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/>
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291 </xml>
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292
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293 <xml name="citations">
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294 <citations>
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295 <citation type="doi">10.1093/bioinformatics/btv146</citation>
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296 </citations>
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297 </xml>
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298 <xml name="infile_analyze75">
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299 <param name="infile" value="" ftype="analyze75">
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300 <composite_data value="Analyze75.hdr"/>
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301 <composite_data value="Analyze75.img"/>
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302 <composite_data value="Analyze75.t2m"/>
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303 </param>
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304 </xml>
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305 <xml name="infile_imzml">
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306 <param name="infile" value="" ftype="imzml">
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307 <composite_data value="Example_Continuous.imzML"/>
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308 <composite_data value="Example_Continuous.ibd"/>
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309 </param>
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310 </xml>
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311 </macros>