Mercurial > repos > galaxyp > cardinal_spectra_plots

annotate macros.xml @ 0:de334e98f1c1 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
author galaxyp
date Mon, 01 Oct 2018 01:01:41 -0400
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children 45fb4dd8400b
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de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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1 <macros>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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2 <token name="@VERSION@">1.12.1</token>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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3
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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4 <xml name="requirements">
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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5 <requirements>
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6 <requirement type="package" version="@VERSION@">bioconductor-cardinal</requirement>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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7 <yield/>
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8 </requirements>
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9 </xml>
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10
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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11 <token name="@INPUT_LINKING@"><![CDATA[
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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12 #if $infile.ext == 'imzml'
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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13 ln -s '${infile.extra_files_path}/imzml' infile.imzML &&
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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14 ln -s '${infile.extra_files_path}/ibd' infile.ibd &&
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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15 #elif $infile.ext == 'analyze75'
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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16 ln -s '${infile.extra_files_path}/hdr' infile.hdr &&
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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17 ln -s '${infile.extra_files_path}/img' infile.img &&
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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18 ln -s '${infile.extra_files_path}/t2m' infile.t2m &&
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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19 #else
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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20 ln -s $infile infile.RData &&
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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21 #end if
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22 ]]></token>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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23
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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24
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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25 <token name="@READING_MSIDATA@"><![CDATA[
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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26 ## importing MSI data files
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27
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28 ## function to read RData files independent of filename
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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29 loadRData <- function(fileName){
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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30 load(fileName)
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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31 get(ls()[ls() != "fileName"])
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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32 }
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33
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34 #if $infile.ext == 'imzml'
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35 #if str($processed_cond.processed_file) == "processed":
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36 msidata <- readImzML('infile', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units")
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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37 centroided(msidata) = $centroids
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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38 #else
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39 msidata <- readImzML('infile')
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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40 centroided(msidata) = $centroids
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41 #end if
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42 #elif $infile.ext == 'analyze75'
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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43 msidata = readAnalyze('infile')
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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44 centroided(msidata) = $centroids
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45 #else
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46 msidata = loadRData('infile.RData')
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47 #end if
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48
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49 ]]></token>
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50
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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51 <token name="@DATA_PROPERTIES@"><![CDATA[
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52 ## Number of features (mz)
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53 maxfeatures = length(features(msidata))
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54 ## Range mz
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55 minmz = round(min(mz(msidata)), digits=2)
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56 maxmz = round(max(mz(msidata)), digits=2)
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57 ## Number of spectra (pixels)
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58 pixelcount = length(pixels(msidata))
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59 ## Range x coordinates
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60 minimumx = min(coord(msidata)[,1])
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61 maximumx = max(coord(msidata)[,1])
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62 ## Range y coordinates
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63 minimumy = min(coord(msidata)[,2])
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64 maximumy = max(coord(msidata)[,2])
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65 ## Range of intensities
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66 minint = round(min(spectra(msidata)[], na.rm=TRUE), digits=2)
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67 maxint = round(max(spectra(msidata)[], na.rm=TRUE), digits=2)
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68 ## Number of intensities > 0, for if conditions
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69 npeaks= sum(spectra(msidata)[]>0, na.rm=TRUE)
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70
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71 properties = c("Number of m/z features",
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72 "Range of m/z values",
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73 "Number of pixels",
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74 "Range of x coordinates",
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75 "Range of y coordinates",
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76 "Range of intensities")
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77
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78 values = c(paste0(maxfeatures),
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79 paste0(minmz, " - ", maxmz),
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80 paste0(pixelcount),
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81 paste0(minimumx, " - ", maximumx),
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82 paste0(minimumy, " - ", maximumy),
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83 paste0(minint, " - ", maxint))
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84
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85 property_df = data.frame(properties, values)
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86 ]]></token>
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87
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88 <token name="@CARDINAL_DESCRIPTION@"><![CDATA[
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89 Cardinal is an R package that implements statistical & computational tools for analyzing mass spectrometry imaging datasets.
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90 `More information on Cardinal <http://cardinalmsi.org/>`_
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91 ]]></token>
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92 <token name="@MSIDATA_INPUT_DESCRIPTION@"><![CDATA[
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93 **Input data**
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94
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95 - MSI data: 3 types of input data can be used:
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96
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97 - 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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98 - Analyze7.5 (upload hdr, img and t2m file via the "composite" function)
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99 - Cardinal "MSImageSet" data saved as .RData
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100 ]]></token>
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101 <token name="@MZ_TABULAR_INPUT_DESCRIPTION@"><![CDATA[
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102 - Optional tabular file with m/z values:
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103
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104 - One column with numeric m/z values (without empty fields or letters)
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105 - 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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106 - m/z features outside the m/z range of the input file are ignored
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107
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108
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109 ::
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110
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111 m/z
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112 100.0
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113 100.01
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114 100.02
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115 ...
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116 ...
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117
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118 ]]></token>
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119 <token name="@MZ_2COLS_TABULAR_INPUT_DESCRIPTION@"><![CDATA[
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120 - Tabular file with m/z values:
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121
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122 - 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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123 - 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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124 - m/z features outside the m/z range of the input file are ignored
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125
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126
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127 ::
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128
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129 m/z name
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130 100.0 analyte1
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131 100.01 analyte2
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132 100.02 analyte3
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133 ...
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134 ...
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135
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136 ]]></token>
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137 <token name="@SPECTRA_TABULAR_INPUT_DESCRIPTION@"><![CDATA[
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138 - Optional file with pixel coordinates and annotation:
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139
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140 - Tabular file: One column with x values, one column wiht y values and one column with annotations
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141 - 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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142 - Pixel with coordinates outside the coordinates of the input file are ignored
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143
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144 ::
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145
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146 x_coord y_coord annotation
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147 1 1 healthy
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148 2 1 healthy
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149 3 1 disease
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150 ...
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151 ...
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152
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153 ]]></token>
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154
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155 <xml name="reading_msidata">
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156 <param name="infile" type="data" format="imzml,rdata,analyze75"
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157 label="Input file as imzML, Analyze7.5 or Cardinal MSImageSet saved as RData"
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158 help="Upload composite datatype imzML (ibd+imzML) or analyze75 (hdr+img+t2m) or regular upload .RData (Cardinal MSImageSet)"/>
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159 <param name="centroids" type="boolean" label="Is the input data centroided (picked)" help="Choose Yes if peak detection has already been done." truevalue="TRUE" falsevalue="FALSE"/>
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160 <conditional name="processed_cond">
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161 <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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162 <option value="no_processed" selected="True">no</option>
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163 <option value="processed">yes</option>
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164 </param>
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165 <when value="no_processed"/>
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166 <when value="processed">
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167 <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"/>
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168 <param name="units" display="radio" type="select" label="Unit of the mass accuracy" help="either m/z or ppm">
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169 <option value="mz" >mz</option>
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170 <option value="ppm" selected="True" >ppm</option>
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171 </param>
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172 </when>
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173 </conditional>
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174 </xml>
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175
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176 <xml name="pdf_filename">
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177 <param name="filename" type="text" value="" label="Title" help="Will appear in the pdf output, if nothing given it will take the dataset name">
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178 <sanitizer invalid_char="">
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179 <valid initial="string.ascii_letters,string.digits">
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180 <add value="_" />
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181 </valid>
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182 </sanitizer>
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183 </param>
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184 </xml>
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185
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186 <xml name="sanitizer_multiple_digits">
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187 <sanitizer invalid_char="">
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188 <valid initial="string.digits">
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189 <add value=":" />
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190 <add value="," />
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191 </valid>
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192 </sanitizer>
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193 </xml>
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194
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195 <xml name="reading_1_column_mz_tabular" token_label="Tabular file with m/z features">
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196 <param name="mz_tabular" type="data" format="tabular" label="@LABEL@" help="Only numeric m/z values are allowed"/>
de334e98f1c1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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197 <param name="feature_column" data_ref="mz_tabular" label="Column with features" type="data_column"/>
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198 <param name="feature_header" type="boolean" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/>
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199 </xml>
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200
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201 <xml name="reading_2_column_mz_tabular">
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202 <param name="calibrant_file" type="data" optional="true" format="tabular"
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203 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)"/>
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204 <param name="mz_column" data_ref="calibrant_file" label="Column with m/z values" type="data_column"/>
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205 <param name="name_column" data_ref="calibrant_file" label="Column with name of m/z values" type="data_column"/>
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206 <param name="calibrant_header" type="boolean" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/>
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207 </xml>
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208
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209 <xml name="reading_pixel_annotations">
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210 <param name="annotation_file" type="data" format="tabular" label="Tabular file with pixel coordinates and annotation"
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211 help="Tabular file with three columns: x values, y values and pixel annotations"/>
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212 <param name="column_x" data_ref="annotation_file" label="Column with x values" type="data_column"/>
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213 <param name="column_y" data_ref="annotation_file" label="Column with y values" type="data_column"/>
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214 <param name="column_names" data_ref="annotation_file" label="Column with pixel annotations" type="data_column"/>
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215 <param name="tabular_header" type="boolean" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/>
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216 </xml>
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217
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218 <xml name="citations">
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219 <citations>
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220 <citation type="doi">10.1093/bioinformatics/btv146</citation>
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221 </citations>
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222 </xml>
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223 <xml name="infile_analyze75">
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224 <param name="infile" value="" ftype="analyze75">
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225 <composite_data value="Analyze75.hdr"/>
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226 <composite_data value="Analyze75.img"/>
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227 <composite_data value="Analyze75.t2m"/>
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228 </param>
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229 </xml>
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230 <xml name="infile_imzml">
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231 <param name="infile" value="" ftype="imzml">
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232 <composite_data value="Example_Continuous.imzML"/>
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233 <composite_data value="Example_Continuous.ibd"/>
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234 </param>
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235 </xml>
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236 </macros>