Mercurial > repos > iuc > dimet_pca_plot

annotate dimet_pca_plot.xml @ 1:78fd9274a21b draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 6da96d865a3a557cfa3ad09e1cfa830519e73748
author iuc
date Tue, 06 Aug 2024 17:31:47 +0000
parents 58498838f0e0
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58498838f0e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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1 <tool id="dimet_@EXECUTABLE@" name="dimet @TOOL_LABEL@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
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2 <description>
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3 Figures of Principal Component Analysis for tracer metabolomics (by DIMet)
58498838f0e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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4 </description>
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5 <macros>
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6 <token name="@TOOL_LABEL@">pca plot</token>
58498838f0e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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7 <token name="@EXECUTABLE@">pca_plot</token>
58498838f0e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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8 <import>macros.xml</import>
58498838f0e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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9 </macros>
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10 <expand macro="requirements"/>
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11 <command detect_errors="exit_code"><![CDATA[
58498838f0e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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12 @INIT_CONFIG@
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13 @INIT_PCA@
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14 @INIT_IMPUTE_VALUES@
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15 @INIT_CONDITIONS@
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16 HYDRA_FULL_ERROR=1 python -m dimet
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17 '++hydra.run.dir=.'
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18 '++figure_path=figures'
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19 '++table_path=tables'
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20 '++analysis={
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21 dataset:{
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22 _target_:dimet.data.DatasetConfig,
58498838f0e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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23 name: "Galaxy DIMet run"
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24 },
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25 method:{
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26 _target_: dimet.method.PcaPlotConfig,
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27 label: pca-plot,
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28 name: "Generate Principal Component Analysis plots",
58498838f0e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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29 pca_split_further:['timepoint'],
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30 draw_ellipses: null,
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31 run_iris_demo: false,
58498838f0e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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32 color: condition,
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33 style: timepoint,
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34 figure_format:${output_options.figure_format},
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35 impute_values:${impute_values}
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36 },
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37 label: pca-plot
58498838f0e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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38 }'
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39 '++analysis.dataset.subfolder='
58498838f0e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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40 '++analysis.dataset.label='
58498838f0e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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41 '++analysis.dataset.conditions=${conds}'
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42 #if $metadata_path:
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43 '++analysis.dataset.metadata=metadata'
58498838f0e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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44 #end if
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45 #if $abundance_file:
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46 '++analysis.dataset.abundances=abundance'
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47 #end if
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48 #if $me_or_frac_contrib_file:
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49 '++analysis.dataset.mean_enrichment=me_or_frac_contrib'
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50 #end if
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51 @REMOVE_CONFIG@
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52 ]]></command>
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53 <inputs>
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54 <expand macro="input_parameters_pca"/>
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55 <expand macro="conditions"/>
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56 <section name="output_options" title="Output options">
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57 <param name="figure_format" type="select" value="pdf" display="radio" label="Select output figure format" help="Please enter at max 1 format">
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58 <option value="pdf">Pdf</option>
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59 <option value="svg">Svg</option>
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60 </param>
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61 </section>
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62 </inputs>
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63
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64 <outputs>
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65 <collection name="report" type="list">
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66 <discover_datasets pattern="__designation_and_ext__" directory="figures"/>
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67 </collection>
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68 </outputs>
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69 <tests>
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70 <test>
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71 <param name="abundance_file" ftype="tabular" value="rawAbundances.csv" />
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72 <param name="metadata_path" ftype="tabular" value="example2_metadata.csv"/>
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73 <param name="conditions" value='Control,L-Cycloserine'/>
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74 <section name="output_options">
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75 <param name="figure_format" value="svg"/>
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76 </section>
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77 <output_collection name="report" type="list" count="18">
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78 <element file="abundances--T0--cell_var.svg" name="abundances--T0--cell_var" ftype="svg" compare="sim_size" delta="100"/>
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79 <element file="abundances--T0--cell--label-n_pc.svg" name="abundances--T0--cell--label-n_pc" ftype="svg" compare="sim_size" delta="100"/>
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80 <element file="abundances--T0--cell--label-y_pc.svg" name="abundances--T0--cell--label-y_pc" ftype="svg" compare="sim_size" delta="100"/>
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81 <element file="abundances--T0--med_var.svg" name="abundances--T0--med_var" ftype="svg" compare="sim_size" delta="100"/>
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82 <element file="abundances--T0--med--label-n_pc.svg" name="abundances--T0--med--label-n_pc" ftype="svg" compare="sim_size" delta="100"/>
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83 <element file="abundances--T0--med--label-y_pc.svg" name="abundances--T0--med--label-y_pc" ftype="svg" compare="sim_size" delta="100"/>
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84 <element file="abundances--T2h--cell--label-n_pc.svg" name="abundances--T2h--cell--label-n_pc" ftype="svg" compare="sim_size" delta="100"/>
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85 <element file="abundances--T2h--cell--label-y_pc.svg" name="abundances--T2h--cell--label-y_pc" ftype="svg" compare="sim_size" delta="100"/>
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86 <element file="abundances--T2h--cell_var.svg" name="abundances--T2h--cell_var" ftype="svg" compare="sim_size" delta="100"/>
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87 <element file="abundances--T2h--med--label-n_pc.svg" name="abundances--T2h--med--label-n_pc" ftype="svg" compare="sim_size" delta="100"/>
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88 <element file="abundances--T2h--med--label-y_pc.svg" name="abundances--T2h--med--label-y_pc" ftype="svg" compare="sim_size" delta="100"/>
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89 <element file="abundances--T2h--med_var.svg" name="abundances--T2h--med_var" ftype="svg" compare="sim_size" delta="100"/>
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90 <element file="abundances--cell--label-n_pc.svg" name="abundances--cell--label-n_pc" ftype="svg" compare="sim_size" delta="100"/>
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91 <element file="abundances--cell--label-y_pc.svg" name="abundances--cell--label-y_pc" ftype="svg" compare="sim_size" delta="100"/>
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92 <element file="abundances--cell_var.svg" name="abundances--cell_var" ftype="svg" compare="sim_size" delta="100"/>
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93 <element file="abundances--med--label-n_pc.svg" name="abundances--med--label-n_pc" ftype="svg" compare="sim_size" delta="100"/>
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94 <element file="abundances--med--label-y_pc.svg" name="abundances--med--label-y_pc" ftype="svg" compare="sim_size" delta="100"/>
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95 <element file="abundances--med_var.svg" name="abundances--med_var" ftype="svg" compare="sim_size" delta="100"/>
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96 </output_collection>
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97 </test>
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98 </tests>
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99 <help><![CDATA[
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100 This module is part of DIMet: Differential analysis of Isotope-labeled targeted Metabolomics data (https://pypi.org/project/DIMet/).
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101
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102 This tool performs the Principal Components Analysis (PCA) on your data,
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103 generating the figures with the results of the PCA, it is, the scatter-plot of the two first principal components or dimensions (eigenvalues), and the barplot of the percentage of explained variances across all the principal components detected in your data.
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104
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105 The figures in .pdf format are of publication quality, and as they are vectorial images you can open them and customize aesthetics with a professional image software such as Inkscape, Adobe Illustrator, Sketch, CorelDRAW, etc.
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106
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107
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108 **Input data files**
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109
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110 This tool requires (at max.) 3 tab-delimited .csv files as inputs. There are two types of files:
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111
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112 - The measures' (or quantifications') files, that can be of 4 types.
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113
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114 - The metadata, a unique file with the description of the samples in your measures' files. This is compulsory.
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115
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116 For running DIMet @EXECUTABLE@ you need **at least one file** of measures:
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117
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118 - The total **abundances** (of the metabolites) file
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119
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120 - The mean **enrichment** or labelled fractional contributions
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121
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122
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123 and one metadata file, WHICH IS COMPULSORY, see section **Metadata File Information**.
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124
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125
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126 **Measures' files**
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127
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128 The measure's files must be organized as matrices:
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129
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130 - The first column must contain Metabolite IDs that are unique (not repeated) within the file.
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131
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132 - The rest of the columns correspond to the samples
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133
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134 - The rows correspond to the metabolites
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135
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136 - The values must be tab separated, with the first row containing the sample/column labels.
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137
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138 See the following examples of measures files:
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139
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140
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141 Example - Metabolites **abundances**:
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142
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143 =============== ================== ================== ================== ================== ================== ==================
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144 ID **MCF001089_TD01** **MCF001089_TD02** **MCF001089_TD03** **MCF001089_TD04** **MCF001089_TD05** **MCF001089_TD06**
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145 =============== ================== ================== ================== ================== ================== ==================
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146 2_3-PG 8698823.9926 10718737.7217 10724373.9 8536484.5 22060650 28898956
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147 2-OHGLu 36924336 424336 92060650 45165 84951950 965165051
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148 Glc6P 2310 2142 2683 1683 012532068 1252172
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149 Gly3P 399298 991656565 525195 6365231 89451625 4952651963
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150 IsoCit 0 0 0 84915613 856236 954651610
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151 =============== ================== ================== ================== ================== ================== ==================
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152
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153 Example - mean **enrichment** or labeled fractional contributions:
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154
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155 =============== ================== ================== ================== ================== ================== ==================
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156 ID **MCF001089_TD01** **MCF001089_TD02** **MCF001089_TD03** **MCF001089_TD04** **MCF001089_TD05** **MCF001089_TD06**
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157 =============== ================== ================== ================== ================== ================== ==================
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158 2_3-PG 0.9711 0.968 0.9909 0.991 0.40 0.9
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159 2-OHGLu 0.01719 0.0246 0.554 0.555 0.73 0.68
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160 Glc6P 0.06 0.66 2683 0.06 2068 2172
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161 Gly3P 0.06 0.06 0.06 1 5 3
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162 IsoCit 0.06 1 0.49 0.36 6 10
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163 =============== ================== ================== ================== ================== ================== ==================
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164
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165
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166 **Metadata File Information**
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167
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168 Provide a tab-separated file that has the names of the samples in the first column and one header row.
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169 Column names must be exactly in this order:
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170
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171 name_to_plot
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172 condition
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173 timepoint
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174 timenum
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175 compartment
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176 original_name
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177
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178
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179 Example **Metadata File**:
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180
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181
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182 ==================== =============== ============= ============ ================ =================
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183 **name_to_plot** **condition** **timepoint** **timenum** **compartment** **original_name**
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184 -------------------- --------------- ------------- ------------ ---------------- -----------------
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185 Control_cell_T0-1 Control T0 0 cell MCF001089_TD01
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186 Control_cell_T0-2 Control T0 0 cell MCF001089_TD02
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187 Control_cell_T0-3 Control T0 0 cell MCF001089_TD03
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188 Tumoral_cell_T0-1 Tumoral T0 0 cell MCF001089_TD04
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189 Tumoral_cell_T0-2 Tumoral T0 0 cell MCF001089_TD05
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190 Tumoral_cell_T0-3 Tumoral T0 0 cell MCF001089_TD06
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191 Tumoral_cell_T24-1 Tumoral T24 24 cell MCF001089_TD07
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192 Tumoral_cell_T24-2 Tumoral T24 24 cell MCF001089_TD08
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193 Tumoral_cell_T24-3 Tumoral T24 24 cell MCF001090_TD01
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194 Control_med_T24-1 Control T24 24 med MCF001090_TD02
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195 Control_med_T24-2 Control T24 24 med MCF001090_TD03
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196 Tumoral_med_T24-1 Tumoral T24 24 med MCF001090_TD04
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197 Tumoral_med_T24-2 Tumoral T24 24 med MCF001090_TD05
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198 Control_med_T0-1 Control T0 0 med MCF001090_TD06
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199 Tumoral_med_T0-1 Tumoral T0 0 med MCF001090_TD07
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200 Tumoral_med_T0-2 Tumoral T0 0 med MCF001090_TD08
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201 ==================== =============== ============= ============ ================ =================
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202
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203
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204 The column **original_name** must have the names of the samples as given in your data.
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205
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206 The column **name_to_plot** must have the names as you want them to be (or set identical to original_name if you prefer). To set names that
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207 are meaningful is a better choice, as we will take them to display the results.
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208
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209 The column **timenum** must contain only the numeric part of the timepoint, for example 2,0, 10, 100 (this means, without letters ("T", "t", "s", "h" etc)
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210 nor any other symbol). Make sure these time numbers are in the same units (but do not write the units here!).
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211
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212 The column **compartment** is an abbreviation, coined by you, for the compartments. This will be used for the results' files names: the longer the
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213 compartments names are, the longer the output files' names! Please pick short and clear abbreviations to fill this column.
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214
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215
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216 **Running the analysis**
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217
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218 You can precise how you want your analysis to be executed, there exist hints on use that will guide you, next to the parameters.
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219
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220 Our tool automatically processes the integrality of your data (global PCA plots), and also splits your data by timepoint to generate PCA plots by timepoint (which is convenient to explore the "grouping" of conditions), but if you only have one condition you can discard them.
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221
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222 The output, for the global PCA, and for each timepoint PCA, consists of :
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223
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224 - a scatter-plot of the first two Principal Components (PC), with labels corresponding to 'name_to_plot'.
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225
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226 - the same scatter-plot as above but without labels.
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227
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228 - a bar-plot of the percentage of explained variances.
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229
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230
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231
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232 **Available data for testing**
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233
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234 You can test our tool with the data from our manuscript https://zenodo.org/record/10579862 (the pertinent
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235 files for you are located in the subfolders inside the data folder).
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236 You can also use the minimal data examples from https://zenodo.org/record/10579891
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237
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238 ]]>
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239 </help>
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240 <expand macro="citations" />
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241 </tool>