annotate dimet_differential_analysis.xml @ 0:c46d33411495 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
author iuc
date Tue, 10 Oct 2023 11:52:44 +0000
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c46d33411495 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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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 Differential analysis of tracer metabolomics data comparing two groups (by DIMet)
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4 </description>
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5 <macros>
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6 <token name="@TOOL_LABEL@">differential analysis</token>
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7 <token name="@EXECUTABLE@">differential_analysis</token>
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8 <import>macros.xml</import>
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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[
c46d33411495 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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12 @INIT_CONFIG@
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13 @INIT_DIFF_ANALYSIS@
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14 @INIT_STAT_TEST@
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15 @INIT_GROUPS@
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16 @INIT_COMPARISONS@
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17 HYDRA_FULL_ERROR=1 python -m dimet
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18 -cp '$__new_file_path__/config'
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19 '++hydra.run.dir=differential_analysis'
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20 '++figure_path=figures'
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21 '++table_path=tables'
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22 '++analysis={
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23 dataset:{
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24 _target_: dimet.data.DatasetConfig,
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25 name: "I am a synthetic data example"
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26 },
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27 method:{
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28 _target_: dimet.method.DifferentialAnalysisConfig,
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29 label: "differential_analysis",
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30 name: "Pairwise computation of statistical differences",
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31 draw_ellipses: null,
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32 run_iris_demo: false
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33 },
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34 label: differential-analysis-example2
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35 }'
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36 '++analysis.method.qualityDistanceOverSpan='${qualityDistanceOverSpan}''
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37 '++analysis.dataset.label='
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38 '++analysis.timepoints=${timepoints}'
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39 '++analysis.comparisons=${comparisons}'
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40 '++analysis.method.statistical_test=${statistical_test}'
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41 '++analysis.method.grouping=${groups}'
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42 '++analysis.method.correction_method=${correction_method}'
c46d33411495 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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43 '++analysis.method.impute_values=${impute_values}'
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44 '++analysis.statistical_test=${statistical_test}'
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45 '++analysis.dataset.subfolder='
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46 '++analysis.dataset.conditions=${conds}'
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47 #if $metadata_path:
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48 '++analysis.dataset.metadata=metadata'
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49 #end if
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50 #if str( $data_input.data_input_selector ) == "abundance":
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51 #if $data_input.abundance_file:
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52 '++analysis.dataset.abundances=abundance'
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53 #end if
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54 #elif str( $data_input.data_input_selector ) == "mean_enrichment":
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55 #if $data_input.me_or_frac_contrib_file:
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56 '++analysis.dataset.mean_enrichment=me_or_frac_contrib'
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57 #end if
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58 #elif str( $data_input.data_input_selector ) == "isotop_prop":
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59 #if $data_input.isotop_prop_file:
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60 '++analysis.dataset.isotopologue_proportions=isotop_prop'
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61 #end if
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62 #else
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63 #if $data_input.isotop_abs_file:
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64 '++analysis.dataset.isotopologues=isotop_abs'
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65 #end if
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66 #end if
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67 @REMOVE_CONFIG@
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68 ]]></command>
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69 <inputs>
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70 <expand macro="input_parameters_diff_analysis"/>
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71 <expand macro="conditions"/>
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72 <expand macro="timepoint"/>
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73 <expand macro="correction_method"/>
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74 <param name="qualityDistanceOverSpan" type="float" min="-1.0" max="-0.1" value="-0.3" label="quality Distance Over Span" help="Default value is -0.3."/>
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75 </inputs>
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76
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77 <outputs>
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78 <collection name="report" type="list">
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79 <discover_datasets pattern="__designation__" directory="tables" format="tabular"/>
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80 </collection>
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81 </outputs>
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82 <tests>
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83 <test>
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84 <param name="data_input_selector" value="abundance" />
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85 <param name="abundance_file" ftype="tabular" value="rawAbundances.csv"/>
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86 <param name="metadata_path" ftype="tabular" value="example2_metadata.csv"/>
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87 <param name="correction_method" value="bonferroni"/>
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88 <param name="stat_test" value="Tt"/>
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89 <param name="qualityDistanceOverSpan" value="-0.3"/>
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90 <param name="conditions" value='Control,L-Cycloserine'/>
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91 <param name="timepoint" value='T0,T2h'/>
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92 <output_collection name="report" type="list" count="4">
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93 <element file="abundance--cell-Control-T0-L-Cycloserine-T0-Tt.tsv" name="abundance--cell-Control-T0-L-Cycloserine-T0-Tt.tsv" ftype="tabular"/>
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94 <element file="abundance--cell-Control-T2h-L-Cycloserine-T2h-Tt.tsv" name="abundance--cell-Control-T2h-L-Cycloserine-T2h-Tt.tsv" ftype="tabular"/>
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95 <element file="abundance--med-Control-T0-L-Cycloserine-T0-Tt.tsv" name="abundance--med-Control-T0-L-Cycloserine-T0-Tt.tsv" ftype="tabular"/>
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96 <element file="abundance--med-Control-T2h-L-Cycloserine-T2h-Tt.tsv" name="abundance--med-Control-T2h-L-Cycloserine-T2h-Tt.tsv" ftype="tabular"/>
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97 </output_collection>
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98 </test>
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99 </tests>
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100 <help><![CDATA[
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101
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102 This module is part of DIMet: Differential analysis of Isotope-labeled targeted Metabolomics data (https://pypi.org/project/DIMet/).
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103
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104 DIMet differential analysis compares groups to evaluate for statistical differences, in a **pairwise** mode.
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105 This pairwise mode accepts one or several defined comparison(s), that will run in a single execution.
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106 In this way, you do not need to re-upload your data several times,
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107 instead, you upload once your data and you compose a list of comparisons:
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108
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109 - Tumoral,T0 vs Control,T0
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110
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111 - Tumoral,T2 vs Control,T2
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112
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113 - Tumoral,T24 vs Control,T24
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114
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115 - ...
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116
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117 then DIMet differential analysis will execute them -one by one- automatically.
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118
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119
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120 **Input data files**
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121
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122 This tool requires (at max.) 5 tab-delimited .csv files as inputs. There are two types of files:
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123
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124 - The measures' (or quantifications') files, that can be of 4 types.
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125
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126 - The metadata, a unique file with the description of the samples in your measures' files. This is compulsory.
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127
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128 For running DIMet @EXECUTABLE@ you need **at least one file** of measures:
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129
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130 - The total **abundances** (of the metabolites) file
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131
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132 - The mean **enrichment** or labelled fractional contributions
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133
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134 - The **isotopologues** absolute values files (optional)
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135
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136 - The **isotopologue proportions** file (optional)
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137
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138 and one metadata file, WHICH IS COMPULSORY, see section **Metadata File Information**.
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139
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140
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141 **Measures' files**
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142
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143 The measure's files must be organized as matrices:
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144
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145 - The first column must contain Metabolite IDs that are unique (not repeated) within the file.
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146
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147 - The rest of the columns correspond to the samples
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148
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149 - The rows correspond to the metabolites
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150
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151 - The values must be tab separated, with the first row containing the sample/column labels.
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152
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153 See the following examples of measures files:
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154
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155
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156 Example - Metabolites **abundances**:
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157
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158 =============== ================== ================== ================== ================== ================== ==================
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159 ID **MCF001089_TD01** **MCF001089_TD02** **MCF001089_TD03** **MCF001089_TD04** **MCF001089_TD05** **MCF001089_TD06**
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160 =============== ================== ================== ================== ================== ================== ==================
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161 2_3-PG 8698823.9926 10718737.7217 10724373.9 8536484.5 22060650 28898956
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162 2-OHGLu 36924336 424336 92060650 45165 84951950 965165051
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163 Glc6P 2310 2142 2683 1683 012532068 1252172
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164 Gly3P 399298 991656565 525195 6365231 89451625 4952651963
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165 IsoCit 0 0 0 84915613 856236 954651610
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166 =============== ================== ================== ================== ================== ================== ==================
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167
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168 Example - mean **enrichment** or labeled fractional contributions:
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169
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170 =============== ================== ================== ================== ================== ================== ==================
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171 ID **MCF001089_TD01** **MCF001089_TD02** **MCF001089_TD03** **MCF001089_TD04** **MCF001089_TD05** **MCF001089_TD06**
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172 =============== ================== ================== ================== ================== ================== ==================
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173 2_3-PG 0.9711 0.968 0.9909 0.991 0.40 0.9
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174 2-OHGLu 0.01719 0.0246 0.554 0.555 0.73 0.68
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175 Glc6P 0.06 0.66 2683 0.06 2068 2172
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176 Gly3P 0.06 0.06 0.06 1 5 3
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177 IsoCit 0.06 1 0.49 0.36 6 10
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178 =============== ================== ================== ================== ================== ================== ==================
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179
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180 Example - **Isotopologues**
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181
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182 =============== ================== ================== ================== ================== ================== ==================
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183 ID **MCF001089_TD01** **MCF001089_TD02** **MCF001089_TD03** **MCF001089_TD04** **MCF001089_TD05** **MCF001089_TD06**
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184 =============== ================== ================== ================== ================== ================== ==================
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185 2_3-PG_m+0 206171.4626 285834.0353 36413.27637 27367.17784 6171.4626 119999
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186 2_3-PG_m+1 123 432 101 127 206171.4626 119999
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187 2_3-PG_m+2 133780.182 161461.2364 182631.3947 132170.3807 358749.348 848754.36
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188 2_3-PG_m+3 8358749.348 10271010.45 10505228.3 8376820.028 62163.30727 1088.8963
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189 2-OHGLu_m+0 5550339.322 6072872.833 3855047.791 3216178.72 8358749.348 10271010.45
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190 2-OHGLu_m+1 0.0 0.0 0.0 0.0 206171.4626 285834.0353
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191 =============== ================== ================== ================== ================== ================== ==================
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192
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193
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194 Example - **Isotopologue proportions**:
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195
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196 =============== ================== ================== ================== ================== ================== ==================
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197 ID **MCF001089_TD01** **MCF001089_TD02** **MCF001089_TD03** **MCF001089_TD04** **MCF001089_TD05** **MCF001089_TD06**
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198 =============== ================== ================== ================== ================== ================== ==================
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199 2_3-PG_m+0 0.023701408 0.026667837 0.003395407 0.05955 0.034383527 0.12
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200 2_3-PG_m+1 0.0 0.0 0.0 0.0 0.4 0.12
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201 2_3-PG_m+2 0.015379329 0.01506 0.017029723 0.35483229 0.54131313 0.743
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202 2_3-PG_m+3 0.960919263 0.958268099 0.97957487 0.581310816 0.017029723 0.017
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203 2-OHGLu_m+0 0.972778716 0.960016157 0.238843937 0.234383527 0.9998888 0.015064063
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204 2-OHGLu_m+1 0.0 0.0 0.0 0.0 0.0001112 0.960919263
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205 =============== ================== ================== ================== ================== ================== ==================
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206
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207
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208
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209 **Metadata File Information**
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210
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211 Provide a tab-separated file that has the names of the samples in the first column and one header row.
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212 Column names must be exactly in this order:
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213
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214 name_to_plot
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215 condition
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216 timepoint
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217 timenum
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218 compartment
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219 original_name
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220
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221
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222 Example **Metadata File**:
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223
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224
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225 ==================== =============== ============= ============ ================ =================
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226 **name_to_plot** **condition** **timepoint** **timenum** **compartment** **original_name**
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227 -------------------- --------------- ------------- ------------ ---------------- -----------------
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228 Control_cell_T0-1 Control T0 0 cell MCF001089_TD01
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229 Control_cell_T0-2 Control T0 0 cell MCF001089_TD02
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230 Control_cell_T0-3 Control T0 0 cell MCF001089_TD03
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231 Tumoral_cell_T0-1 Tumoral T0 0 cell MCF001089_TD04
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232 Tumoral_cell_T0-2 Tumoral T0 0 cell MCF001089_TD05
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233 Tumoral_cell_T0-3 Tumoral T0 0 cell MCF001089_TD06
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234 Tumoral_cell_T24-1 Tumoral T24 24 cell MCF001089_TD07
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235 Tumoral_cell_T24-2 Tumoral T24 24 cell MCF001089_TD08
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236 Tumoral_cell_T24-3 Tumoral T24 24 cell MCF001090_TD01
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237 Control_med_T24-1 Control T24 24 med MCF001090_TD02
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238 Control_med_T24-2 Control T24 24 med MCF001090_TD03
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239 Tumoral_med_T24-1 Tumoral T24 24 med MCF001090_TD04
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240 Tumoral_med_T24-2 Tumoral T24 24 med MCF001090_TD05
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241 Control_med_T0-1 Control T0 0 med MCF001090_TD06
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242 Tumoral_med_T0-1 Tumoral T0 0 med MCF001090_TD07
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243 Tumoral_med_T0-2 Tumoral T0 0 med MCF001090_TD08
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244 ==================== =============== ============= ============ ================ =================
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245
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246
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247 The column **original_name** must have the names of the samples as given in your data.
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248
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249 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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250 are meaningful is a better choice, as we will take them to display the results.
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251
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252 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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253 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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254
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255 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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256 compartments names are, the longer the output files' names! Please pick short and clear abbreviations to fill this column.
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257
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258
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259 **Running the analysis**
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260
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261 You can precise how you want your analysis to be executed, with the parameters:
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262
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263 - **conditions**: the conditions present in your data, specifying in first place your CONTROL condition (this ordering is crucial to make the comparisons in a coherent sense).
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264
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265 - **comparisons** : the pairs of [condition, timepoint] groups to compare
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266
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267 - **datatypes** : the measures type(s) that you want to run
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268
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269 - **statistical_test** : choose, by type of measure, the specific statistical test to be applied.
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270
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271 Kruskal-Wallis, Mann-Whitney, Wilcoxon’s signed rank test, Wilcoxon’s rank sum test
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272 t-test, and permutation test are currently offered (we use the trusted functions from scipy library https://docs.scipy.org/doc/scipy/reference/stats.html).
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273
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274 For the permutation test, we have established as test statistic, the absolute difference of geometric means of the two compared groups.
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275
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276 - **qualityDistanceOverSpan**: a normalized distance between the intervals of values of the compared groups, that is the cutoff for
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277
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278 considering a minimal acceptable "separation", and therefore, to be suitable for statistical testing. A 'distance/span' == 1 is a perfect separation,
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279 whereas if 'distance/span' < 0 there is no separation.
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280 To use with caution in case of important dispersion of your intra-group values. Default is -0.3 (not stringent)
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281
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282 - **correction_method** : one of the methods for multiple testing correction available in statsmodels library (bonferroni, fdr_bh, sidak, among others, see https://www.statsmodels.org/dev/generated/statsmodels.stats.multitest.multipletests.html).
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283
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284 There exist hints on use that will guide you, next to the parameters.
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285
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286
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287 **Available data for testing**
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288
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289 You can test our tool with the data from our manuscript https://zenodo.org/record/8378887 (the pertinent
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290 files for you are located in the subfolders inside the data folder).
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291 You can also use the minimal data examples from https://zenodo.org/record/8380706
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292
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293 ]]>
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294 </help>
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295 <expand macro="citations" />
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296 </tool>