Mercurial > repos > iuc > dimet_differential_multigroup_analysis

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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 17:30:36 +0000
parents de2f85da4e1d
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de2f85da4e1d 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 Differential analysis of 3 or more chosen groups of tracer metabolomics data (by DIMet)
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4 </description>
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5 <macros>
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6 <token name="@TOOL_LABEL@">differential multigroup analysis</token>
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7 <token name="@EXECUTABLE@">differential_multigroup_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[
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12 @INIT_CONFIG@
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13 @INIT_DIFF_MULTIGROUP_ANALYSIS@
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14 @INIT_DATATYPES@
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15 @INIT_GROUPS@
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16 @INIT_PLOT_CONDITIONS@
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17 @INIT_TIMEPOINTS@
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18 @INIT_MULTIGROUP_COMPARISONS@
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19 HYDRA_FULL_ERROR=1 python -m dimet
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20 '++hydra.run.dir=.'
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21 '++figure_path=figures'
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22 '++table_path=tables'
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23 '++analysis={
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24 dataset:{
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25 _target_:dimet.data.DatasetConfig,
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26 name: "Galaxy DIMet run"
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27 },
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28 method:{
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29 _target_: dimet.method.MultiGroupComparisonConfig,
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30 label: multi_group_comparison,
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31 name: "Multi group statistical comparison using Kruskal-Wallis test"
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32 },
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33 label: multi_group_comparison,
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34 datatypes:${datatypes_avail}
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35 }'
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36 '++analysis.method.datatypes=${datatypes_avail}'
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37 '++analysis.timepoints=${timepoints}'
de2f85da4e1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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38 '++analysis.conditions=${comparisons}'
de2f85da4e1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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39 '++analysis.dataset.label='
de2f85da4e1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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40 '++analysis.method.correction_method=${correction_method}'
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41 '++analysis.method.impute_values=${impute_values}'
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42 '++analysis.dataset.subfolder='
de2f85da4e1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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43 '++analysis.method.grouping=${groups}'
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44 '++analysis.dataset.conditions=${conditions}'
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45 #if $metadata_path:
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46 '++analysis.dataset.metadata=metadata'
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47 #end if
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48 #if str( $data_input.data_input_selector ) == "abundance":
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49 #if $data_input.abundance_file:
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50 '++analysis.dataset.abundances=abundance'
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51 #end if
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52 #elif str( $data_input.data_input_selector ) == "mean_enrichment":
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53 #if $data_input.me_or_frac_contrib_file:
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54 '++analysis.dataset.mean_enrichment=me_or_frac_contrib'
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55 #end if
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56 #elif str( $data_input.data_input_selector ) == "isotop_prop":
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57 #if $data_input.isotop_prop_file:
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58 '++analysis.dataset.isotopologue_proportions=isotop_prop'
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59 #end if
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60 #else
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61 #if $data_input.isotop_abs_file:
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62 '+analysis.dataset.isotopologues=isotop_abs'
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63 #end if
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64 #end if
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65 @REMOVE_CONFIG@
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66 ]]></command>
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67 <inputs>
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68 <expand macro="input_parameters_multi_diff_analysis"/>
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69 <expand macro="plot_factor_list"/>
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70 <expand macro="timepoint_multigroup"/>
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71 <expand macro="compartments"/>
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72 <expand macro="correction_method"/>
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73 </inputs>
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74
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75 <outputs>
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76 <collection name="report" type="list">
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77 <discover_datasets pattern="__designation__" directory="tables" format="tabular"/>
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78 </collection>
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79 </outputs>
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80 <tests>
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81 <test>
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82 <param name="data_input_selector" value="abundance" />
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83 <param name="abundance_file" ftype="tabular" value="rawAbundances3.csv"/>
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84 <param name="metadata_path" ftype="tabular" value="example3_metadata.csv"/>
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85 <param name="correction_method" value="bonferroni"/>
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86 <repeat name="plot_factor_list">
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87 <param name="condition" value="Control"/>
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88 </repeat>
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89 <repeat name="plot_factor_list">
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90 <param name="condition" value="Cond1"/>
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91 </repeat>
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92 <repeat name="plot_factor_list">
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93 <param name="condition" value="Cond2"/>
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94 </repeat>
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95 <param name="timepoint" value="T0h,T2h"/>
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96 <param name="compartments" value="cell"/>
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97
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98 <output_collection name="report" type="list" count="1">
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99 <element file="abundance--cell--multigroup.tsv" name="abundance--cell--multigroup.tsv" ftype="tabular"/>
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100 </output_collection>
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101 </test>
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102 </tests>
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103 <help><![CDATA[
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104 This module is part of DIMet: Differential analysis of Isotope-labeled targeted Metabolomics data (https://pypi.org/project/DIMet/).
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105
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106 **Input data files**
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107
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108 This tool computes the Kruskal-Wallis test over 3 or more groups,
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109 to evaluate if at least one group is significantly different to the other groups (H0: median of all of the groups is equal). For illustration see the section **Metadata File Information** which contains three conditions: Control, Core_mass and Edge_tissue, across one single time point, thus 3 groups (number-of-groups-in-my-data = number-of-conditions x number-of-timepoints)).
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110
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111 This tool requires (at max.) 5 tab-delimited .csv files as inputs. There are two types of files:
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112
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113 - The measures' (or quantifications') files, that can be of 4 types.
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114
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115 - The metadata, a unique file with the description of the samples in your measures' files. This is compulsory.
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116
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117 For running DIMet @EXECUTABLE@ you need **at least one** file of measures:
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118
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119
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120 - The total **abundances** (of the metabolites) file
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121
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122 - The mean **enrichment** or labelled fractional contributions
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123
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124 - The **isotopologues** absolute values files (optional)
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125
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126 - The **isotopologue proportions** file (optional)
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127
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128 and one metadata file, WHICH IS COMPULSORY, see section **Metadata File Information**.
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129
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130 The measure's files must be organized as matrices:
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131
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132 - The first column must contain Metabolite IDs that are unique (not repeated) within the file.
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133
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134 - The rest of the columns correspond to the samples
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135
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136 - The rows correspond to the metabolites
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137
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138 - The values must be tab separated, with the first row containing the sample/column labels.
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139
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140 See the following examples of measures' files:
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141
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142
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143 Example - Metabolites **abundances**:
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144
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145 =============== ================== ================== ================== ================== ================== ==================
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146 ID **MCF001089_TD01** **MCF001089_TD02** **MCF001089_TD03** **MCF001089_TD04** **MCF001089_TD05** **MCF001089_TD06**
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147 =============== ================== ================== ================== ================== ================== ==================
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148 2_3-PG 8698823.9926 10718737.7217 10724373.9 8536484.5 22060650 28898956
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149 2-OHGLu 36924336 424336 92060650 45165 84951950 965165051
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150 Glc6P 2310 2142 2683 1683 012532068 1252172
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151 Gly3P 399298 991656565 525195 6365231 89451625 4952651963
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152 IsoCit 0 0 0 84915613 856236 954651610
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153 =============== ================== ================== ================== ================== ================== ==================
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154
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155 Example - mean **enrichment** or labeled fractional contributions:
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156
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157 =============== ================== ================== ================== ================== ================== ==================
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158 ID **MCF001089_TD01** **MCF001089_TD02** **MCF001089_TD03** **MCF001089_TD04** **MCF001089_TD05** **MCF001089_TD06**
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159 =============== ================== ================== ================== ================== ================== ==================
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160 2_3-PG 0.9711 0.968 0.9909 0.991 0.40 0.9
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161 2-OHGLu 0.01719 0.0246 0.554 0.555 0.73 0.68
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162 Glc6P 0.06 0.66 2683 0.06 2068 2172
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163 Gly3P 0.06 0.06 0.06 1 5 3
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164 IsoCit 0.06 1 0.49 0.36 6 10
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165 =============== ================== ================== ================== ================== ================== ==================
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166
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167 Example - **Isotopologues**
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168
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169 =============== ================== ================== ================== ================== ================== ==================
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170 ID **MCF001089_TD01** **MCF001089_TD02** **MCF001089_TD03** **MCF001089_TD04** **MCF001089_TD05** **MCF001089_TD06**
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171 =============== ================== ================== ================== ================== ================== ==================
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172 2_3-PG_m+0 206171.4626 285834.0353 36413.27637 27367.17784 6171.4626 119999
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173 2_3-PG_m+1 123 432 101 127 206171.4626 119999
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174 2_3-PG_m+2 133780.182 161461.2364 182631.3947 132170.3807 358749.348 848754.36
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175 2_3-PG_m+3 8358749.348 10271010.45 10505228.3 8376820.028 62163.30727 1088.8963
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176 2-OHGLu_m+0 5550339.322 6072872.833 3855047.791 3216178.72 8358749.348 10271010.45
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177 2-OHGLu_m+1 0.0 0.0 0.0 0.0 206171.4626 285834.0353
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178 =============== ================== ================== ================== ================== ================== ==================
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179
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180
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181 Example - **Isotopologue proportions**:
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182
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183 =============== ================== ================== ================== ================== ================== ==================
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184 ID **MCF001089_TD01** **MCF001089_TD02** **MCF001089_TD03** **MCF001089_TD04** **MCF001089_TD05** **MCF001089_TD06**
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185 =============== ================== ================== ================== ================== ================== ==================
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186 2_3-PG_m+0 0.023701408 0.026667837 0.003395407 0.05955 0.034383527 0.12
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187 2_3-PG_m+1 0.0 0.0 0.0 0.0 0.4 0.12
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188 2_3-PG_m+2 0.015379329 0.01506 0.017029723 0.35483229 0.54131313 0.743
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189 2_3-PG_m+3 0.960919263 0.958268099 0.97957487 0.581310816 0.017029723 0.017
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190 2-OHGLu_m+0 0.972778716 0.960016157 0.238843937 0.234383527 0.9998888 0.015064063
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191 2-OHGLu_m+1 0.0 0.0 0.0 0.0 0.0001112 0.960919263
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192 =============== ================== ================== ================== ================== ================== ==================
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193
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194
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195
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196 **Metadata File Information**
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197
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198 Provide a tab-separated file that has the names of the samples in the first column and one header row.
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199 Column names must be exactly in this order:
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200
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201 name_to_plot
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202 condition
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203 timepoint
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204 timenum
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205 compartment
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206 original_name
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207
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208
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209 Example **Metadata File**:
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210
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211
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212 ==================== =============== ============= ============ ================ =================
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213 **name_to_plot** **condition** **timepoint** **timenum** **compartment** **original_name**
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214 -------------------- --------------- ------------- ------------ ---------------- -----------------
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215 Control_cell-1 Control T0 0 cell MCF001089_TD01
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216 Control_cell-2 Control T0 0 cell MCF001089_TD02
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217 Control_cell-3 Control T0 0 cell MCF001089_TD03
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218 CoreMass_cell-1 Core_mass T0 0 cell MCF001089_TD04
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219 CoreMass_cell-2 Core_mass T0 0 cell MCF001089_TD05
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220 CoreMass_cell-3 Core_mass T0 0 cell MCF001089_TD06
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221 EdgeTiss_cell-1 Edge_tissue T0 0 cell MCF001089_TD07
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222 EdgeTiss_cell-2 Edge_tissue T0 0 cell MCF001089_TD08
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223 EdgeTiss_cell-3 Edge_tissue T0 0 cell MCF001089_TD09
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224 ==================== =============== ============= ============ ================ =================
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225
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226
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227 The column **original_name** must have the names of the samples as given in your data.
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228
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229 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 are meaningful is a better choice, as we will take them to display the results.
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230
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231 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) 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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232
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233 The column **compartment** is an abbreviation, coined by you, for the compartments. This will be used for the results' files names: the longer the compartments names are, the longer the output files' names! Please pick short and clear abbreviations to fill this column.
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234
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235
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236 **Running the analysis**
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237
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238
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239 You can precise how you want your analysis to be executed, with the parameters:
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240
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241 - **comparisons** : the groups you want to select for comparison in the multigroup analysis
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242
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243 (Note that **comparisons** parameter in the multigroup analysis does not have the same usage as in the pairwise differential analysis).
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244
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245 - **datatypes** : the measures type(s) that you want to run
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246
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247 - **correction_method** : one of the methods for multiple testinc 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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248
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249 There exist hints on use that will guide you, next to the parameters.
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250
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251 For more information about the implemented statistical tests, please visit: https://github.com/cbib/DIMet/wiki/2-Statistical-tests
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252
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253 The output files are explained in https://github.com/cbib/DIMet/wiki/3-Output
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254
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255 **Available data for testing**
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256
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257 You can test our tool with the data from our manuscript https://zenodo.org/record/10579862 (the pertinent
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258 files for you are located in the subfolders inside the data folder).
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259 You can also use the minimal data examples from https://zenodo.org/record/10579891
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260
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261 ]]>
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262 </help>
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263 <expand macro="citations"/>
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264 </tool>