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comparison dimet_metabologram.xml @ 7:06f8d9ba09cd 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 17:36:05 +0000
parents c7ff01bd331b
children
comparison
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6:c7ff01bd331b 7:06f8d9ba09cd
30 name: "Perform data integration via metabologram visualization", 30 name: "Perform data integration via metabologram visualization",
31 abs_values_scale_color_bar: {transcripts: null, metabolites:null}, 31 abs_values_scale_color_bar: {transcripts: null, metabolites:null},
32 colors_divergent_palette: ['royalblue', 'white', 'red'], 32 colors_divergent_palette: ['royalblue', 'white', 'red'],
33 edge_color: ['black','black'], 33 edge_color: ['black','black'],
34 line_width:['1','1.2'], 34 line_width:['1','1.2'],
35 display_label_and_value: true, 35 display_label_and_value: ${output_options.write_values},
36 font_size: ${output_options.font_size}, 36 font_size: ${output_options.font_size},
37 fig_width: ${output_options.fig_width}, 37 fig_width: ${output_options.fig_width},
38 figure_format:${output_options.figure_format}, 38 figure_format:${output_options.figure_format},
39 color_nan_elements:'gray', 39 color_nan_elements:'gray',
40 fig_height: ${output_options.fig_height} 40 fig_height: ${output_options.fig_height}
74 ]]></command> 74 ]]></command>
75 <inputs> 75 <inputs>
76 <expand macro="input_parameters_metabologram"/> 76 <expand macro="input_parameters_metabologram"/>
77 <expand macro="deg_list"/> 77 <expand macro="deg_list"/>
78 <expand macro="compartments_metabologram"/> 78 <expand macro="compartments_metabologram"/>
79
79 <param name="correction_method" type="select" value="bonferroni" display="radio" label="Select multiple test correction to apply" help="Please enter at max 1 method"> 80 <param name="correction_method" type="select" value="bonferroni" display="radio" label="Select multiple test correction to apply" help="Please enter at max 1 method">
80 <option value="bonferroni">bonferroni</option> 81 <option value="bonferroni">bonferroni</option>
81 <option value="holm-sidak">holm-sidak</option> 82 <option value="holm-sidak">holm-sidak</option>
82 <option value="holm">holm</option> 83 <option value="holm">holm</option>
83 <option value="simes-hochberg">simes-hochberg</option> 84 <option value="simes-hochberg">simes-hochberg</option>
91 <section name="output_options" title="Output options"> 92 <section name="output_options" title="Output options">
92 <param name="figure_format" type="select" value="pdf" display="radio" label="Select output figure format" help="Please enter at max 1 format"> 93 <param name="figure_format" type="select" value="pdf" display="radio" label="Select output figure format" help="Please enter at max 1 format">
93 <option value="pdf">Pdf</option> 94 <option value="pdf">Pdf</option>
94 <option value="svg">Svg</option> 95 <option value="svg">Svg</option>
95 </param> 96 </param>
97 <param name="write_values" type="boolean" value="false" label="Write the values alongside the metabolites and genes names (e.g. L-Alanine: -0.44)"
98 help="Default value is false."/>
96 <param name="fig_width" type="integer" min="5" max="20" value="7" label="width of figures" 99 <param name="fig_width" type="integer" min="5" max="20" value="7" label="width of figures"
97 help="Default value is 7."/> 100 help="Default value is 7."/>
98 <param name="fig_height" type="integer" min="5" max="20" value="7" label="heigt of each figure" 101 <param name="fig_height" type="integer" min="5" max="20" value="7" label="heigt of each figure"
99 help="Default value is 7."/> 102 help="Default value is 7."/>
100 <param name="font_size" type="integer" min="1" max="20" value="12" label=" figure font size" 103 <param name="font_size" type="integer" min="1" max="20" value="12" label=" figure font size"
113 116
114 <param name="path_kegg_metabolites" ftype="tabular" value="pathways_kegg_metabolites.csv"/> 117 <param name="path_kegg_metabolites" ftype="tabular" value="pathways_kegg_metabolites.csv"/>
115 <param name="path_kegg_transcripts" ftype="tabular" value="pathways_kegg_transcripts.csv"/> 118 <param name="path_kegg_transcripts" ftype="tabular" value="pathways_kegg_transcripts.csv"/>
116 <param name="abundance_file" ftype="tabular" value="rawAbundances.csv"/> 119 <param name="abundance_file" ftype="tabular" value="rawAbundances.csv"/>
117 <param name="metadata_path" ftype="tabular" value="example2_metadata.csv"/> 120 <param name="metadata_path" ftype="tabular" value="example2_metadata.csv"/>
118 <param name="metabolites_list" value="Fumaric_acid,Glycine,L-Proline"/>
119 <param name="statistical_test_type" value="parametric"/> 121 <param name="statistical_test_type" value="parametric"/>
120 <param name="stat_test" value="Tt"/> 122 <param name="stat_test" value="Tt"/>
121 <repeat name="deg_list"> 123 <repeat name="deg_list">
122 <param name="input" ftype="tabular" value="DEG_comparison_1.csv"/> 124 <param name="input" ftype="tabular" value="DEG_comparison_1.csv"/>
123 <param name="idcol" ftype="integer" value="2"/> 125 <param name="idcol" ftype="integer" value="2"/>
124 <param name="valuecol" ftype="integer" value="3"/> 126 <param name="valuecol" ftype="integer" value="3"/>
125 <param name="timepoint" value='T0'/> 127 <param name="timepoint" value='T0'/>
126 <repeat name="factor_list"> 128 <repeat name="factor_list">
127 <param name="condition" value="Control"/> 129 <param name="condition" value="L-Cycloserine"/>
128 </repeat> 130 </repeat>
129 <repeat name="factor_list"> 131 <repeat name="factor_list">
130 <param name="condition" value="L-Cycloserine"/> 132 <param name="condition" value="Control"/>
131 </repeat> 133 </repeat>
132 </repeat> 134 </repeat>
133 <section name="output_options"> 135 <section name="output_options">
136 <param name="show_values" value="false"/>
134 <param name="figure_format" value="svg"/> 137 <param name="figure_format" value="svg"/>
135 <param name="figure_width" value="7"/> 138 <param name="figure_width" value="7"/>
136 <param name="figure_height" value="7"/> 139 <param name="figure_height" value="7"/>
137 <param name="font_size" value="12"/> 140 <param name="font_size" value="12"/>
138 </section> 141 </section>
139 <output_collection name="report" type="list" count="3"> 142 <output_collection name="report" type="list" count="3">
140 <element file="AMINOACIDS-Control-T0-L-Cycloserine-T0--DEG_comparison1-abundances-cell.svg" name="AMINOACIDS-Control-T0-L-Cycloserine-T0--DEG_comparison1-abundances-cell" ftype="svg" compare="sim_size" delta="100"/> 143 <element file="AMINOACIDS-L-Cycloserine-T0-Control-T0--DEG_comparison1-abundances-cell.svg" name="AMINOACIDS-L-Cycloserine-T0-Control-T0--DEG_comparison1-abundances-cell" ftype="svg" compare="sim_size" delta="100"/>
141 <element file="CENTRAL_CARBON_METABOLISM-Control-T0-L-Cycloserine-T0--DEG_comparison1-abundances-cell.svg" name="CENTRAL_CARBON_METABOLISM-Control-T0-L-Cycloserine-T0--DEG_comparison1-abundances-cell" ftype="svg" compare="sim_size" delta="100"/> 144 <element file="CENTRAL_CARBON_METABOLISM-L-Cycloserine-T0-Control-T0--DEG_comparison1-abundances-cell.svg" name="CENTRAL_CARBON_METABOLISM-L-Cycloserine-T0-Control-T0--DEG_comparison1-abundances-cell" ftype="svg" compare="sim_size" delta="100"/>
142 <element file="legend-abundances-cell.svg" name="legend-abundances-cell" ftype="svg" compare="sim_size" delta="100"/> 145 <element file="legend-abundances-cell.svg" name="legend-abundances-cell" ftype="svg" compare="sim_size" delta="100"/>
143 </output_collection> 146 </output_collection>
144 </test> 147 </test>
145 </tests> 148 </tests>
146 <help><![CDATA[ 149 <help><![CDATA[
169 1.2 The metadata, a unique file with the description of the samples in your measures' files. This is compulsory, see section **Metadata File Information**. 172 1.2 The metadata, a unique file with the description of the samples in your measures' files. This is compulsory, see section **Metadata File Information**.
170 173
171 174
172 2. **The transcriptomics data**: 175 2. **The transcriptomics data**:
173 176
174 2.1 The table with the results of the differential expression analysis (performed with an external tool) 177 2.1 The table with the results of the differential expression analysis (performed with an external tool). Please provide the file with the results of the differential expression analysis of your transcriptomics data. It is recommended to use only the statistically significant **Differentially Expressed Genes (DEG)**. We provide examples in the zenodo (see section **Available data for testing**)
178
175 179
176 180
177 3. **The pathways files**: 181 3. **The pathways files**:
178 182
179 183
294 compartments names are, the longer the output files' names! Please pick short and clear abbreviations to fill this column. 298 compartments names are, the longer the output files' names! Please pick short and clear abbreviations to fill this column.
295 299
296 300
297 **Running the analysis** 301 **Running the analysis**
298 302
299 You can precise how you want your analysis to be executed, with the parameters: 303 You can precise how you want your analysis to be executed with the parameters, which are of two types:
300 304
301 305 **a. Parameters proper to the metabolome differential analysis (that runs automatically before the integration)**:
302 a. Parameters proper to the metabolomics analysis (that runs automatically before the integration): 306
303 307 - **Conditions and timepoint**:
304 - **comparisons** : the pairs of [condition, timepoint] groups to compare 308
305 309 For each comparison to run on the metabolomics data, you can define the Conditions to compare, at a chosen time point, through the box 'Deregulated gene set': follow the instructions and choose the correct order of Conditions (the last must be the reference or control).
306 - **datatypes** : the measures type that you want to run, that must be only one (see above in **Input data files** section) 310 To add a second comparison, click the 'Insert Deregulated gene set' button.
307 311 You can insert and define as many boxes ('Deregulated gene set') as comparisons you want to perform.
308 - **statistical_test** : choose the specific statistical test to be applied. 312
313 - **statistical_test**: choose the specific statistical test to be applied.
309 314
310 Kruskal-Wallis, Mann-Whitney, Wilcoxon’s signed rank test, Wilcoxon’s rank sum test 315 Kruskal-Wallis, Mann-Whitney, Wilcoxon’s signed rank test, Wilcoxon’s rank sum test
311 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). 316 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).
312 317
313 For the permutation test, we have established as test statistic, the absolute difference of geometric means of the two compared groups. 318 For the permutation test, we have established as test statistic, the absolute difference of geometric means of the two compared groups.
316 321
317 considering a minimal acceptable "separation", and therefore, to be suitable for statistical testing. A 'distance/span' == 1 is a perfect separation, 322 considering a minimal acceptable "separation", and therefore, to be suitable for statistical testing. A 'distance/span' == 1 is a perfect separation,
318 whereas if 'distance/span' < 0 there is no separation. 323 whereas if 'distance/span' < 0 there is no separation.
319 To use with caution in case of important dispersion of your intra-group values. Default is -0.3 (not stringent) 324 To use with caution in case of important dispersion of your intra-group values. Default is -0.3 (not stringent)
320 325
321 - **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). 326 - **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).
322 327
323 - **compartment** : one of the compartments present in your data. 328 - **compartment**: one of the compartments present in your data.
324 329
325 b. Parameters proper to the integration (that runs automatically after the metabolites analysis): 330 **b. Parameters proper to the integration with transcriptomics (that runs automatically after the metabolome differential analysis)**:
326 331
327 332 - **Deregulated genes set file**: Corresponds to the transcriptomics data, as explained in **Input data files** section.
328 - **transcripts** : the file(s) with the results of the differential expression analysis. They must be as many as the number of comparisons (metabolomics analysis) and keep a coherent order with them. 333
334 For each 'Deregulated gene set' box, a single **Differentially Expressed Genes (DEG)** file must be added, and must match with the metabolomics comparison set in the same box. Additional files can be added with the 'Insert deregulated gene set' button,
335 see also the subsection 'Conditions and timepoint' above.
329 336
330 - **pathways** : files for the pathways, as explained in **Input data files** section 337 - **pathways** : files for the pathways, as explained in **Input data files** section
331 338
332 339
333 There exist hints on use that will guide you, next to the parameters. 340 Overall, the metabologram module provides hints on use that will guide you, in the same menus and boxes of the parameters.
341
342
343 **Output**
334 344
335 The output consists of one figure by metabologram, and a color key bar legend valid for all metabolograms produced 345 The output consists of one figure by metabologram, and a color key bar legend valid for all metabolograms produced
336 346
337 **Available data for testing** 347 **Available data for testing**
338 348