Mercurial > repos > iuc > dimet_metabologram
diff dimet_metabologram.xml @ 2:7ff4f61789de draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
| author | iuc |
|---|---|
| date | Thu, 15 Feb 2024 12:49:51 +0000 |
| parents | 8d8ae3697a65 |
| children | b6e621c83f94 |
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--- a/dimet_metabologram.xml Tue Jan 23 14:58:39 2024 +0000 +++ b/dimet_metabologram.xml Thu Feb 15 12:49:51 2024 +0000 @@ -12,7 +12,7 @@ @INIT_METABOLOGRAM@ @INIT_TRANSCRIPTS@ @INIT_GROUPS@ - @INIT_COMPARISONS@ + @INIT_COMPARISONS_METABOLOGRAM@ @INIT_PATHWAYS@ @INIT_STAT_TEST@ HYDRA_FULL_ERROR=1 python -m dimet @@ -42,7 +42,7 @@ }, columns_metabolites: {ID: metabolite, values: log2FC}, columns_transcripts: {ID: ${deg_one_id}, values: ${deg_one_values}}, - compartment: cell, + compartment: ${compartments}, label: metabologram }' '++analysis.method.qualityDistanceOverSpan='${qualityDistanceOverSpan}'' @@ -54,7 +54,7 @@ '++analysis.method.impute_values=${impute_values}' '++analysis.statistical_test=${statistical_test}' '++analysis.dataset.subfolder=' - '++analysis.dataset.conditions=${conds}' + '++analysis.dataset.conditions=${$conditions}' '++analysis.dataset.pathways=${pathways}' '++analysis.dataset.transcripts=${transcripts}' '++analysis.comparisons=${comparisons}' @@ -75,8 +75,7 @@ <inputs> <expand macro="input_parameters_metabologram"/> <expand macro="deg_list"/> - <expand macro="conditions"/> - <expand macro="timepoint"/> + <expand macro="compartments_metabologram"/> <param name="correction_method" type="select" value="bonferroni" display="radio" label="Select multiple test correction to apply" help="Please enter at max 1 method"> <option value="bonferroni">bonferroni</option> <option value="holm-sidak">holm-sidak</option> @@ -111,17 +110,26 @@ </outputs> <tests> <test> - <param name="input" ftype="tabular" value="DEG_comparison_1.csv"/> - <param name="idcol" ftype="integer" value="2"/> - <param name="valuecol" ftype="integer" value="3"/> + <param name="path_kegg_metabolites" ftype="tabular" value="pathways_kegg_metabolites.csv"/> <param name="path_kegg_transcripts" ftype="tabular" value="pathways_kegg_transcripts.csv"/> <param name="abundance_file" ftype="tabular" value="rawAbundances.csv"/> <param name="metadata_path" ftype="tabular" value="example2_metadata.csv"/> <param name="metabolites_list" value="Fumaric_acid,Glycine,L-Proline"/> + <param name="statistical_test_type" value="parametric"/> <param name="stat_test" value="Tt"/> - <param name="conditions" value='Control,L-Cycloserine'/> - <param name="timepoint" value='T0'/> + <repeat name="deg_list"> + <param name="input" ftype="tabular" value="DEG_comparison_1.csv"/> + <param name="idcol" ftype="integer" value="2"/> + <param name="valuecol" ftype="integer" value="3"/> + <param name="timepoint" value='T0'/> + <repeat name="factor_list"> + <param name="condition" value="Control"/> + </repeat> + <repeat name="factor_list"> + <param name="condition" value="L-Cycloserine"/> + </repeat> + </repeat> <section name="output_options"> <param name="figure_format" value="svg"/> <param name="figure_width" value="7"/> @@ -140,7 +148,7 @@ DIMet Metabologram integrates tracer metabolomics and transcriptomics, in a pathway based fashion. More precisely, the differential information (Fold Changes (log2 transformed, or not)) of both types of omics -must be given as input, plus the files defining the pathways. You can use the minimal data examples from https://zenodo.org/records/8380706 that contain a minimal example data for running our DIMet Metabologram tool. +must be given as input, plus the files defining the pathways. You can use the minimal data examples from https://zenodo.org/records/10579891 that contain a minimal example data for running our DIMet Metabologram tool. 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. @@ -168,12 +176,32 @@ 3. **The pathways files**: - 3.1 A file with the pathways and respective gene symbols, which must match with those present in the transcriptomics data. The names of the columns must be the pathways' names, see the minimal data example downloaded from zenodo as explained above. + + 3.1 A file with the pathways and respective gene symbols, which must match with those present in the transcriptomics data. The names of the columns must be the pathways' names, see the minimal data example downloaded from zenodo as explained above. Example: - 3.2 A file with the pathways and respective metabolites ID, that must match with those in your metabolomics data. The names of the columns must be the pathways' names, see the minimal data example downloaded from zenodo as explained above. + ====================== ================== ================== + **PENTHOSE PHOSPHATE** **FATTY ACIDS** ... + ====================== ================== ================== + RPE SCD ... + PGM1 FADS1 ... + PKF BAAT ... + DERA ACOT2 ... + ... ... ... + ====================== ================== ================== + 3.2 A file with the pathways and respective metabolites ID, that must match with those in your metabolomics data. The names of the columns must be the pathways' names, see the minimal data example downloaded from zenodo as explained above. Example: + + ====================== ================== ================== + **PENTHOSE PHOSPHATE** **FATTY ACIDS** ... + ====================== ================== ================== + Xyl_P Acetyl_CoA ... + Glc_6P Palmitate ... + Rib_6P Stearate ... + ... ... ... + ====================== ================== ================== + **Measures' files** The measure's files must be organized as matrices: @@ -308,9 +336,9 @@ **Available data for testing** -You can test our tool with the data from our manuscript https://zenodo.org/record/8378887 (the pertinent +You can test our tool with the data from our manuscript https://zenodo.org/record/10579862 (the pertinent files for you are located in the subfolders inside the data folder). -You can also use the minimal data examples from https://zenodo.org/record/8380706 +You can also use the minimal data examples from https://zenodo.org/record/10579891 ]]> </help>