Mercurial > repos > iuc > dimet_differential_analysis
changeset 7:fff032d6115a draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 6da96d865a3a557cfa3ad09e1cfa830519e73748
author | iuc |
---|---|
date | Tue, 06 Aug 2024 17:40:47 +0000 |
parents | 6a63c1d832db |
children | |
files | dimet_differential_analysis.xml macros.xml test-data/AMINOACIDS-Control-T0-L-Cycloserine-T0--DEG_comparison1-abundances-cell.svg test-data/AMINOACIDS-L-Cycloserine-T0-Control-T0--DEG_comparison1-abundances-cell.svg test-data/CENTRAL_CARBON_METABOLISM-Control-T0-L-Cycloserine-T0--DEG_comparison1-abundances-cell.svg test-data/CENTRAL_CARBON_METABOLISM-L-Cycloserine-T0-Control-T0--DEG_comparison1-abundances-cell.svg |
diffstat | 6 files changed, 2723 insertions(+), 3239 deletions(-) [+] |
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--- a/dimet_differential_analysis.xml Fri Jun 21 18:50:24 2024 +0000 +++ b/dimet_differential_analysis.xml Tue Aug 06 17:40:47 2024 +0000 @@ -266,11 +266,11 @@ You can precise how you want your analysis to be executed, with the parameters: -- **conditions**: the conditions present in your data, to perform the pairwise comparison. +- **datatypes** : the measures type(s) that you want to run (see above in Input data files section) -- **comparisons** : the pairs of [condition, timepoint] groups to compare +- **conditions**: the two 'Conditions' boxes must be filled in a coherent order, keeping in mind that the last specified condition is the reference or control. -- **datatypes** : the measures type(s) that you want to run (see above in Input data files section) +- **timepoint** : the time point at which the two conditions will be compared. - **statistical_test** : choose, by type of measure, the specific statistical test to be applied.
--- a/macros.xml Fri Jun 21 18:50:24 2024 +0000 +++ b/macros.xml Tue Aug 06 17:40:47 2024 +0000 @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">0.2.4</token> - <token name="@VERSION_SUFFIX@">3</token> + <token name="@VERSION_SUFFIX@">4</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">dimet</requirement> @@ -49,6 +49,7 @@ </xml> <xml name="citations"> <citations> + <citation type="doi">10.1093/bioinformatics/btae282</citation> <citation type="bibtex"> @software{Galvis_Rodriguez_DIMet, author = {Galvis Rodriguez, Johanna and Guyon, Joris and Dartigues, Benjamin and Specque, Florian and Daubon, Thomas and Karkar, Slim and Nikolski, Macha}, @@ -56,7 +57,6 @@ title = {{DIMet}}, url = {https://github.com/cbib/DIMet} } - </citation> </citations> @@ -95,58 +95,23 @@ </xml> <xml name="input_parameters_metabologram"> <conditional name="data_input"> - <param name="data_input_selector" type="select" label="Abundance, Enrichment or Isotopologues quantification files" help="Select between raw abundance and mean enrichment files"> + <param name="data_input_selector" type="select" label="Abundance or Enrichment quantification files" help="Select between metabolite total abundances and mean enrichment files"> <option value="abundance" selected="True">abundance</option> <option value="mean_enrichment">mean_enrichment</option> </param> <when value="abundance"> <expand macro="abundance_file_macros"/> - <param name="metabolites_list" type="select" optional="false" multiple="true" - label="Select Metabolite(s) for condition 1 to plot (1 Min.). You have to load a abundance file prior to have access to metabolite list"> - <validator type="length" min="1" message="Please enter at max 2 compartments"/> - <options from_dataset="abundance_file"> - <column name="metabolite_or_isotopologue" index="0"/> - <column name="value" index="0"/> - <filter type="unique_value" name="metabolite_or_isotopologue" column="0"/> - <filter type="remove_value" value="metabolite_or_isotopologue"/> - </options> - <sanitizer> - <valid initial="default"> - <add preset="string.printable"/> - <add value="\t"/> - <remove value="""/> - <remove value="'"/> - </valid> - </sanitizer> - </param> <expand macro="statistical_test"/> + </when> <when value="mean_enrichment"> <expand macro="enrichment_file_macros"/> - <param name="metabolites_list" type="select" optional="false" multiple="true" - label="Select Metabolite(s) for condition 1 to plot (1 Min.). You have to load a abundance file prior to have access to metabolite list"> - <validator type="length" min="1" message="Please enter at max 2 compartments"/> - <options from_dataset="me_or_frac_contrib_file"> - <column name="metabolite_or_isotopologue" index="0"/> - <column name="value" index="0"/> - <filter type="unique_value" name="metabolite_or_isotopologue" column="0"/> - <filter type="remove_value" value="metabolite_or_isotopologue"/> - </options> - <sanitizer> - <valid initial="default"> - <add preset="string.printable"/> - <add value="\t"/> - <remove value="""/> - <remove value="'"/> - </valid> - </sanitizer> - </param> <expand macro="statistical_test"/> </when> </conditional> + <expand macro="metadata_file_macros"/> <param name="path_kegg_metabolites" type="data" format="tabular" label="Pathways kegg metabolites file" help="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. (see help below for more details)"/> <param name="path_kegg_transcripts" type="data" format="tabular" label="Pathways kegg transcripts file" help="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. (see help below for more details)"/> - <expand macro="metadata_file_macros"/> </xml> <xml name="input_parameters_bivar_analysis"> <conditional name="data_input">
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