Mercurial > repos > iuc > dimet_pca_analysis
changeset 4:3b9226db8ab6 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit afc87f0254b4399b71e53735966032ba1a32434d
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--- a/dimet_pca_analysis.xml Mon Mar 04 19:58:22 2024 +0000 +++ b/dimet_pca_analysis.xml Wed Mar 27 16:48:52 2024 +0000 @@ -64,18 +64,18 @@ <param name="metadata_path" ftype="tabular" value="example2_metadata.csv"/> <param name="conditions" value='Control,L-Cycloserine'/> <output_collection name="report" type="list" count="12"> - <element file="abundances--cell_pc.csv" name="abundances--cell_pc.csv" ftype="tabular"/> - <element file="abundances--cell_var.csv" name="abundances--cell_var.csv" ftype="tabular"/> - <element file="abundances--med_pc.csv" name="abundances--med_pc.csv" ftype="tabular"/> - <element file="abundances--med_var.csv" name="abundances--med_var.csv" ftype="tabular"/> - <element file="abundances--T0--cell_pc.csv" name="abundances--T0--cell_pc.csv" ftype="tabular"/> - <element file="abundances--T0--cell_var.csv" name="abundances--T0--cell_var.csv" ftype="tabular"/> - <element file="abundances--T0--med_pc.csv" name="abundances--T0--med_pc.csv" ftype="tabular"/> - <element file="abundances--T0--med_var.csv" name="abundances--T0--med_var.csv" ftype="tabular"/> - <element file="abundances--T2h--cell_pc.csv" name="abundances--T2h--cell_pc.csv" ftype="tabular"/> - <element file="abundances--T2h--cell_var.csv" name="abundances--T2h--cell_var.csv" ftype="tabular"/> - <element file="abundances--T2h--med_pc.csv" name="abundances--T2h--med_pc.csv" ftype="tabular"/> - <element file="abundances--T2h--med_var.csv" name="abundances--T2h--med_var.csv" ftype="tabular"/> + <element file="abundances--cell_pc.tsv" name="abundances--cell_pc.tsv" ftype="tabular"/> + <element file="abundances--cell_var.tsv" name="abundances--cell_var.tsv" ftype="tabular"/> + <element file="abundances--med_pc.tsv" name="abundances--med_pc.tsv" ftype="tabular"/> + <element file="abundances--med_var.tsv" name="abundances--med_var.tsv" ftype="tabular"/> + <element file="abundances--T0--cell_pc.tsv" name="abundances--T0--cell_pc.tsv" ftype="tabular"/> + <element file="abundances--T0--cell_var.tsv" name="abundances--T0--cell_var.tsv" ftype="tabular"/> + <element file="abundances--T0--med_pc.tsv" name="abundances--T0--med_pc.tsv" ftype="tabular"/> + <element file="abundances--T0--med_var.tsv" name="abundances--T0--med_var.tsv" ftype="tabular"/> + <element file="abundances--T2h--cell_pc.tsv" name="abundances--T2h--cell_pc.tsv" ftype="tabular"/> + <element file="abundances--T2h--cell_var.tsv" name="abundances--T2h--cell_var.tsv" ftype="tabular"/> + <element file="abundances--T2h--med_pc.tsv" name="abundances--T2h--med_pc.tsv" ftype="tabular"/> + <element file="abundances--T2h--med_var.tsv" name="abundances--T2h--med_var.tsv" ftype="tabular"/> </output_collection> </test> </tests>
--- a/macros.xml Mon Mar 04 19:58:22 2024 +0000 +++ b/macros.xml Wed Mar 27 16:48:52 2024 +0000 @@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">0.2.2</token> + <token name="@TOOL_VERSION@">0.2.4</token> <token name="@VERSION_SUFFIX@">1</token> <token name="@EXECUTABLE@">pca</token> <xml name="requirements"> @@ -12,6 +12,12 @@ <option value="KW">Kruskal-Wallis</option> </param> </xml> + <xml name="statistical_test_for_bivariate_analysis"> + <param name="stat_test" type="select" value="pearson" display="radio" label="Select statistical to apply" help="Please enter at max 1 statistical test by file"> + <option value="pearson">pearson</option> + <option value="spearman">spearman</option> + </param> + </xml> <xml name="statistical_test"> <conditional name="statistics"> <param name="statistical_test_type" type="select" label="Choose which type of statistical test to perform" help="Choose which type of statistical test to perform"> @@ -166,6 +172,7 @@ </when> </conditional> <expand macro="metadata_file_macros"/> + <expand macro="statistical_test_for_bivariate_analysis"/> </xml> <xml name="input_parameters_diff_analysis"> <conditional name="data_input"> @@ -638,14 +645,23 @@ #if $metadata_path: ln -s '$metadata_path' data/metadata.csv && #end if + + #set conditions_MDV_comparison = {} - #silent $conditions_MDV_comparison['isotopologue_proportions']='pearson' #set timepoints_MDV_comparison = {} - #silent $timepoints_MDV_comparison['isotopologue_proportions']='pearson' #set conditions_metabolite_time_profiles = {} - #silent $conditions_metabolite_time_profiles['abundances']='pearson' - #silent $conditions_metabolite_time_profiles['mean_enrichment']='pearson' + #if str( $stat_test ) == "pearson": + #silent $conditions_MDV_comparison['isotopologue_proportions']='pearson' + #silent $timepoints_MDV_comparison['isotopologue_proportions']='pearson' + #silent $conditions_metabolite_time_profiles['abundances']='pearson' + #silent $conditions_metabolite_time_profiles['mean_enrichment']='pearson' + #else + #silent $conditions_MDV_comparison['isotopologue_proportions']='spearman' + #silent $timepoints_MDV_comparison['isotopologue_proportions']='spearman' + #silent $conditions_metabolite_time_profiles['abundances']='spearman' + #silent $conditions_metabolite_time_profiles['mean_enrichment']='spearman' + #end if #set $impute_values = {} #if str( $data_input.data_input_selector ) == "abundance": #if $data_input.abundance_file:
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