| Previous changeset 3:7897a5cadcf5 (2024-03-04) Next changeset 5:0bba1203264f (2024-05-21) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit afc87f0254b4399b71e53735966032ba1a32434d |
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modified:
macros.xml test-data/abundances--T0--cell--label-n_pc.svg test-data/abundances--T0--cell--label-y_pc.svg test-data/abundances--T0--cell_var.svg test-data/abundances--T0--med--label-n_pc.svg test-data/abundances--T0--med--label-y_pc.svg test-data/abundances--T0--med_var.svg test-data/abundances--T2h--cell--label-n_pc.svg test-data/abundances--T2h--cell--label-y_pc.svg test-data/abundances--T2h--cell_var.svg test-data/abundances--T2h--med--label-n_pc.svg test-data/abundances--T2h--med--label-y_pc.svg test-data/abundances--T2h--med_var.svg test-data/abundances--cell--label-n_pc.svg test-data/abundances--cell--label-y_pc.svg test-data/abundances--cell_var.svg test-data/abundances--med--label-n_pc.svg test-data/abundances--med--label-y_pc.svg test-data/abundances--med_var.svg test-data/bars_endo_Fru1P-total_abundance.svg test-data/legend.svg |
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added:
test-data/abundances--T0--cell_pc.tsv test-data/abundances--T0--cell_var.tsv test-data/abundances--T0--med_pc.tsv test-data/abundances--T0--med_var.tsv test-data/abundances--T2h--cell_pc.tsv test-data/abundances--T2h--cell_var.tsv test-data/abundances--T2h--med_pc.tsv test-data/abundances--T2h--med_var.tsv test-data/abundances--cell_pc.tsv test-data/abundances--cell_var.tsv test-data/abundances--med_pc.tsv test-data/abundances--med_var.tsv |
| b |
| diff -r 7897a5cadcf5 -r daefbae2aacf macros.xml --- a/macros.xml Mon Mar 04 20:02:11 2024 +0000 +++ b/macros.xml Wed Mar 27 16:47:56 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: |
| b |
| diff -r 7897a5cadcf5 -r daefbae2aacf test-data/abundances--T0--cell--label-n_pc.svg --- a/test-data/abundances--T0--cell--label-n_pc.svg Mon Mar 04 20:02:11 2024 +0000 +++ b/test-data/abundances--T0--cell--label-n_pc.svg Wed Mar 27 16:47:56 2024 +0000 |
| b |
| b'@@ -6,11 +6,11 @@\n <rdf:RDF xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:cc="http://creativecommons.org/ns#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">\n <cc:Work>\n <dc:type rdf:resource="http://purl.org/dc/dcmitype/StillImage"/>\n- <dc:date>2023-10-08T10:14:24.244122</dc:date>\n+ <dc:date>2024-03-26T10:28:20.939491</dc:date>\n <dc:format>image/svg+xml</dc:format>\n <dc:creator>\n <cc:Agent>\n- <dc:title>Matplotlib v3.7.3, https://matplotlib.org/</dc:title>\n+ <dc:title>Matplotlib v3.8.3, https://matplotlib.org/</dc:title>\n </cc:Agent>\n </dc:creator>\n </cc:Work>\n@@ -37,29 +37,26 @@\n z\n " style="fill: #ffffff"/>\n </g>\n- <g id="PathCollection_1"/>\n- <g id="PathCollection_2"/>\n- <g id="PathCollection_3"/>\n <g id="line2d_1">\n <path d="M 57.6 188.317452 \n L 414.72 188.317452 \n-" clip-path="url(#pd89567ce0b)" style="fill: none; stroke-dasharray: 5.55,2.4; stroke-dashoffset: 0; stroke: #808080; stroke-width: 1.5"/>\n+" clip-path="url(#pab131b2223)" style="fill: none; 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| b |
| diff -r 7897a5cadcf5 -r daefbae2aacf test-data/abundances--T0--cell--label-y_pc.svg --- a/test-data/abundances--T0--cell--label-y_pc.svg Mon Mar 04 20:02:11 2024 +0000 +++ b/test-data/abundances--T0--cell--label-y_pc.svg Wed Mar 27 16:47:56 2024 +0000 |
| b |
| b'@@ -6,11 +6,11 @@\n <rdf:RDF xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:cc="http://creativecommons.org/ns#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">\n <cc:Work>\n <dc:type rdf:resource="http://purl.org/dc/dcmitype/StillImage"/>\n- <dc:date>2023-10-08T10:14:24.195225</dc:date>\n+ <dc:date>2024-03-26T10:28:20.904175</dc:date>\n <dc:format>image/svg+xml</dc:format>\n <dc:creator>\n <cc:Agent>\n- <dc:title>Matplotlib v3.7.3, https://matplotlib.org/</dc:title>\n+ <dc:title>Matplotlib v3.8.3, https://matplotlib.org/</dc:title>\n </cc:Agent>\n </dc:creator>\n </cc:Work>\n@@ -37,29 +37,26 @@\n z\n " style="fill: #ffffff"/>\n </g>\n- <g id="PathCollection_1"/>\n- <g id="PathCollection_2"/>\n- <g id="PathCollection_3"/>\n <g id="line2d_1">\n <path d="M 57.6 188.317452 \n L 414.72 188.317452 \n-" clip-path="url(#pb6ed43a42b)" style="fill: none; stroke-dasharray: 5.55,2.4; stroke-dashoffset: 0; stroke: #808080; stroke-width: 1.5"/>\n+" clip-path="url(#p4516990cc5)" style="fill: none; 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| diff -r 7897a5cadcf5 -r daefbae2aacf test-data/abundances--T0--cell_var.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abundances--T0--cell_var.tsv Wed Mar 27 16:47:56 2024 +0000 |
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| @@ -0,0 +1,5 @@ +Explained Variance % PC +74.487179 PC1 +22.939254 PC2 +2.573566 PC3 +0.0 PC4 |
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| diff -r 7897a5cadcf5 -r daefbae2aacf test-data/abundances--T0--med_var.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abundances--T0--med_var.tsv Wed Mar 27 16:47:56 2024 +0000 |
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| @@ -0,0 +1,5 @@ +Explained Variance % PC +58.686028 PC1 +22.949429 PC2 +18.364542 PC3 +0.0 PC4 |
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| @@ -0,0 +1,5 @@ +PC1 PC2 PC3 PC4 name_to_plot condition timepoint timenum compartment original_name +3.418013 2.018827 -0.624963 0.0 Ctrl_cell_T2h-1 Control T2h 2 cell MCF001089_TD07 +-5.121119 -1.029264 -0.970952 0.0 Ctrl_cell_T2h-2 Control T2h 2 cell MCF001089_TD08 +5.604413 -1.686558 0.356619 0.0 L-Cyc_cell_T2h-1 L-Cycloserine T2h 2 cell MCF001089_TD25 +-3.901307 0.696996 1.239296 0.0 L-Cyc_cell_T2h-2 L-Cycloserine T2h 2 cell MCF001089_TD26 |
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| diff -r 7897a5cadcf5 -r daefbae2aacf test-data/abundances--T2h--cell_var.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abundances--T2h--cell_var.tsv Wed Mar 27 16:47:56 2024 +0000 |
| b |
| @@ -0,0 +1,5 @@ +Explained Variance % PC +88.060744 PC1 +8.81805 PC2 +3.121206 PC3 +0.0 PC4 |
| b |
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| @@ -0,0 +1,5 @@ +PC1 PC2 PC3 PC4 name_to_plot condition timepoint timenum compartment original_name +-3.78242 2.157774 0.512581 0.0 Ctrl_med_T2h-1 Control T2h 2 med MCF001089_TD43 +-3.977769 -1.955737 -0.734513 0.0 Ctrl_med_T2h-2 Control T2h 2 med MCF001089_TD44 +3.226932 -0.99365 1.522596 0.0 L-Cyc_med_T2h-1 L-Cycloserine T2h 2 med MCF001089_TD61 +4.533256 0.791612 -1.300663 0.0 L-Cyc_med_T2h-2 L-Cycloserine T2h 2 med MCF001089_TD62 |
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| diff -r 7897a5cadcf5 -r daefbae2aacf test-data/abundances--T2h--med_var.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abundances--T2h--med_var.tsv Wed Mar 27 16:47:56 2024 +0000 |
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| @@ -0,0 +1,5 @@ +Explained Variance % PC +80.38532 PC1 +13.282744 PC2 +6.331936 PC3 +0.0 PC4 |
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| diff -r 7897a5cadcf5 -r daefbae2aacf test-data/abundances--med_var.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abundances--med_var.tsv Wed Mar 27 16:47:56 2024 +0000 |
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| @@ -0,0 +1,9 @@ +Explained Variance % PC +62.995949 PC1 +13.724146 PC2 +10.351207 PC3 +6.560286 PC4 +3.031798 PC5 +2.187543 PC6 +1.149071 PC7 +0.0 PC8 |
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| b |
| diff -r 7897a5cadcf5 -r daefbae2aacf test-data/legend.svg --- a/test-data/legend.svg Mon Mar 04 20:02:11 2024 +0000 +++ b/test-data/legend.svg Wed Mar 27 16:47:56 2024 +0000 |
| b |
| @@ -6,11 +6,11 @@ <rdf:RDF xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:cc="http://creativecommons.org/ns#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <cc:Work> <dc:type rdf:resource="http://purl.org/dc/dcmitype/StillImage"/> - <dc:date>2023-10-08T10:14:52.311672</dc:date> + <dc:date>2024-03-26T10:26:04.837231</dc:date> <dc:format>image/svg+xml</dc:format> <dc:creator> <cc:Agent> - <dc:title>Matplotlib v3.7.3, https://matplotlib.org/</dc:title> + <dc:title>Matplotlib v3.8.3, https://matplotlib.org/</dc:title> </cc:Agent> </dc:creator> </cc:Work> |
