# HG changeset patch
# User iuc
# Date 1711558132 0
# Node ID 3b9226db8ab644572ab9cb3aa986eaefbdd966f0
# Parent  04c26050d2d08920b5a6d89772b07db696f71ef5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit afc87f0254b4399b71e53735966032ba1a32434d

diff -r 04c26050d2d0 -r 3b9226db8ab6 dimet_pca_analysis.xml
--- 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>
diff -r 04c26050d2d0 -r 3b9226db8ab6 macros.xml
--- 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:
diff -r 04c26050d2d0 -r 3b9226db8ab6 test-data/abundances--T0--cell--label-n_pc.svg
--- a/test-data/abundances--T0--cell--label-n_pc.svg	Mon Mar 04 19:58:22 2024 +0000
+++ b/test-data/abundances--T0--cell--label-n_pc.svg	Wed Mar 27 16:48:52 2024 +0000
@@ -6,11 +6,11 @@
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-    <dc:date>2023-10-08T10:14:24.244122</dc:date>
+    <dc:date>2024-03-26T10:28:20.939491</dc:date>
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     <dc:creator>
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-      <dc:title>Matplotlib v3.7.3, https://matplotlib.org/</dc:title>
+      <dc:title>Matplotlib v3.8.3, https://matplotlib.org/</dc:title>
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@@ -37,29 +37,26 @@
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diff -r 04c26050d2d0 -r 3b9226db8ab6 test-data/abundances--T0--cell_pc.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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+PC1	PC2	PC3	PC4	name_to_plot	condition	timepoint	timenum	compartment	original_name
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+5.95666	0.032379	-0.791794	0.0	L-Cyc_cell_T0-2	L-Cycloserine	T0	0	cell	MCF001089_TD20
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diff -r 04c26050d2d0 -r 3b9226db8ab6 test-data/abundances--T0--cell_var.tsv
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diff -r 04c26050d2d0 -r 3b9226db8ab6 test-data/abundances--T0--med_pc.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/abundances--T0--med_pc.tsv	Wed Mar 27 16:48:52 2024 +0000
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diff -r 04c26050d2d0 -r 3b9226db8ab6 test-data/abundances--T0--med_var.tsv
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diff -r 04c26050d2d0 -r 3b9226db8ab6 test-data/abundances--T2h--med_pc.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/abundances--T2h--med_pc.tsv	Wed Mar 27 16:48:52 2024 +0000
@@ -0,0 +1,5 @@
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diff -r 04c26050d2d0 -r 3b9226db8ab6 test-data/abundances--T2h--med_var.tsv
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diff -r 04c26050d2d0 -r 3b9226db8ab6 test-data/abundances--cell_pc.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/abundances--cell_pc.tsv	Wed Mar 27 16:48:52 2024 +0000
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+PC1	PC2	PC3	PC4	PC5	PC6	PC7	PC8	name_to_plot	condition	timepoint	timenum	compartment	original_name
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diff -r 04c26050d2d0 -r 3b9226db8ab6 test-data/abundances--cell_var.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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diff -r 04c26050d2d0 -r 3b9226db8ab6 test-data/abundances--med_pc.tsv
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diff -r 04c26050d2d0 -r 3b9226db8ab6 test-data/abundances--med_var.svg
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diff -r 04c26050d2d0 -r 3b9226db8ab6 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 16:48:52 2024 +0000
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+Explained Variance %	PC
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+L 171.371813 123.318922 
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+L 176.492662 123.318922 
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-   <g id="patch_5">
-    <path d="M 34.240625 355.809449 
-L 34.240625 60.56655 
+   <g id="patch_7">
+    <path d="M 51.885313 311.770896 
+L 51.885313 60.56655 
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-   <g id="patch_6">
-    <path d="M 34.240625 355.809449 
-L 222.395625 355.809449 
+   <g id="patch_8">
+    <path d="M 51.885312 311.770896 
+L 222.580312 311.770896 
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    <g id="text_9">
     <!-- Fru1P -->
-    <g transform="translate(93.205469 26.348063) scale(0.252 -0.252)">
+    <g transform="translate(102.120156 26.348062) scale(0.252 -0.252)">
      <defs>
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-    <g transform="translate(128.318125 54.56655) scale(0.252 -0.252)"/>
+    <g transform="translate(137.232812 54.56655) scale(0.252 -0.252)"/>
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+  <clipPath id="p6ced50d961">
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diff -r 04c26050d2d0 -r 3b9226db8ab6 test-data/legend.svg
--- a/test-data/legend.svg	Mon Mar 04 19:58:22 2024 +0000
+++ b/test-data/legend.svg	Wed Mar 27 16:48:52 2024 +0000
@@ -6,11 +6,11 @@
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-    <dc:date>2023-10-08T10:14:52.311672</dc:date>
+    <dc:date>2024-03-26T10:26:04.837231</dc:date>
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     <dc:creator>
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-      <dc:title>Matplotlib v3.7.3, https://matplotlib.org/</dc:title>
+      <dc:title>Matplotlib v3.8.3, https://matplotlib.org/</dc:title>
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    </cc:Work>