# HG changeset patch
# User iuc
# Date 1711557978 0
# Node ID e814718ecb074ce3c76494b2167d1a6bfc989a74
# Parent  b856fcb1346e348aa7a41ff4d5c9289b88b91823
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit afc87f0254b4399b71e53735966032ba1a32434d

diff -r b856fcb1346e -r e814718ecb07 macros.xml
--- a/macros.xml	Mon Mar 04 19:57:45 2024 +0000
+++ b/macros.xml	Wed Mar 27 16:46:18 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 b856fcb1346e -r e814718ecb07 test-data/abundances--T0--cell--label-n_pc.svg
--- a/test-data/abundances--T0--cell--label-n_pc.svg	Mon Mar 04 19:57:45 2024 +0000
+++ b/test-data/abundances--T0--cell--label-n_pc.svg	Wed Mar 27 16:46:18 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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diff -r b856fcb1346e -r e814718ecb07 test-data/abundances--T0--cell_pc.tsv
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diff -r b856fcb1346e -r e814718ecb07 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 16:46:18 2024 +0000
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+PC1	PC2	PC3	PC4	name_to_plot	condition	timepoint	timenum	compartment	original_name
+-3.647549	-2.371648	-1.342906	0.0	Ctrl_med_T0-1	Control	T0	0	med	MCF001089_TD37
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+4.873764	0.136899	-1.737705	0.0	L-Cyc_med_T0-1	L-Cycloserine	T0	0	med	MCF001089_TD55
+1.229634	-1.039134	3.021683	0.0	L-Cyc_med_T0-2	L-Cycloserine	T0	0	med	MCF001089_TD56
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diff -r b856fcb1346e -r e814718ecb07 test-data/abundances--T0--med_var.tsv
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+++ b/test-data/abundances--T0--med_var.tsv	Wed Mar 27 16:46:18 2024 +0000
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diff -r b856fcb1346e -r e814718ecb07 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 16:46:18 2024 +0000
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+PC1	PC2	PC3	PC4	name_to_plot	condition	timepoint	timenum	compartment	original_name
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diff -r b856fcb1346e -r e814718ecb07 test-data/abundances--cell_var.tsv
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+Explained Variance %	PC
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diff -r b856fcb1346e -r e814718ecb07 test-data/abundances--med_pc.tsv
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diff -r b856fcb1346e -r e814718ecb07 test-data/abundances--med_var.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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+Explained Variance %	PC
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+    <g transform="translate(137.232812 54.56655) scale(0.252 -0.252)"/>
    </g>
   </g>
  </g>
  <defs>
-  <clipPath id="pdc3a65a28b">
-   <rect x="34.240625" y="60.56655" width="188.155" height="295.242899"/>
+  <clipPath id="p6ced50d961">
+   <rect x="51.885313" y="60.56655" width="170.695" height="251.204346"/>
   </clipPath>
  </defs>
 </svg>
diff -r b856fcb1346e -r e814718ecb07 test-data/legend.svg
--- a/test-data/legend.svg	Mon Mar 04 19:57:45 2024 +0000
+++ b/test-data/legend.svg	Wed Mar 27 16:46:18 2024 +0000
@@ -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>