changeset 4:3b9226db8ab6 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit afc87f0254b4399b71e53735966032ba1a32434d
author iuc
date Wed, 27 Mar 2024 16:48:52 +0000
parents 04c26050d2d0
children 06b6d0c16833
files dimet_pca_analysis.xml 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_pc.tsv test-data/abundances--T0--cell_var.svg test-data/abundances--T0--cell_var.tsv test-data/abundances--T0--med--label-n_pc.svg test-data/abundances--T0--med--label-y_pc.svg test-data/abundances--T0--med_pc.tsv test-data/abundances--T0--med_var.svg test-data/abundances--T0--med_var.tsv test-data/abundances--T2h--cell--label-n_pc.svg test-data/abundances--T2h--cell--label-y_pc.svg test-data/abundances--T2h--cell_pc.tsv test-data/abundances--T2h--cell_var.svg test-data/abundances--T2h--cell_var.tsv test-data/abundances--T2h--med--label-n_pc.svg test-data/abundances--T2h--med--label-y_pc.svg test-data/abundances--T2h--med_pc.tsv test-data/abundances--T2h--med_var.svg test-data/abundances--T2h--med_var.tsv test-data/abundances--cell--label-n_pc.svg test-data/abundances--cell--label-y_pc.svg test-data/abundances--cell_pc.tsv test-data/abundances--cell_var.svg test-data/abundances--cell_var.tsv test-data/abundances--med--label-n_pc.svg test-data/abundances--med--label-y_pc.svg test-data/abundances--med_pc.tsv test-data/abundances--med_var.svg test-data/abundances--med_var.tsv test-data/bars_endo_Fru1P-total_abundance.svg test-data/legend.svg
diffstat 34 files changed, 1265 insertions(+), 1121 deletions(-) [+]
line wrap: on
line diff
--- 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:
--- 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:type rdf:resource="http://purl.org/dc/dcmitype/StillImage"/>
-    <dc:date>2023-10-08T10:14:24.244122</dc:date>
+    <dc:date>2024-03-26T10:28:20.939491</dc:date>
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      <cc:Agent>
-      <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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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/abundances--T0--cell_pc.tsv	Wed Mar 27 16:48:52 2024 +0000
@@ -0,0 +1,5 @@
+PC1	PC2	PC3	PC4	name_to_plot	condition	timepoint	timenum	compartment	original_name
+-4.612574	-2.881005	-0.432059	0.0	Ctrl_cell_T0-1	Control	T0	0	cell	MCF001089_TD01
+-3.303276	3.622393	-0.061907	0.0	Ctrl_cell_T0-2	Control	T0	0	cell	MCF001089_TD02
+1.95919	-0.773766	1.28576	0.0	L-Cyc_cell_T0-1	L-Cycloserine	T0	0	cell	MCF001089_TD19
+5.95666	0.032379	-0.791794	0.0	L-Cyc_cell_T0-2	L-Cycloserine	T0	0	cell	MCF001089_TD20
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/abundances--T0--cell_var.tsv	Wed Mar 27 16:48:52 2024 +0000
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--- /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
@@ -0,0 +1,5 @@
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+-3.647549	-2.371648	-1.342906	0.0	Ctrl_med_T0-1	Control	T0	0	med	MCF001089_TD37
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+1.229634	-1.039134	3.021683	0.0	L-Cyc_med_T0-2	L-Cycloserine	T0	0	med	MCF001089_TD56
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/abundances--T0--med_var.tsv	Wed Mar 27 16:48:52 2024 +0000
@@ -0,0 +1,5 @@
+Explained Variance %	PC
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+++ b/test-data/abundances--T2h--cell_pc.tsv	Wed Mar 27 16:48:52 2024 +0000
@@ -0,0 +1,5 @@
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+++ b/test-data/abundances--T2h--cell_var.tsv	Wed Mar 27 16:48:52 2024 +0000
@@ -0,0 +1,5 @@
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+++ b/test-data/abundances--T2h--med_pc.tsv	Wed Mar 27 16:48:52 2024 +0000
@@ -0,0 +1,5 @@
+PC1	PC2	PC3	PC4	name_to_plot	condition	timepoint	timenum	compartment	original_name
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+++ b/test-data/abundances--T2h--med_var.tsv	Wed Mar 27 16:48:52 2024 +0000
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+++ b/test-data/abundances--cell_pc.tsv	Wed Mar 27 16:48:52 2024 +0000
@@ -0,0 +1,9 @@
+PC1	PC2	PC3	PC4	PC5	PC6	PC7	PC8	name_to_plot	condition	timepoint	timenum	compartment	original_name
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+++ b/test-data/abundances--cell_var.tsv	Wed Mar 27 16:48:52 2024 +0000
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+Explained Variance %	PC
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+Explained Variance %	PC
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+   <g id="patch_8">
+    <path d="M 51.885312 311.770896 
+L 222.580312 311.770896 
 " style="fill: none; stroke: #000000; stroke-width: 0.8; stroke-linejoin: miter; stroke-linecap: square"/>
    </g>
    <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>
       <path id="DejaVuSans-46" d="M 628 4666 
 L 3309 4666 
@@ -734,13 +738,13 @@
      <use xlink:href="#DejaVuSans-50" x="218.384766"/>
     </g>
     <!--  -->
-    <g transform="translate(128.318125 54.56655) scale(0.252 -0.252)"/>
+    <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>
--- 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 @@
   <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>