--- a/ml_visualization_ex.xml	Thu Aug 11 09:29:32 2022 +0000
+++ b/ml_visualization_ex.xml	Wed Aug 09 13:08:43 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="ml_visualization_ex" name="Machine Learning Visualization Extension" version="@VERSION@" profile="20.05">
+<tool id="ml_visualization_ex" name="Machine Learning Visualization Extension" version="@VERSION@" profile="@PROFILE@">
     <description>includes several types of plotting for machine learning</description>
     <macros>
         <import>main_macros.xml</import>
@@ -21,11 +21,6 @@
             --infile1 '$plotting_selection.infile1'
             #elif $plotting_selection.plot_type == 'keras_plot_model'
             --model_config '$plotting_selection.infile_model_config'
-            #elif $plotting_selection.plot_type == 'classification_confusion_matrix'
-            --true_labels '$plotting_selection.infile_true'
-            --predicted_labels '$plotting_selection.infile_predicted'
-            --plot_color '$plotting_selection.plot_color'
-            --title '$plotting_selection.title'
             #end if
         ]]>
     </command>
@@ -41,7 +36,6 @@
                 <option value="rfecv_gridscores">Number of features vs. Recursive Feature Elimination gridscores with corss-validation</option>
                 <option value="feature_importances">Feature Importances plot</option>
                 <option value="keras_plot_model">keras plot model - plot configuration of a neural network model</option>
-                <option value="classification_confusion_matrix">Confusion matrix for classes</option>
             </param>
             <when value="learning_curve">
                 <param name="infile1" type="data" format="tabular" label="Select the dataset containing values for plotting learning curve." help="This dataset should be the output of tool model_validation->learning_curve." />
@@ -85,7 +79,7 @@
                 </param>
             </when>
             <when value="feature_importances">
-                <param name="infile_estimator" type="data" format="zip" label="Select the dataset containing fitted estimator/pipeline" />
+                <param name="infile_estimator" type="data" format="h5mlm" label="Select the dataset containing fitted estimator/pipeline" />
                 <param name="infile1" type="data" format="tabular" label="Select the dataset containing feature names" help="Make sure the headers (first row) are feature names." />
                 <conditional name="column_selector_options">
                     <expand macro="samples_column_selector_options" multiple="true" />
@@ -102,32 +96,6 @@
                 <param name="title" type="hidden" value="" optional="true" label="Plot title" help="Optional. If change is desired." />
                 <param name="plot_format" type="hidden" value="png" label="The output format and library" />
             </when>
-
-            <when value="classification_confusion_matrix">
-                <param name="infile_true" type="data" format="tabular" label="Select dataset containing true labels" />
-                <param name="header_true" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Does the dataset contain header:" />
-                <conditional name="column_selector_options_true">
-                    <expand macro="samples_column_selector_options" multiple="true" column_option="selected_column_selector_option" col_name="col1" infile="infile_true" />
-                </conditional>
-
-                <param name="infile_predicted" type="data" format="tabular" label="Select dataset containing predicted labels" />
-                <param name="header_predicted" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Does the dataset contain header:" />
-                <param name="title" type="text" value="Confusion matrix between true and predicted labels" label="Plot title" />
-                <param name="plot_format" type="hidden" value="png" label="The output format and library" />
-                <param name="plot_color" type="select" label="Choose plot color">
-                    <option value="Greys">Greys</option>
-                    <option value="Purples">Purples</option>
-                    <option value="Blues">Blues</option>
-                    <option value="Greens" selected="true">Greens</option>
-                    <option value="Oranges">Oranges</option>
-                    <option value="Reds">Reds</option>
-                    <option value="Summer">Summer</option>
-                    <option value="Autumn">Autumn</option>
-                    <option value="RdYlGn">RdYlGn</option>
-                    <option value="Spectral">Spectral</option>
-                    <option value="winter">winter</option>
-                </param>
-            </when>
         </conditional>
     </inputs>
     <outputs>
@@ -146,7 +114,7 @@
         </test>
         <test>
             <param name="plot_type" value="feature_importances" />
-            <param name="infile_estimator" value="best_estimator_.zip" ftype="zip" />
+            <param name="infile_estimator" value="best_estimator_.h5mlm" ftype="h5mlm" />
             <param name="infile1" value="regression_X.tabular" ftype="tabular" />
             <param name="selected_column_selector_option" value="all_columns" />
             <output name="output" file="ml_vis01.html" compare="sim_size" />
@@ -172,28 +140,6 @@
             <param name="infile_model_config" value="deepsear_1feature.json" ftype="json" />
             <output name="output" file="ml_vis05.png" compare="sim_size" delta="20000" />
         </test>
-        <test>
-            <param name="plot_type" value="classification_confusion_matrix" />
-            <param name="infile_true" value="ml_confusion_true.tabular" ftype="tabular" />
-            <param name="header_true" value="False" />
-            <param name="selected_column_selector_option" value="all_columns" />
-            <param name="infile_predicted" value="ml_confusion_predicted.tabular" ftype="tabular" />
-            <param name="header_predicted" value="False" />
-            <param name="title" value="Confusion matrix" />
-            <param name="plot_color" value="winter" />
-            <output name="output" file="ml_confusion_viz.png" compare="sim_size" />
-        </test>
-        <test>
-            <param name="plot_type" value="classification_confusion_matrix" />
-            <param name="infile_true" value="true_header.tabular" ftype="tabular" />
-            <param name="header_true" value="True" />
-            <param name="selected_column_selector_option" value="all_columns" />
-            <param name="infile_predicted" value="predicted_header.tabular" ftype="tabular" />
-            <param name="header_predicted" value="True" />
-            <param name="title" value="Confusion matrix" />
-            <param name="plot_color" value="winter" />
-            <output name="output" file="ml_confusion_viz.png" compare="sim_size" />
-        </test>
     </tests>
     <help>
         <![CDATA[