--- a/macros.xml	Mon Jun 30 17:19:21 2025 +0000
+++ b/macros.xml	Fri Jul 04 14:57:52 2025 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">0.2.20</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@VERSION_SUFFIX@">2</token>
     <token name="@PROFILE@">24.1</token>
     <xml name="requirements">
         <requirements>
@@ -49,17 +49,17 @@
         </param>
     </xml>
     <xml name="main_inputs">
-        <param name="train_clin" type="data" format="csv" label="Training clinical data"/>
-        <param name="test_clin" type="data" format="csv" label="Test clinical data"/>
-        <param name="train_omics_main" type="data" format="csv" label="Training omics data"/>
-        <param name="test_omics_main" type="data" format="csv" label="Test omics data"/>
+        <param name="train_clin" type="data" format="tabular" label="Training clinical data"/>
+        <param name="test_clin" type="data" format="tabular" label="Test clinical data"/>
+        <param name="train_omics_main" type="data" format="tabular" label="Training omics data"/>
+        <param name="test_omics_main" type="data" format="tabular" label="Test omics data"/>
         <param name="assay_main" type="text" optional="true" label="What type of assay is your input?" help="This would be used as output name.">
             <expand macro="sanitizer_letters"/>
         </param>
     </xml>
     <xml name="extra_inputs">
-        <param name="train_omics" type="data" optional="true" format="csv" label="Training omics data"/>
-        <param name="test_omics" type="data" optional="true" format="csv" label="Test omics data"/>
+        <param name="train_omics" type="data" optional="true" format="tabular" label="Training omics data"/>
+        <param name="test_omics" type="data" optional="true" format="tabular" label="Test omics data"/>
         <param name="assay" type="text" optional="true" label="What type of assay is your input?" help="This would be used as output name." >
             <expand macro="sanitizer_letters"/>
         </param>
@@ -103,7 +103,7 @@
     </xml>
     <xml name="plots_common_input">
         <yield/>
-        <param argument="--labels" type="data" format="tabular,csv" label="Predicted labels" help="Generated by flexynesis"/>
+        <param argument="--labels" type="data" format="tabular" label="Predicted labels" help="Generated by flexynesis"/>
     </xml>
     <token name="@PLOT_COMMON_CONFIG@"><![CDATA[
 label_data = load_labels('inputs/$plot_conditional.labels.element_identifier.$plot_conditional.labels.ext')
@@ -216,22 +216,24 @@
         <param name="non_commercial_use" value="True"/>
         <conditional name="training_type">
             <param name="model" value="s_train"/>
-            <param name="train_clin" value="train/clin" ftype="csv"/>
-            <param name="test_clin" value="test/clin" ftype="csv"/>
-            <param name="train_omics_main" value="train/gex" ftype="csv"/>
-            <param name="test_omics_main" value="test/gex" ftype="csv"/>
+            <param name="train_clin" value="train/clin" ftype="tabular"/>
+            <param name="test_clin" value="test/clin" ftype="tabular"/>
+            <param name="train_omics_main" value="train/gex" ftype="tabular"/>
+            <param name="test_omics_main" value="test/gex" ftype="tabular"/>
             <param name="assay_main" value="bar"/>
             <repeat name="omics">
-                <param name="train_omics" value="train/cnv" ftype="csv"/>
-                <param name="test_omics" value="test/cnv" ftype="csv"/>
+                <param name="train_omics" value="train/cnv" ftype="tabular"/>
+                <param name="test_omics" value="test/cnv" ftype="tabular"/>
                 <param name="assay" value="foo"/>
             </repeat>
             <conditional name="model_class">
                 <param name="model_class" value="DirectPred"/>
             </conditional>
-            <param name="target_variables" value="Erlotinib"/>
-            <param name="surv_event_var" value="OS_STATUS"/>
-            <param name="surv_time_var" value="OS_MONTHS"/>
+            <repeat name="targets">
+                <param name="target_variables" value="3"/>
+            </repeat>
+            <param name="surv_event_var" value="15"/>
+            <param name="surv_time_var" value="14"/>
             <section name="advanced">
                 <param name="hpo_iter" value="1"/>
             </section>
@@ -250,15 +252,15 @@
             </element>
             <element name="job.feature_importance.GradientShap">
                 <assert_contents>
-                    <has_text_matching expression="Erlotinib,0,,bar,A2M,"/>
-                    <has_text_matching expression="Erlotinib,0,,bar,ABCC4,"/>
+                    <has_text_matching expression="Erlotinib\t0\t\tbar\tA2M\t"/>
+                    <has_text_matching expression="Erlotinib\t0\t\tbar\tABCC4\t"/>
                     <has_text_matching expression="GradientShap"/>
                 </assert_contents>
             </element>
             <element name="job.feature_importance.IntegratedGradients">
                 <assert_contents>
-                    <has_text_matching expression="Erlotinib,0,,bar,A2M,"/>
-                    <has_text_matching expression="Erlotinib,0,,bar,ABCC4,"/>
+                    <has_text_matching expression="Erlotinib\t0\t\tbar\tA2M\t"/>
+                    <has_text_matching expression="Erlotinib\t0\t\tbar\tABCC4\t"/>
                     <has_text_matching expression="IntegratedGradients"/>
                 </assert_contents>
             </element>
@@ -274,15 +276,15 @@
             </element>
             <element name="job.predicted_labels">
                 <assert_contents>
-                    <has_text_matching expression="source_dataset:A-704,Erlotinib,"/>
-                    <has_text_matching expression="target_dataset:KMRC-20,Erlotinib,"/>
+                    <has_text_matching expression="source_dataset:A-704\tErlotinib\t"/>
+                    <has_text_matching expression="target_dataset:KMRC-20\tErlotinib\t"/>
                 </assert_contents>
             </element>
             <element name="job.stats">
                 <assert_contents>
-                    <has_text_matching expression="DirectPred,Erlotinib,numerical,mse,"/>
-                    <has_text_matching expression="DirectPred,Erlotinib,numerical,r2,"/>
-                    <has_text_matching expression="DirectPred,Erlotinib,numerical,pearson_corr,"/>
+                    <has_text_matching expression="DirectPred\tErlotinib\tnumerical\tmse\t"/>
+                    <has_text_matching expression="DirectPred\tErlotinib\tnumerical\tr2\t"/>
+                    <has_text_matching expression="DirectPred\tErlotinib\tnumerical\tpearson_corr\t"/>
                 </assert_contents>
             </element>
         </output_collection>