Mercurial > repos > bgruening > flexynesis_plot

diff macros.xml @ 3:52b6f2ac38c7 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
author bgruening
date Wed, 23 Jul 2025 07:49:52 +0000
parents 3c5d82bf6e8a
children
line wrap: on
line diff
--- a/macros.xml	Fri Jul 04 14:57:52 2025 +0000
+++ b/macros.xml	Wed Jul 23 07:49:52 2025 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">0.2.20</token>
-    <token name="@VERSION_SUFFIX@">2</token>
+    <token name="@VERSION_SUFFIX@">3</token>
     <token name="@PROFILE@">24.1</token>
     <xml name="requirements">
         <requirements>
@@ -91,14 +91,24 @@
             </param>
         </section>
     </xml>
-    <xml name="plots_common_param">
-        <yield/>
+    <xml name="plots_common_format">
         <param name="format" type="select" label="Output format">
             <option value="jpg" selected="true">jpg</option>
             <option value="png">png</option>
             <option value="pdf">pdf</option>
+            <yield/>
+        </param>
+    </xml>
+    <xml name="plots_common_param">
+        <yield/>
+        <expand macro="plots_common_format"/>
+        <param name="dpi" type="integer" min="0" max="1200" value="300" label="DPI"/>
+    </xml>
+    <xml name="plots_common_param_svg">
+        <yield/>
+        <expand macro="plots_common_format">
             <option value="svg">svg</option>
-        </param>
+        </expand>
         <param name="dpi" type="integer" min="0" max="1200" value="300" label="DPI"/>
     </xml>
     <xml name="plots_common_input">
@@ -229,16 +239,14 @@
             <conditional name="model_class">
                 <param name="model_class" value="DirectPred"/>
             </conditional>
-            <repeat name="targets">
-                <param name="target_variables" value="3"/>
-            </repeat>
+            <param name="target_variables" value="3"/>
             <param name="surv_event_var" value="15"/>
             <param name="surv_time_var" value="14"/>
             <section name="advanced">
                 <param name="hpo_iter" value="1"/>
             </section>
+            <yield/>
         </conditional>
-        <yield/>
         <output_collection name="results" type="list">
             <element name="job.embeddings_test">
                 <assert_contents>
@@ -269,7 +277,7 @@
                     <has_n_lines n="25"/>
                 </assert_contents>
             </element>
-            <element name="job.feature_logs.omics_foo">
+            <element name="job.feature_logs.foo">
                 <assert_contents>
                     <has_n_lines n="25"/>
                 </assert_contents>
@@ -289,6 +297,81 @@
             </element>
         </output_collection>
     </xml>
+    <xml name="common_test_class">
+        <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="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="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="16"/>
+            <param name="surv_event_var" value="15"/>
+            <param name="surv_time_var" value="14"/>
+            <section name="advanced">
+                <param name="hpo_iter" value="1"/>
+            </section>
+            <yield/>
+        </conditional>
+        <output_collection name="results" type="list">
+            <element name="job.embeddings_test">
+                <assert_contents>
+                    <has_n_lines n="50"/>
+                </assert_contents>
+            </element>
+            <element name="job.embeddings_train">
+                <assert_contents>
+                    <has_n_lines n="50"/>
+                </assert_contents>
+            </element>
+            <element name="job.feature_importance.GradientShap">
+                <assert_contents>
+                    <has_text_matching expression="class\t0\tbuz\tbar\tA2M\t"/>
+                    <has_text_matching expression="class\t0\tbuz\tbar\tABCC4\t"/>
+                    <has_text_matching expression="GradientShap"/>
+                </assert_contents>
+            </element>
+            <element name="job.feature_importance.IntegratedGradients">
+                <assert_contents>
+                    <has_text_matching expression="class\t0\tbuz\tbar\tA2M\t"/>
+                    <has_text_matching expression="class\t0\tbuz\tbar\tABCC4\t"/>
+                    <has_text_matching expression="IntegratedGradients"/>
+                </assert_contents>
+            </element>
+            <element name="job.feature_logs.bar">
+                <assert_contents>
+                    <has_n_lines n="25"/>
+                </assert_contents>
+            </element>
+            <element name="job.feature_logs.foo">
+                <assert_contents>
+                    <has_n_lines n="25"/>
+                </assert_contents>
+            </element>
+            <element name="job.predicted_labels">
+                <assert_contents>
+                    <has_text_matching expression="source_dataset:A-704\tclass\t"/>
+                    <has_text_matching expression="target_dataset:KMRC-20\tclass\t"/>
+                </assert_contents>
+            </element>
+            <element name="job.stats">
+                <assert_contents>
+                    <has_text_matching expression="DirectPred\tclass\tcategorical\tbalanced_acc\t"/>
+                    <has_text_matching expression="DirectPred\tclass\tcategorical\tf1_score\t"/>
+                    <has_text_matching expression="DirectPred\tclass\tcategorical\taverage_auroc\t"/>
+                </assert_contents>
+            </element>
+        </output_collection>
+    </xml>
     <token name="@COMMON_HELP@">
 
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