diff batch.xml @ 3:97d2b6742760 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 9d922676808c5f57e9c01b148eec6cc0a63c53e5

--- a/batch.xml	Mon Apr 22 17:44:06 2024 +0000
+++ b/batch.xml	Fri Dec 13 23:59:44 2024 +0000
@@ -147,16 +147,20 @@
     </outputs>
     <tests>
         <test expect_num_outputs="13">
-            <conditional name="reference_source">
-                <param name="ref_selector" value="history"/>
-                <param name="fasta" ftype="fasta" value="genome.fasta" />
+            <conditional name="CNV_reference">
+                <conditional name="reference_source">
+                    <param name="ref_selector" value="history"/>
+                    <param name="fasta" ftype="fasta" value="genome.fasta" />
+                </conditional>
+                <param name="CNV_reference_availabel" value="no" />
+                <param name="input_sample_file" ftype="bam" value="tumor.bam" />
+                <param name="normal" ftype="bam" value="normal.bam" />
+                <param name="targets" ftype="bed" value="capture.bed" />
             </conditional>
-            <param name="CNV_reference_availabel" value="no" />
-            <param name="input_sample_file" ftype="bam" value="tumor.bam" />
-            <param name="normal" ftype="bam" value="normal.bam" />
-            <param name="targets" ftype="bed" value="capture.bed" />
-            <param name="scatter" value="1"/>
-            <param name="diagram" value="1"/>
+            <section name="output_section">
+                <param name="scatter" value="1"/>
+                <param name="diagram" value="1"/>
+            </section>
             <output name="out_sample_bintest" file="tumor.bintest.cns" />
             <output name="out_sample_antitargetcoverage">
                 <assert_contents><has_text text="chromosome"/></assert_contents>
@@ -190,16 +194,20 @@
             </output>
         </test>
         <test expect_num_outputs="13">
-            <conditional name="reference_source">
-                <param name="ref_selector" value="cached"/>
-                <param name="fasta" value="test_buildid"/>
+            <conditional name="CNV_reference">
+                <conditional name="reference_source">
+                    <param name="ref_selector" value="cached"/>
+                    <param name="fasta" value="test_buildid"/>
+                </conditional>
+                <param name="CNV_reference_availabel" value="no" />
+                <param name="input_sample_file" ftype="bam" value="tumor.bam" />
+                <param name="normal" ftype="bam" value="normal.bam" />
+                <param name="targets" ftype="bed" value="capture.bed" />
             </conditional>
-            <param name="CNV_reference_availabel" value="no" />
-            <param name="input_sample_file" ftype="bam" value="tumor.bam" />
-            <param name="normal" ftype="bam" value="normal.bam" />
-            <param name="targets" ftype="bed" value="capture.bed" />
-            <param name="scatter" value="1"/>
-            <param name="diagram" value="1"/>
+            <section name="output_section">
+                <param name="scatter" value="1"/>
+                <param name="diagram" value="1"/>
+            </section>
             <output name="out_sample_bintest" file="tumor.bintest.cns" />
             <output name="out_sample_antitargetcoverage">
                 <assert_contents><has_text text="chromosome"/></assert_contents>
@@ -233,11 +241,15 @@
             </output>
         </test>
         <test expect_num_outputs="10">
-            <param name="CNV_reference_availabel" value="yes" />
-            <param name="input_sample_file" ftype="bam" value="tumor.bam" />
-            <param name="reference" ftype="tabular" value="reference.cnn" />
-            <param name="scatter" value="1"/>
-            <param name="diagram" value="1"/>
+            <conditional name="CNV_reference">
+                <param name="CNV_reference_availabel" value="yes" />
+                <param name="input_sample_file" ftype="bam" value="tumor.bam" />
+                <param name="reference" ftype="tabular" value="reference.cnn" />
+            </conditional>
+            <section name="output_section">
+                <param name="scatter" value="1"/>
+                <param name="diagram" value="1"/>
+            </section>
             <output name="out_sample_bintest" file="tumor.bintest.cns" />
             <output name="out_sample_antitargetcoverage">
                 <assert_contents><has_text text="chromosome"/></assert_contents>