# HG changeset patch
# User iuc
# Date 1734133926 0
# Node ID b551442cf2a0c14e8cb9f187a035a3a00e0575bf
# Parent  a7beca110b848e72b639ce671ff6652db3d195d1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 9d922676808c5f57e9c01b148eec6cc0a63c53e5

diff -r a7beca110b84 -r b551442cf2a0 macros.xml
--- a/macros.xml	Fri Sep 29 15:31:52 2023 +0000
+++ b/macros.xml	Fri Dec 13 23:52:06 2024 +0000
@@ -1,10 +1,10 @@
 <macros>
-    <token name="@VERSION_SUFFIX@">0.1</token>
-    <token name="@TOOL_VERSION@">0.9.10</token>
+    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@TOOL_VERSION@">0.9.11</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">cnvkit</requirement>
-            <requirement type="package" version="1.0.2">scikit-learn</requirement>
+            <requirement type="package" version="1.4.2">scikit-learn</requirement>
         </requirements>
     </xml>
     <xml name="reference_interface">
diff -r a7beca110b84 -r b551442cf2a0 reference.xml
--- a/reference.xml	Fri Sep 29 15:31:52 2023 +0000
+++ b/reference.xml	Fri Dec 13 23:52:06 2024 +0000
@@ -98,60 +98,90 @@
     </outputs>
     <tests>
         <test expect_num_outputs="1">
-            <conditional name="reference_source">
-                <param name="ref_selector" value="history"/>
-                <param name="fasta" ftype="fasta" value="genome.fasta" />
+            <conditional name="CNV_reference">
+                <param name="CNV_reference_availabel" value="yes" />
+                <section name="advanced_settings">
+                    <conditional name="reference_source">
+                        <param name="ref_selector" value="history"/>
+                        <param name="fasta" ftype="fasta" value="genome.fasta" />
+                    </conditional>
+                </section>
+                <param name="input_cnn_file" ftype="tabular" value="tumor.targetcoverage.cnn" />
+                <section name="disable_some_of_the_bias_corrections">
+                    <param name="no_gc" value="1" />
+                </section>
             </conditional>
-            <param name="CNV_reference_availabel" value="yes" />
-            <param name="input_cnn_file" ftype="tabular" value="tumor.targetcoverage.cnn" />
-            <param name="no_gc" value="1" />
             <output name="out_referene_tas" file="ref-tas.cnn" /> 
         </test>
         <test expect_num_outputs="1">
-            <conditional name="reference_source">
-                <param name="ref_selector" value="cached"/>
-                <param name="fasta" value="test_buildid"/>
+            <conditional name="CNV_reference">
+                <param name="CNV_reference_availabel" value="yes" />
+                <section name="advanced_settings">
+                    <conditional name="reference_source">
+                        <param name="ref_selector" value="cached"/>
+                        <param name="fasta" value="test_buildid"/>
+                    </conditional>
+                </section>
+                <param name="input_cnn_file" ftype="tabular" value="tumor.targetcoverage.cnn" />
+                <section name="disable_some_of_the_bias_corrections">
+                    <param name="no_gc" value="1" />    
+                </section>
             </conditional>
-            <param name="CNV_reference_availabel" value="yes" />
-            <param name="input_cnn_file" ftype="tabular" value="tumor.targetcoverage.cnn" />
-            <param name="no_gc" value="1" />
             <output name="out_referene_tas" file="ref-tas.cnn" />
         </test>
         <test expect_num_outputs="1">
-            <conditional name="reference_source">
-                <param name="ref_selector" value="cached"/>
-                <param name="fasta" value="test_buildid"/>
+            <conditional name="CNV_reference">
+                <param name="CNV_reference_availabel" value="yes" />
+                <section name="advanced_settings">
+                    <conditional name="reference_source">
+                        <param name="ref_selector" value="cached"/>
+                        <param name="fasta" value="test_buildid"/>
+                    </conditional>
+                </section>
+                <param name="input_cnn_file" ftype="tabular" value="tumor.targetcoverage.cnn,test.targetcoverage.cnn" />
+                <section name="disable_some_of_the_bias_corrections">
+                    <param name="no_gc" value="1" />
+                </section>
             </conditional>
-            <param name="CNV_reference_availabel" value="yes" />
-            <param name="input_cnn_file" ftype="tabular" value="tumor.targetcoverage.cnn,test.targetcoverage.cnn" />
-            <param name="no_gc" value="1" />
             <output name="out_referene_tas">
                 <assert_contents><has_text text="chromosome"/></assert_contents>
             </output>
         </test>
         <test expect_num_outputs="1">
-            <conditional name="reference_source">
-                <param name="ref_selector" value="cached"/>
-                <param name="fasta" value="test_buildid"/>
+            <conditional name="CNV_reference">
+                <param name="CNV_reference_availabel" value="no" />
+                <section name="advanced_settings">
+                    <conditional name="reference_source">
+                        <param name="ref_selector" value="cached"/>
+                        <param name="fasta" value="test_buildid"/>
+                    </conditional>
+                </section>
+                <param name="targets" ftype="bed" value="capture.target.bed" />
+                <section name="disable_some_of_the_bias_corrections">
+                    <param name="no_gc" value="1" />
+                </section>
             </conditional>
-            <param name="CNV_reference_availabel" value="no" />
-            <param name="targets" ftype="bed" value="capture.target.bed" />
-            <param name="no_gc" value="1" />
             <output name="out_referene_tas">
                 <assert_contents><has_text text="chromosome"/></assert_contents>
             </output>
         </test>
         <test expect_num_outputs="1">
-            <conditional name="reference_source">
-                <param name="ref_selector" value="cached"/>
-                <param name="fasta" value="test_buildid"/>
+            <conditional name="CNV_reference">
+                <param name="CNV_reference_availabel" value="no" />
+                <section name="advanced_settings">
+                    <conditional name="reference_source">
+                        <param name="ref_selector" value="cached"/>
+                        <param name="fasta" value="test_buildid"/>
+                    </conditional>
+                    <conditional name="Sample_sex">
+                        <param name="sex" value="no" />
+                    </conditional>
+                </section>
+                <param name="targets" ftype="bed" value="capture.target.bed" />
+                <section name="disable_some_of_the_bias_corrections">
+                    <param name="no_gc" value="1" />
+                </section>
             </conditional>
-            <conditional name="Sample_sex">
-                <param name="sex" value="no" />
-            </conditional>
-            <param name="CNV_reference_availabel" value="no" />
-            <param name="targets" ftype="bed" value="capture.target.bed" />
-            <param name="no_gc" value="1" />
             <output name="out_referene_tas">
                 <assert_contents><has_text text="chromosome"/></assert_contents>
             </output>