From 8242257d90647a1f83630c926c3002ebd601f066 Mon Sep 17 00:00:00 2001
From: planemo-autoupdate <planemo-autoupdate@users.noreply.github.com>
Date: Mon, 22 Apr 2024 04:21:07 +0000
Subject: [PATCH 1/2] Updating tools/cnvkit from version 0.9.10 to 0.9.11

---
 tools/cnvkit/macros.xml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tools/cnvkit/macros.xml b/tools/cnvkit/macros.xml
index 424fdaec671..2dca689e660 100644
--- a/tools/cnvkit/macros.xml
+++ b/tools/cnvkit/macros.xml
@@ -1,10 +1,10 @@
 <macros>
-    <token name="@VERSION_SUFFIX@">0.1</token>
-    <token name="@TOOL_VERSION@">0.9.10</token>
+    <token name="@VERSION_SUFFIX@">0</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">

From ce1943a5c035122a99f3d13c2b4908813cfed282 Mon Sep 17 00:00:00 2001
From: Khaled196 <56037954+khaled196@users.noreply.github.com>
Date: Mon, 22 Apr 2024 14:42:07 +0100
Subject: [PATCH 2/2] fix refence.cnn file difference

---
 tools/cnvkit/batch.xml | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/tools/cnvkit/batch.xml b/tools/cnvkit/batch.xml
index 7e047381191..1ca2803ca46 100644
--- a/tools/cnvkit/batch.xml
+++ b/tools/cnvkit/batch.xml
@@ -176,7 +176,9 @@
             <output name="out_capture_antitarget" file="capture.antitarget.bed" />
             <output name="out_control_targetcoverage" file="normal.targetcoverage.cnn" />
             <output name="out_control_antitargetcoverage" file="normal.antitargetcoverage.cnn" />
-            <output name="out_reference_cnn" file="reference.cnn" />
+            <output name="out_reference_cnn" file="reference.cnn" ftype="tabular" compare="sim_size">
+                <assert_contents><has_size value="3000" delta="2000" /></assert_contents>
+            </output>
             <output name="out_capture_target">
                 <assert_contents><has_text_matching expression="chrM"/></assert_contents>
             </output>
@@ -217,7 +219,9 @@
             <output name="out_capture_antitarget" file="capture.antitarget.bed" />
             <output name="out_control_targetcoverage" file="normal.targetcoverage.cnn" />
             <output name="out_control_antitargetcoverage" file="normal.antitargetcoverage.cnn" />
-            <output name="out_reference_cnn" file="reference.cnn" />
+            <output name="out_reference_cnn" file="reference.cnn" ftype="tabular" compare="sim_size">
+                <assert_contents><has_size value="3000" delta="2000" /></assert_contents>
+            </output>
             <output name="out_capture_target">
                 <assert_contents><has_text_matching expression="chrM"/></assert_contents>
             </output>