Updating tools/cnvkit from version 0.9.10 to 0.9.11 (#5961)

* Updating tools/cnvkit from version 0.9.10 to 0.9.11 * fix refence.cnn file difference --------- Co-authored-by: planemo-autoupdate <[email protected]> Co-authored-by: Khaled196 <[email protected]> Co-authored-by: Björn Grüning <[email protected]>
galaxyproject · Apr 22, 2024 · bced16a · bced16a
1 parent db30370
commit bced16a
Show file tree

Hide file tree

Showing 2 changed files with 9 additions and 5 deletions.
diff --git 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>

diff --git 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">