From fdc1baed5f2208a4cdef046191b914c02bd40465 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Fri, 13 Dec 2024 20:03:38 +0100
Subject: [PATCH 1/3] text is txt

---
 tools/cnvkit/breaks.xml      | 2 +-
 tools/cnvkit/genemetrics.xml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/tools/cnvkit/breaks.xml b/tools/cnvkit/breaks.xml
index 7e5b30ec3dc..17661117b85 100644
--- a/tools/cnvkit/breaks.xml
+++ b/tools/cnvkit/breaks.xml
@@ -23,7 +23,7 @@
         <param argument="--min-probes" optional="true" type="integer" label="Minimum propes" value="1" help="Minimum number of covered probes to label a gene" />     
     </inputs>
     <outputs>
-        <data name="gene_breaks" format="text" label="${tool.name} on ${on_string}:genes with copy number breakpoints" from_work_dir="gene-breaks.txt" />
+        <data name="gene_breaks" format="txt" label="${tool.name} on ${on_string}:genes with copy number breakpoints" from_work_dir="gene-breaks.txt" />
     </outputs>
     <tests>
         <test expect_num_outputs="1">
diff --git a/tools/cnvkit/genemetrics.xml b/tools/cnvkit/genemetrics.xml
index 3afe9eabe09..89ce5109cb7 100644
--- a/tools/cnvkit/genemetrics.xml
+++ b/tools/cnvkit/genemetrics.xml
@@ -61,7 +61,7 @@
       </section>
    </inputs>
     <outputs>
-        <data name="gene_genemetrics" format="text" label="${tool.name} on ${on_string}: Sample copy number ratios table" from_work_dir="gene_genemetrics.txt" />
+        <data name="gene_genemetrics" format="txt" label="${tool.name} on ${on_string}: Sample copy number ratios table" from_work_dir="gene_genemetrics.txt" />
     </outputs>
     <tests>
         <test expect_num_outputs="1">

From b3a5698230e91ae61729ac9eaeb964140aaad841 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Fri, 13 Dec 2024 20:35:49 +0100
Subject: [PATCH 2/3] fix TestsCaseValidation

---
 tools/cnvkit/autobin.xml    | 20 ++++----
 tools/cnvkit/batch.xml      | 58 +++++++++++++---------
 tools/cnvkit/call.xml       | 24 ++++++----
 tools/cnvkit/diagram.xml    | 22 +++++----
 tools/cnvkit/heatmap.xml    | 14 ++++--
 tools/cnvkit/reference.xml  | 96 ++++++++++++++++++++++++-------------
 tools/cnvkit/scatter.xml    | 10 +++-
 tools/cnvkit/segment.xml    | 10 ++--
 tools/cnvkit/segmetrics.xml |  8 ++--
 9 files changed, 167 insertions(+), 95 deletions(-)

diff --git a/tools/cnvkit/autobin.xml b/tools/cnvkit/autobin.xml
index e32e2b7b188..66364ede988 100644
--- a/tools/cnvkit/autobin.xml
+++ b/tools/cnvkit/autobin.xml
@@ -93,20 +93,24 @@
     </outputs>
     <tests>
         <test expect_num_outputs="2">
-            <conditional name="reference_source">
-                <param name="ref_selector" value="history"/>
-                <param name="fasta" ftype="fasta" value="genome.fasta" />
-            </conditional>
+            <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="bams" ftype="bam" value="tumor.bam" />
             <param name="targets" ftype="bed" value="capture.bed" />
             <output name="out_capture_target" file="capture.target.bed" /> 
             <output name="out_capture_antitarget" file="capture.antitarget.bed" /> 
         </test>
         <test expect_num_outputs="2">
-            <conditional name="reference_source">
-                <param name="ref_selector" value="cached"/>
-                <param name="fasta" value="test_buildid"/>
-            </conditional>
+            <section name="advanced_settings">
+                <conditional name="reference_source">
+                    <param name="ref_selector" value="cached"/>
+                    <param name="fasta" value="test_buildid"/>
+                </conditional>
+            </section>
             <param name="bams" ftype="bam" value="tumor.bam" />
             <param name="targets" ftype="bed" value="capture.bed" />
             <output name="out_capture_target" file="capture.target.bed" /> 
diff --git a/tools/cnvkit/batch.xml b/tools/cnvkit/batch.xml
index 1ca2803ca46..030c218d84e 100644
--- a/tools/cnvkit/batch.xml
+++ b/tools/cnvkit/batch.xml
@@ -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>
diff --git a/tools/cnvkit/call.xml b/tools/cnvkit/call.xml
index d2eb54765dd..4bdd6c8647c 100644
--- a/tools/cnvkit/call.xml
+++ b/tools/cnvkit/call.xml
@@ -98,20 +98,28 @@
     <tests>
         <test expect_num_outputs="1">
             <param name="input_sample_file" ftype="tabular" value="tumor.cns" />
-            <param name="zygosity_freq" value="0.25" />
-            <param name="min_variant_depth" value="40" />
-            <param name="purity" value="1" />
+            <section name="additional_SNP_allelic_process">
+                <param name="zygosity_freq" value="0.25" />
+                <param name="min_variant_depth" value="40" />
+            </section>
+            <section name="advanced_settings">
+                <param name="purity" value="1" />
+            </section>
             <output name="out_sample_Bintest">
                 <assert_contents><has_text_matching expression="chrM"/></assert_contents>
             </output>
         </test>
         <test expect_num_outputs="1">
-            <conditional name="Sample_sex">
-                <param name="sex" value="yes" />
-            </conditional>
+            <section name="advanced_settings">
+                <conditional name="Sample_sex">
+                    <param name="sex" value="yes" />
+                </conditional>
+                <param name="purity" value="1" />
+            </section>
             <param name="input_sample_file" ftype="tabular" value="tumor.cns" />
-            <param name="min_variant_depth" value="40" />
-            <param name="purity" value="1" />
+            <section name="additional_SNP_allelic_process">
+                <param name="min_variant_depth" value="40" />
+            </section>
             <output name="out_sample_Bintest">
                 <assert_contents><has_text_matching expression="chrM"/></assert_contents>
             </output>
diff --git a/tools/cnvkit/diagram.xml b/tools/cnvkit/diagram.xml
index 583a0e3433d..36d327da7e2 100644
--- a/tools/cnvkit/diagram.xml
+++ b/tools/cnvkit/diagram.xml
@@ -57,21 +57,25 @@
     <tests>
         <test expect_num_outputs="1">
             <param name="input_cnr_file" ftype="tabular" value="tumor.cnr" />
-            <param name="segment" ftype="tabular" value="sample.cns" />
-            <param name="threshold" value="10" />
-            <param name="male_reference" value="1" />
+            <section name="advanced_settings">
+                <param name="segment" ftype="tabular" value="sample.cns" />
+                <param name="threshold" value="10" />
+                <param name="male_reference" value="1" />
+            </section>
             <output name="out_diagram_file" file="sample-diagram.pdf" ftype="pdf" compare="sim_size" > 
                 <assert_contents><has_size value="6000" delta="2000" /></assert_contents>
             </output>
         </test>
         <test expect_num_outputs="1">
-            <conditional name="Sample_sex">
-                <param name="sex" value="yes" />
-            </conditional>
             <param name="input_cnr_file" ftype="tabular" value="tumor.cnr" />
-            <param name="segment" ftype="tabular" value="sample.cns" />
-            <param name="threshold" value="10" />
-            <param name="male_reference" value="1" />
+            <section name="advanced_settings">
+                <conditional name="Sample_sex">
+                    <param name="sex" value="yes" />
+                </conditional>
+                <param name="segment" ftype="tabular" value="sample.cns" />
+                <param name="threshold" value="10" />
+                <param name="male_reference" value="1" />
+            </section>
             <output name="out_diagram_file" file="sample-diagram.pdf" ftype="pdf" compare="sim_size" > 
                 <assert_contents><has_size value="6000" delta="2000" /></assert_contents>
             </output>
diff --git a/tools/cnvkit/heatmap.xml b/tools/cnvkit/heatmap.xml
index 5b970571e5c..657dbda4a15 100644
--- a/tools/cnvkit/heatmap.xml
+++ b/tools/cnvkit/heatmap.xml
@@ -55,17 +55,21 @@
     <tests>
         <test expect_num_outputs="1">
             <param name="filenames" ftype="tabular" value="tumor.cns,sample.cns" />
-            <param name="desaturate" value="1" />
+            <section name="advanced_settings">
+                <param name="desaturate" value="1" />
+            </section>
             <output name="out_heatmap_png" file="sample-heatmap.png" ftype="png" compare="sim_size" >
                 <assert_contents><has_size value="9000" delta="5000" /></assert_contents>
             </output> 
         </test>
         <test expect_num_outputs="1">
-            <conditional name="Sample_sex">
-                <param name="sex" value="no" />
-            </conditional>
             <param name="filenames" ftype="tabular" value="tumor.cns,sample.cns" />
-            <param name="desaturate" value="1" />
+            <section name="advanced_settings">
+                <param name="desaturate" value="1" />
+                <conditional name="Sample_sex">
+                    <param name="sex" value="no" />
+                </conditional>
+            </section>
             <output name="out_heatmap_png" file="sample-heatmap.png" ftype="png" compare="sim_size" >
                 <assert_contents><has_size value="9000" delta="5000" /></assert_contents>
             </output> 
diff --git a/tools/cnvkit/reference.xml b/tools/cnvkit/reference.xml
index b4bfa90312c..01518e60f84 100644
--- a/tools/cnvkit/reference.xml
+++ b/tools/cnvkit/reference.xml
@@ -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>
-            <conditional name="Sample_sex">
-                <param name="sex" value="no" />
+            <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>
-            <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>
diff --git a/tools/cnvkit/scatter.xml b/tools/cnvkit/scatter.xml
index 732dfeff13d..44d1ac85271 100644
--- a/tools/cnvkit/scatter.xml
+++ b/tools/cnvkit/scatter.xml
@@ -89,8 +89,14 @@
     <tests>
         <test expect_num_outputs="1">
             <param name="input_cnr_file" ftype="tabular" value="tumor.cnr" />
-            <param name="zygosity_freq" value="0.25" />
-            <param name="by_bin" value="1" />
+            <section name="advanced_settings">
+                <section name="additional_SNP_allelic_process">
+                    <param name="zygosity_freq" value="0.25" />
+                </section>
+                <section name="plot_aesthetics">
+                    <param name="by_bin" value="1" />
+                </section>
+            </section>
             <output name="out_scatter_file" file="sample-scatter.pdf" ftype="pdf" compare="sim_size">
                 <assert_contents><has_size value="12000" delta="5000" /></assert_contents>
             </output>
diff --git a/tools/cnvkit/segment.xml b/tools/cnvkit/segment.xml
index d885ca86c71..ec00142fb9e 100644
--- a/tools/cnvkit/segment.xml
+++ b/tools/cnvkit/segment.xml
@@ -64,10 +64,12 @@
     <tests>
         <test expect_num_outputs="1">
             <param name="filename" ftype="tabular" value="tumor.cnr" />
-            <param name="method" value="hmm" />
-            <param name="threshold" value="2" />
-            <param name="drop_outliers" value="2" />
-            <param name="drop_low_coverage" value="1" />
+            <section name="advanced_settings">
+                <param name="method" value="hmm" />
+                <param name="threshold" value="2" />
+                <param name="drop_outliers" value="2" />
+                <param name="drop_low_coverage" value="1" />
+            </section>
             <output name="out_sample_segment">
                 <assert_contents><has_text text="chromosome"/></assert_contents>
             </output>
diff --git a/tools/cnvkit/segmetrics.xml b/tools/cnvkit/segmetrics.xml
index 5062151eee3..d896ac2a6f0 100644
--- a/tools/cnvkit/segmetrics.xml
+++ b/tools/cnvkit/segmetrics.xml
@@ -48,9 +48,11 @@
             <param name="input_filename_file" ftype="tabular" value="sample.cnr" />
             <param name="segments" ftype="tabular" value="sample.cns" />
             <param name="drop_low_coverage" value="1" />
-            <param name="mean" value="1" />
-            <param name="median" value="1" />
-            <param name="mode" value="0" />
+            <section name="advanced_settings">
+                <param name="mean" value="1" />
+                <param name="median" value="1" />
+                <param name="mode" value="0" />
+            </section>
             <output name="gene_segmetrics">
                 <assert_contents><has_text text="chromosome"/></assert_contents>
             </output> 

From a7d7b81718bd0324a442a316690d92ae57026129 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Sat, 14 Dec 2024 00:37:50 +0100
Subject: [PATCH 3/3] bump

---
 tools/cnvkit/macros.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/cnvkit/macros.xml b/tools/cnvkit/macros.xml
index 2dca689e660..fbe778a6bbb 100644
--- a/tools/cnvkit/macros.xml
+++ b/tools/cnvkit/macros.xml
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@TOOL_VERSION@">0.9.11</token>
     <xml name="requirements">
         <requirements>