# HG changeset patch
# User iuc
# Date 1728645536 0
# Node ID cb441f258c3781cc4537d9ca0035dbfe2468d877
# Parent  23d7e75d850e19f350e5a00b221c85c537121faf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit 963634ce66fcee0fe9d4ecd229cafbb2c4be263c

diff -r 23d7e75d850e -r cb441f258c37 cutesv.xml
--- a/cutesv.xml	Sat Oct 05 16:42:23 2024 +0000
+++ b/cutesv.xml	Fri Oct 11 11:18:56 2024 +0000
@@ -8,7 +8,7 @@
     </xrefs>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">cutesv</requirement>
-        <requirement type="package" version="1.10">samtools</requirement>
+        <requirement type="package" version="1.21">samtools</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         ln -s '$input_sample_file' ./sample.bam &&
@@ -51,7 +51,7 @@
             --diff_ratio_filtering_TRA '$sel_method.adv_settings.diff_ratio_filtering_TRA'
     ]]></command>
     <inputs>
-        <param name="input_sample_file" type="data" format="bam" label="Sample file" help="Sample file in .BAM format." />
+        <param name="input_sample_file" type="data" format="bam" label="Sample file" help="Sample file in .BAM format."/>
         <expand macro="reference_interface" />
         <param name="sample" type="text" value="Sample" label="Sample name/id" help="">
             <validator type="length" min="1" message="Please enter a sample name/id"/>
@@ -66,30 +66,30 @@
             </param>
             <when value="pb_clr">
                 <section name="adv_settings" title="Advanced settings" expanded="false">
-                    <expand macro="adv_shared_1" />
-                    <expand macro="adv_pb_clr" />
-                    <expand macro="adv_shared_2" />
+                    <expand macro="adv_shared_1"/>
+                    <expand macro="adv_pb_clr"/>
+                    <expand macro="adv_shared_2"/>
                 </section>
             </when>
             <when value="pb_ccs">
                 <section name="adv_settings" title="Advanced settings" expanded="false">
-                    <expand macro="adv_shared_1" />
-                    <expand macro="adv_pb_ccs" />
-                    <expand macro="adv_shared_2" />
+                    <expand macro="adv_shared_1"/>
+                    <expand macro="adv_pb_ccs"/>
+                    <expand macro="adv_shared_2"/>
                 </section>
             </when>
             <when value="pb_ont">
                 <section name="adv_settings" title="Advanced settings" expanded="false">
-                    <expand macro="adv_shared_1" />
-                    <expand macro="adv_ont" />
-                    <expand macro="adv_shared_2" />
+                    <expand macro="adv_shared_1"/>
+                    <expand macro="adv_ont"/>
+                    <expand macro="adv_shared_2"/>
                 </section>
             </when>
             <when value="other">
                 <section name="adv_settings" title="Advanced settings" expanded="true">
-                    <expand macro="adv_shared_1" />
-                    <expand macro="adv_other" />
-                    <expand macro="adv_shared_2" />
+                    <expand macro="adv_shared_1"/>
+                    <expand macro="adv_other"/>
+                    <expand macro="adv_shared_2"/>
                 </section>
             </when>
         </conditional>
@@ -101,14 +101,14 @@
         <test expect_num_outputs="1">
             <conditional name="reference_source">
                 <param name="ref_selector" value="history"/>
-                <param name="ref" ftype="fasta" value="genome.fasta" />
+                <param name="ref" ftype="fasta" value="genome.fasta"/>
             </conditional>
-            <param name="sel_method|meth_selector" value="pb_ccs" />
-            <param name="input_sample_file" ftype="bam" value="sample.bam" />
+            <param name="sel_method|meth_selector" value="pb_ccs"/>
+            <param name="input_sample_file" ftype="bam" value="sample.bam"/>
             <output name="out_sample">
                 <assert_contents>
                     <has_text text="##fileformat=VCFv4.2"/>
-                    <has_text text="##source=cuteSV-1.0.8"/>
+                    <has_text text="##contig=&lt;ID=chrM,length=16571&gt;"/>
                 </assert_contents>
             </output>
         </test>
@@ -117,12 +117,12 @@
                 <param name="ref_selector" value="cached"/>
                 <param name="ref" value="test_buildid"/>
             </conditional>
-            <param name="sel_method|meth_selector" value="pb_ccs" />
-            <param name="input_sample_file" ftype="bam" value="sample.bam" />
+            <param name="sel_method|meth_selector" value="pb_ccs"/>
+            <param name="input_sample_file" ftype="bam" value="sample.bam"/>
             <output name="out_sample">
                 <assert_contents>
                     <has_text text="##fileformat=VCFv4.2"/>
-                    <has_text text="##source=cuteSV-1.0.8"/>
+                    <has_text text="##contig=&lt;ID=chrM,length=16571&gt;"/>
                 </assert_contents>
             </output>
         </test>
diff -r 23d7e75d850e -r cb441f258c37 macros.xml
--- a/macros.xml	Sat Oct 05 16:42:23 2024 +0000
+++ b/macros.xml	Fri Oct 11 11:18:56 2024 +0000
@@ -1,6 +1,6 @@
 <macros>
-    <token name="@VERSION_SUFFIX@">1</token>
-    <token name="@TOOL_VERSION@">1.0.8</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@TOOL_VERSION@">2.1.1</token>
     <xml name="reference_interface">
         <conditional name="reference_source">
             <param name="ref_selector" type="select" label="Choose the source for the reference genome">