diff bcftools_view.xml @ 18:3ca3de4e5291 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49

--- a/bcftools_view.xml	Fri Aug 19 20:04:14 2022 +0000
+++ b/bcftools_view.xml	Tue Sep 20 13:04:09 2022 +0000
@@ -1,5 +1,5 @@
 <?xml version='1.0' encoding='utf-8'?>
-<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@">
+<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>VCF/BCF conversion, view, subset and filter VCF/BCF files</description>
     <macros>
         <token name="@EXECUTABLE@">view</token>
@@ -375,6 +375,27 @@
                 </assert_contents>
             </output>
         </test>
+        <!-- Test region overlap option -->
+        <test>
+            <param name="input_file" ftype="vcf" value="view.vcf" />
+            <param name="min_ac" value="1" />
+            <param name="max_ac" value="1" />
+            <param name="samples" value="NA00002" />
+            <param name="types" value="snps" />
+            <param name="output_type" value="v" />
+            <section name="sec_restrict">
+                <param name="regions_overlap" value="1"/>
+            </section>
+            <output name="output_file">
+                <assert_contents>
+                    <has_text text="rs2298108" />
+                    <not_has_text text="rs6111385" />
+                </assert_contents>
+            </output>
+            <assert_command>
+                <has_text text="--regions-overlap" />
+            </assert_command>
+        </test>
     </tests>
     <help><![CDATA[
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