Mercurial > repos > iuc > bcftools_cnv

diff bcftools_cnv.xml @ 16:3a7084316a6e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
author iuc
date Tue, 20 Sep 2022 12:58:03 +0000
parents 8d637025a905
children 143796b504eb
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--- a/bcftools_cnv.xml	Sat Jul 23 13:38:06 2022 +0000
+++ b/bcftools_cnv.xml	Tue Sep 20 12:58:03 2022 +0000
@@ -1,5 +1,5 @@
 <?xml version='1.0' encoding='utf-8'?>
-<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy1">
+<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Call copy number variation from VCF B-allele frequency (BAF) and Log R Ratio intensity (LRR) values</description>
     <macros>
         <token name="@EXECUTABLE@">cnv</token>
@@ -231,6 +231,17 @@
             </conditional>
             <output name="output_summary" file="cnv_summary.tab" compare="re_match" />
         </test>
+        <!-- Test region overlap option -->
+        <test expect_num_outputs="3">
+            <param name="input_file" ftype="vcf" value="cnv.vcf" />
+            <section name="sec_restrict">
+                <param name="regions_overlap" value="1"/>
+            </section>
+            <output name="output_summary" file="cnv_summary.tab" compare="re_match" />
+            <assert_command>
+                <has_text text="--regions-overlap" />
+            </assert_command>
+        </test>
     </tests>
     <help><![CDATA[
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