Mercurial > repos > iuc > bcftools_query

diff bcftools_query.xml @ 16:3ce32adc55b2 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 13:12:13 +0000
parents 94c5f302f0ea
children
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--- a/bcftools_query.xml	Sat Jul 23 13:55:56 2022 +0000
+++ b/bcftools_query.xml	Tue Sep 20 13:12:13 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>Extracts fields from VCF/BCF file and prints them in user-defined format</description>
     <macros>
         <token name="@EXECUTABLE@">query</token>
@@ -82,6 +82,19 @@
             <param name="tsv" value="True" />
             <output name="output_file" file="query.out" />
         </test>
+        <!-- Test region overlap option-->
+        <test>
+            <param name="input_files" ftype="vcf" value="query.vcf" />
+            <param name="format" value="%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n" />
+            <param name="tsv" value="True" />
+            <section name="sec_restrict">
+                <param name="regions_overlap" value="1"/>
+            </section>
+            <output name="output_file" file="query.out" />
+            <assert_command>
+                <has_text text="--regions-overlap" />
+            </assert_command>
+        </test>
     </tests>
     <help><![CDATA[ 
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