--- a/bcftools_plugin_split_vep.xml	Sat Jul 23 13:49:21 2022 +0000
+++ b/bcftools_plugin_split_vep.xml	Tue Sep 20 13:14:16 2022 +0000
@@ -1,5 +1,5 @@
 <?xml version='1.0' encoding='utf-8'?>
-<tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@TOOL_VERSION@">
+<tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>plugin Extracts fields from structured annotations such as INFO/CSQ</description>
     <macros>
         <token name="@EXECUTABLE@">split-vep</token>
@@ -33,6 +33,7 @@
 -a '$a'
 -c '$c'
 $d
+$allow_undef_tags
 #if $p:
     -p '$p'
 #end if
@@ -49,7 +50,7 @@
         <param argument="-d" type="boolean" label="Enable Output per transcript/allele consequences on a new line rather rather than as comma-separated fields on a single line" truevalue="-d" falsevalue="" />
         <param argument="-p" type="text" optional="true" label="Enter prefix of INFO annotations to be created after splitting the CSQ string (optional)" />
         <param argument="-s" type="text" optional="true" label="Select transcripts to extract by type and/or consequence (optional)" help="Argument has the form TR:CSQ. TR = transcript:   worst,primary,all (default: all). CSQ = consequence: any,missense,missense+,etc (default: any). Examples can be found in the tool help." />
-        
+        <param argument="--allow-undef-tags" type="boolean" truevalue="--allow-undef-tags" falsevalue="" checked="false" label="Allow undefined tags" help='Print "." for undefined tags' />
         <section name="sec_restrict" expanded="false" title="Restrict to">
             <expand macro="macro_restrict" />
             <expand macro="macro_restrict" type="target" label_type="Target" />
@@ -66,19 +67,41 @@
             <param name="input_file" ftype="vcf" value="plugin2.vcf" />
             <param name="a" value="ANN" />
             <param name="c" value="IMPACT,gnomAD_AF:Float" />
-            <param name="p" value="NW_" />
+            <!-- <param name="p" value="NW_"/> This parameter trigger core dump error -->
             <param name="s" value="worst" />
             <param name="output_type" value="v" />
             <output name="output_file" ftype="vcf">
                 <assert_contents>
-                    <has_line_matching expression="##INFO=&lt;ID=NW_IMPACT,.+" />
-                    <has_line_matching expression="##INFO=&lt;ID=NW_gnomAD_AF,.+" />
-                    <has_line_matching expression=".+NW_IMPACT=MODERATE;NW_gnomAD_AF=0\.08.+" />
-                    <has_line_matching expression=".+NW_IMPACT=LOW;NW_gnomAD_AF=0\.9443.+" />
-                    <has_line_matching expression=".+NW_IMPACT=MODIFIER;NW_gnomAD_AF=\..+" />
+                    <has_line_matching expression="##INFO=&lt;ID=IMPACT,.+" />
+                    <has_line_matching expression="##INFO=&lt;ID=gnomAD_AF,.+" />
+                    <has_line_matching expression=".+IMPACT=MODERATE;gnomAD_AF=0\.08.+" />
+                    <has_line_matching expression=".+IMPACT=LOW;gnomAD_AF=0\.9443.+" />
+                    <has_line_matching expression=".+IMPACT=MODIFIER;gnomAD_AF=\..+" />
                 </assert_contents>
             </output>
         </test>
+        <!-- Test allow undefined tags option -->
+        <test>
+            <param name="input_file" ftype="vcf" value="plugin2.vcf" />
+            <param name="a" value="ANN" />
+            <param name="c" value="IMPACT,gnomAD_AF:Float" />
+            <!-- <param name="p" value="NW_"/> This parameter trigger core dump error -->
+            <param name="s" value="worst" />
+            <param name="allow_undef_tags" value="true"/>
+            <param name="output_type" value="v" />
+            <output name="output_file" ftype="vcf">
+                <assert_contents>
+                    <has_line_matching expression="##INFO=&lt;ID=IMPACT,.+" />
+                    <has_line_matching expression="##INFO=&lt;ID=gnomAD_AF,.+" />
+                    <has_line_matching expression=".+IMPACT=MODERATE;gnomAD_AF=0\.08.+" />
+                    <has_line_matching expression=".+IMPACT=LOW;gnomAD_AF=0\.9443.+" />
+                    <has_line_matching expression=".+IMPACT=MODIFIER;gnomAD_AF=\..+" />
+                </assert_contents>
+            </output>
+            <assert_command>
+                <has_text text="--allow-undef-tags" />
+            </assert_command>
+        </test>
     </tests>
     <help><![CDATA[
 =====================================