--- a/bcftools_csq.xml	Sat Jul 23 13:35:18 2022 +0000
+++ b/bcftools_csq.xml	Tue Sep 20 13:15:15 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>Haplotype aware consequence predictor</description>
     <macros>
         <token name="@EXECUTABLE@">csq</token>
@@ -38,6 +38,9 @@
 #if str($sec_csq_opts.custom_tag):
     --custom-tag '$sec_csq_opts.custom_tag'
 #end if
+#if str($sec_csq_opts.trim_protein_seq)
+    --trim-protein-seq $sec_csq_opts.trim_protein_seq
+#end if
 
 ## Subset section
 #set $section = $sec_subset
@@ -82,6 +85,8 @@
                  label="use this custom tag to store consequences rather than the default BCSQ tag">
                  <validator type="regex" message="">^(\w+)?$</validator>
             </param>
+            <param argument="--trim-protein-seq" type="integer" min="0" value="" optional="true" label="Abbreviate protein-changing predictions" 
+                help="Abbreviate protein-changing predictions to max INT aminoacids" />
         </section>
 
         <section name="sec_restrict" expanded="false" title="Restrict to">
@@ -111,7 +116,7 @@
             </output>
         </test>
         <test>
-            <param name="input_file" ftype="vcf" dbkey="?" value="csq.vcf" />
+            <param name="input_file" ftype="vcf" value="csq.vcf" />
             <expand macro="test_using_reference" select_from="cached" ref="csq" />
             <param name="gff_annot" ftype="gff3" value="csq.gff3" />
             <param name="output_type" value="v" />
@@ -121,7 +126,42 @@
                 </assert_contents>
             </output>
         </test>
-
+        <!-- Test protein seq prediction-->
+        <test>
+            <param name="input_file" ftype="vcf" value="csq.vcf" />
+            <expand macro="test_using_reference" select_from="cached" ref="csq" />
+            <param name="gff_annot" ftype="gff3" value="csq.gff3" />
+            <param name="output_type" value="v" />
+            <section name="sec_csq_opts">
+                <param name="trim_protein_seq" value="10"/>
+            </section>
+            <output name="output_file">
+                <assert_contents>
+                    <has_text text="BCSQ" />
+                </assert_contents>
+            </output>
+            <assert_command>
+                <has_text text="--trim-protein-seq" />
+            </assert_command>
+        </test>
+        <!-- Test region overlap-->
+        <test>
+            <param name="input_file" ftype="vcf" value="csq.vcf" />
+            <expand macro="test_using_reference" select_from="cached" ref="csq" />
+            <param name="gff_annot" ftype="gff3" value="csq.gff3" />
+            <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="BCSQ" />
+                </assert_contents>
+            </output>
+            <assert_command>
+                <has_text text="--regions-overlap" />
+            </assert_command>
+        </test>
     </tests>
     <help><![CDATA[
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