--- a/lofreq_call.xml	Wed Feb 12 18:45:42 2020 -0500
+++ b/lofreq_call.xml	Sat Mar 21 10:52:04 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="lofreq_call" name="Call variants" version="@TOOL_VERSION@+galaxy1">
+<tool id="lofreq_call" name="Call variants" version="@TOOL_VERSION@+galaxy2">
     <description>with LoFreq</description>
     <macros>
         <import>macros.xml</import>
@@ -126,10 +126,10 @@
         </conditional>
         <param name="variant_types" type="select"
         label="Types of variants to call"
-        help="Note: When including indels in the called variants you should preprocess your input data to include indel alignment qualities">
+        help="Note: To have indels included in the called variants you HAVE to preprocess your input data using lofreq indelqual to include indel qualities. In addition, it is highly recommended that you calculate and make use of indel alignment qualities. See the detailed tool help below.">
             <option value="--call-indels">SNVs and indels</option>
             <option value="" selected="True">Only SNVs</option>
-            <option value="--only-indels">Only indels</option>
+            <option value="--call-indels --only-indels">Only indels</option>
         </param>
         <conditional name="call_control">
             <param name="set_call_options" type="select"
@@ -326,6 +326,16 @@
             </conditional>
             <output name="variants" file="call-out2.vcf" lines_diff="4" />
         </test>
+        <test>
+            <param name="reads" ftype="bam" value="indelqual-out3.bam" />
+            <param name="ref_selector" value="history" />
+            <param name="ref" ftype="fasta" value="pBR322.fa" />
+            <param name="variant_types" value="--call-indels --only-indels" />
+            <conditional name="filter_control">
+                <param name="filter_type" value="set_all_off" />
+            </conditional>
+            <output name="variants" file="indel-call-out.vcf" lines_diff="4" />
+        </test>
     </tests>
     <help><![CDATA[
 lofreq call: call variants from BAM file
@@ -364,7 +374,7 @@
   responsible for adding indel qualitites, which are required for indel
   calling with lofreq, to your input.
 
-  For doing so, you can use ``lofreq indelqual`` or GATK's BQSR.
+  For doing so, you can use ``lofreq indelqual``.
 
 - Base/indel alignment quality