--- a/variant.xml	Fri Oct 16 17:03:16 2020 +0000
+++ b/variant.xml	Wed Feb 10 08:25:36 2021 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="medaka_variant" name="medaka variant tool" version="@TOOL_VERSION@+galaxy3" profile="@PROFILE@">
+<tool id="medaka_variant" name="medaka variant tool" version="@TOOL_VERSION@+galaxy4" profile="@PROFILE@">
     <description>Probability decoding</description>
     <macros>
         <import>macros.xml</import>
@@ -47,12 +47,11 @@
     2>&1 | tee '$out_log'
 #end if
 
-#if $out_annotated
-    && samtools faidx reference.fa
-    && grep -v "^#" '$out_result' > tmp.txt
-    && cut -f 1,2 tmp.txt > positions.txt
-    && samtools mpileup -d 0 --positions positions.txt -Q $output_annotated.min_basequal -q $output_annotated.min_mapqual -f reference.fa '$output_annotated.in_bam' > mpileup.txt
-    && python '$__tool_directory__/annotateVCF.py' '$out_result' mpileup.txt '$out_annotated'
+#if $out_annotated:
+    && ln -s '$output_annotated.in_bam' in.bam
+    && ln -s '$output_annotated.in_bam.metadata.bam_index' in.bai
+    && medaka tools annotate --pad $output_annotated.pad '$out_result' reference.fa in.bam tmp.vcf
+    && '$__tool_directory__/convert_VCF_info_fields.py' tmp.vcf '$out_annotated'
 #end if
     ]]></command>
     <inputs>
@@ -85,9 +84,8 @@
                 <option value="false">Don't output annotated VCF</option>
             </param>
             <when value="true">
-                <param name="in_bam" type="data" format="bam" optional="false" label="BAM to annotate the VCF" />
-                <param name="min_basequal" type="integer" value="0" min="0" max="50" label="Minimum base quality" help="The minimum base quality (default: 0) at a given variant position required to include a read in the calculation of variant statistics (samtools mpileup -Q)" />
-                <param name="min_mapqual" type="integer" value="0" min="0" max="60" label="Minimum mapping quality" help="The minimum mapping quality (default: 0) required for a read to be considered in calculation of variant statistics (samtools mpileup -q)" />
+                <param name="in_bam" type="data" format="bam" optional="false" label="BAM to annotate the VCF"/>
+                <param name="pad" type="integer" min="1" value="25" label="Padding width on either side of variant for realignment in medaka tools anntotate, used to calculate DPSP, DPSPS, AF, FAF, RAF, SB, DP4, and AS in the output annotated VCF"/>
             </when>
             <when value="false"/>
         </conditional>
@@ -98,7 +96,7 @@
         <data name="out_result" format="vcf" label="${tool.name} on ${on_string}: Result"/>
         <!-- optional -->
         <data name="out_annotated" format="vcf" label="${tool.name} on ${on_string}: Annotated">
-            <filter>output_annotated_select</filter>
+            <filter>output_annotated['output_annotated_select']!='false'</filter>
         </data>
         <data name="out_log" format="tabular" label="${tool.name} on ${on_string}: Log">
             <filter>output_log_bool</filter>
@@ -125,15 +123,15 @@
                 <assert_contents>
                     <has_n_lines n="9"/>
                     <has_line line="##fileformat=VCFv4.1" />
-                    <has_line line="##medaka_version=1.0.3" />
+                    <has_line_matching expression="##medaka_version=[0-9]+\.[0-9]+\.[0-9]+" />
                 </assert_contents>
             </output>
             <output name="out_annotated">
                 <assert_contents>
-                    <has_n_lines n="16"/>
+                    <has_n_lines n="22"/>
                     <has_line line="##fileformat=VCFv4.1" />
-                    <has_line line="##medaka_version=1.0.3" />
-                    <has_line line="##annotateVCFVersion=0.2" />
+                    <has_line_matching expression="##medaka_version=[0-9]+\.[0-9]+\.[0-9]+" />
+                    <has_line_matching expression="##convert_VCF_info_fields=[0-9]+\.[0-9]+" />
                 </assert_contents>
             </output>
             <output name="out_log">
@@ -162,15 +160,15 @@
                 <assert_contents>
                     <has_n_lines n="9"/>
                     <has_line line="##fileformat=VCFv4.1" />
-                    <has_line line="##medaka_version=1.0.3" />
+                    <has_line_matching expression="##medaka_version=[0-9]+\.[0-9]+\.[0-9]+" />
                 </assert_contents>
             </output>
             <output name="out_annotated">
                 <assert_contents>
-                    <has_n_lines n="16"/>
+                    <has_n_lines n="22"/>
                     <has_line line="##fileformat=VCFv4.1" />
                     <has_line line="##medaka_version=1.0.3" />
-                    <has_line line="##annotateVCFVersion=0.2" />
+                    <has_line_matching expression="##medaka_version=[0-9]+\.[0-9]+\.[0-9]+" />
                 </assert_contents>
             </output>
             <output name="out_log">
@@ -179,6 +177,29 @@
                 </assert_contents>
             </output>
         </test>
+        <!--No annotation or log-->
+        <test expect_num_outputs="1">
+            <conditional name="pool">
+                <param name="pool_mode" value="No"/>
+                <param name="input" value="medaka_test.hdf"/>
+            </conditional>
+            <conditional name="reference_source">
+                <param name="reference_source_selector" value="history"/>
+                <param name="ref_file" value="ref.fasta"/>
+            </conditional>
+            <conditional name="output_annotated">
+                <param name="output_annotated_select" value="false"/>
+            </conditional>
+            <param name="output_log_bool" value="false"/>
+            
+            <output name="out_result">
+                <assert_contents>
+                    <has_n_lines n="9"/>
+                    <has_line line="##fileformat=VCFv4.1" />
+                    <has_line_matching expression="##medaka_version=[0-9]+\.[0-9]+\.[0-9]+" />
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help><![CDATA[
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