--- a/macros.xml	Thu Apr 22 12:58:55 2021 +0000
+++ b/macros.xml	Tue Sep 28 16:14:29 2021 +0000
@@ -5,10 +5,16 @@
             <yield/>
         </requirements>
     </xml>
-    <token name="@TOOL_VERSION@">1.9</token>
-    <token name="@FLAGS@">#set $flags = sum(map(int, str($filter).split(',')))</token>
+    <token name="@TOOL_VERSION@">1.13</token>
+    <token name="@PROFILE@">20.05</token>
+    <token name="@FLAGS@"><![CDATA[
+        #set $flags = 0
+        #if $filter
+            #set $flags = sum(map(int, str($filter).split(',')))
+        #end if
+    ]]></token>
     <token name="@PREPARE_IDX@"><![CDATA[
-        ##prepare input and indices 
+        ##prepare input and indices
         ln -s '$input' infile &&
         #if $input.is_of_type('bam'):
             #if str( $input.metadata.bam_index ) != "None":
@@ -25,7 +31,7 @@
         #end if
     ]]></token>
     <token name="@PREPARE_IDX_MULTIPLE@"><![CDATA[
-        ##prepare input and indices 
+        ##prepare input and indices
         #for $i, $bam in enumerate( $input_bams ):
             ln -s '$bam' '${i}' &&
             #if $bam.is_of_type('bam'):
@@ -63,6 +69,51 @@
             #set reffai=None
         #end if
     ]]></token>
+
+    <xml name="optional_reference">
+        <conditional name="addref_cond">
+            <param name="addref_select" type="select" label="Use a reference sequence">
+                <help>@HELP@</help>
+                <option value="no">No</option>
+                <option value="history">Use a genome/index from the history</option>
+                <option value="cached">Use a built-in genome</option>
+            </param>
+            <when value="no"/>
+            <when value="history">
+                <param name="ref" argument="@ARGUMENT@" type="data" format="fasta,fasta.gz" label="Reference"/>
+            </when>
+            <when value="cached">
+                <param name="ref" argument="@ARGUMENT@" type="select" label="Reference">
+                    <options from_data_table="fasta_indexes">
+                        <filter type="data_meta" ref="input" key="dbkey" column="dbkey"/>
+                    </options>
+                    <validator  type="no_options" message="No reference genome is available for the build associated with the selected input dataset"/>
+                </param>
+            </when>
+        </conditional>
+    </xml>
+    <xml name="mandatory_reference" token_help="" token_argument="">
+        <conditional name="addref_cond">
+            <param name="addref_select" type="select" label="Use a reference sequence">
+                <help>@HELP@</help>
+                <option value="history">Use a genome/index from the history</option>
+                <option value="cached">Use a built-in genome</option>
+            </param>
+            <when value="history">
+                <param name="ref" argument="@ARGUMENT@" type="data" format="fasta,fasta.gz" label="Reference"/>
+            </when>
+            <when value="cached">
+                <param name="ref" argument="@ARGUMENT@" type="select" label="Reference">
+                    <options from_data_table="fasta_indexes">
+                        <filter type="data_meta" ref="input" key="dbkey" column="dbkey"/>
+                        <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" />
+                    </options>
+                </param>
+            </when>
+        </conditional>
+    </xml>
+
+
     <token name="@ADDTHREADS@"><![CDATA[
         ##compute the number of ADDITIONAL threads to be used by samtools (-@)
         addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) &&
@@ -70,28 +121,28 @@
     <token name="@ADDMEMORY@"><![CDATA[
         ##compute the number of memory available to samtools sort (-m)
         ##use only 75% of available: https://github.com/samtools/samtools/issues/831
-        addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} && 
+        addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} &&
         ((addmemory=addmemory*75/100)) &&
     ]]></token>
     <xml name="seed_input">
-       <param name="seed" type="integer" optional="True" label="Seed for random number generator" help="If empty a random seed is used." /> 
+       <param name="seed" type="integer" optional="True" label="Seed for random number generator" help="If empty a random seed is used." />
     </xml>
-    <xml name="flag_options">
-        <option value="1">Read is paired</option>
-        <option value="2">Read is mapped in a proper pair</option>
-        <option value="4">Read is unmapped</option>
-        <option value="8">Mate is unmapped</option>
-        <option value="16">Read is mapped to the reverse strand of the reference</option>
-        <option value="32">Mate is mapped to the reverse strand of the reference</option>
-        <option value="64">Read is the first in a pair</option>
-        <option value="128">Read is the second in a pair</option>
-        <option value="256">Alignment of the read is not primary</option>
-        <option value="512">Read fails platform/vendor quality checks</option>
-        <option value="1024">Read is a PCR or optical duplicate</option>
-        <option value="2048">Alignment is supplementary</option>
+    <xml name="flag_options" token_s1="false" token_s2="false" token_s4="false" token_s8="false" token_s16="false" token_s32="false" token_s64="false" token_s128="false" token_s256="false" token_s512="false" token_s1024="false" token_s2048="false">
+        <option value="1" selected="@S1@">Read is paired</option>
+        <option value="2" selected="@S2@">Read is mapped in a proper pair</option>
+        <option value="4" selected="@S4@">Read is unmapped</option>
+        <option value="8" selected="@S8@">Mate is unmapped</option>
+        <option value="16" selected="@S16@">Read is mapped to the reverse strand of the reference</option>
+        <option value="32" selected="@S32@">Mate is mapped to the reverse strand of the reference</option>
+        <option value="64" selected="@S64@">Read is the first in a pair</option>
+        <option value="128" selected="@S128@">Read is the second in a pair</option>
+        <option value="256" selected="@S256@">Alignment of the read is not primary</option>
+        <option value="512" selected="@S512@">Read fails platform/vendor quality checks</option>
+        <option value="1024" selected="@S1024@">Read is a PCR or optical duplicate</option>
+        <option value="2048" selected="@S2048@">Alignment is supplementary</option>
     </xml>
 
-    <!-- region specification macros and tokens for tools that allow the specification 
+    <!-- region specification macros and tokens for tools that allow the specification
          of region by bed file / space separated list of regions -->
     <token name="@REGIONS_FILE@"><![CDATA[
         #if $cond_region.select_region == 'tab':