--- a/macros.xml	Thu Jul 15 15:45:43 2021 +0000
+++ b/macros.xml	Thu Jan 27 08:20:15 2022 +0000
@@ -1,11 +1,11 @@
 <macros>
-    <token name="@TOOL_VERSION@">11.25.1</token>
+    <token name="@TOOL_VERSION@">12.27.1</token>
     <token name="@PROFILE@">20.01</token>
     <token name="@LICENSE@">MIT</token>
     <token name="@PROFILE_AND_LICENSE@">profile="@PROFILE@" license="@LICENSE@"</token>
     <token name="@SETUP_CERTIFICATES@"><![CDATA[
 ## If running in container use certificate from ca-certificates instead of outdated / missing container certificates
-[ -f /usr/local/ssl/cacert.pem ] && export export SSL_CERT_FILE="/usr/local/ssl/cacert.pem";
+[ -f /usr/local/ssl/cacert.pem ] && export SSL_CERT_FILE="/usr/local/ssl/cacert.pem";
         ]]></token>
     <xml name="requirements">
         <requirements>
@@ -51,7 +51,7 @@
         </conditional>
     </xml>
     <xml name="chromosomes">
-        <param argument="--chromosomes" type="text" value="all" label="Limit chromosomes to a comma-delimited list of chromosomes">
+        <param argument="--chromosomes" type="text" label="Limit chromosomes to a comma-delimited list of chromosomes">
             <sanitizer invalid_char="">
                 <valid initial="string.letters,string.digits">
                     <add value="_" />
@@ -61,14 +61,25 @@
             </sanitizer>
         </param>
     </xml>
+    <xml name="include" token_include_what="gbff" token_include_label="Include GenBank flat file sequence and annotation, if available">
+        <param argument="--include-@INCLUDE_WHAT@" type="boolean" truevalue="--include-@INCLUDE_WHAT@" falsevalue="" label="@INCLUDE_LABEL@" />
+    </xml>
+    <xml name="includes_genome">
+        <expand macro="include" include_what="gbff" include_label="Include GenBank flat file sequence and annotation, if available"/>
+        <expand macro="include" include_what="gtf" include_label="Include gtf annotation file, if available"/>
+    </xml>
     <xml name="exclude" token_exclude_what="gff3" token_exclude_label="Exclude gff3 annotation file">
         <param argument="--exclude-@EXCLUDE_WHAT@" type="boolean" truevalue="--exclude-@EXCLUDE_WHAT@" falsevalue="" label="@EXCLUDE_LABEL@" />
     </xml>
+    <xml name="anti-exclude" token_exclude_what="gff3" token_exclude_label="Include gff3 annotation file" token_checked="false">
+        <param argument="--exclude-@EXCLUDE_WHAT@" type="boolean" falsevalue="--exclude-@EXCLUDE_WHAT@" truevalue="" label="@EXCLUDE_LABEL@" checked="@CHECKED@"/>
+    </xml>
     <xml name="excludes_genome">
-        <expand macro="exclude" exclude_what="gff3" exclude_label="Exclude gff3 annotation file"/>
-        <expand macro="exclude" exclude_what="protein" exclude_label="Exclude protein sequence file"/>
-        <expand macro="exclude" exclude_what="rna" exclude_label="Exclude transcript sequence file"/>
-        <expand macro="exclude" exclude_what="seq" exclude_label="Exclude genomic sequence file"/>
+        <expand macro="anti-exclude" exclude_what="seq" exclude_label="Include genomic sequence file" checked="true"/>
+        <expand macro="anti-exclude" exclude_what="gff3" exclude_label="Include gff3 annotation file"/>
+        <expand macro="anti-exclude" exclude_what="genomic-cds" exclude_label="Include cds from genomic sequence file"/>
+        <expand macro="anti-exclude" exclude_what="protein" exclude_label="Include protein sequence file"/>
+        <expand macro="anti-exclude" exclude_what="rna" exclude_label="Include transcript sequence file"/>
     </xml>
     <xml name="excludes_gene">
         <expand macro="exclude" exclude_what="gene" exclude_label="Exclude gene sequence file"/>
@@ -87,31 +98,24 @@
             <expand macro="exclude" exclude_what="seq" exclude_label="Exclude genomic sequence file"/>
         </expand>
     </xml>
-    <token name="@EXCLUDES_GENOME@">$exclude_gff3 $exclude_protein $exclude_rna $exclude_seq</token>
+    <token name="@EXCLUDES_GENOME@">$file_choices.exclude_gff3 $file_choices.exclude_genomic_cds $file_choices.exclude_protein $file_choices.exclude_rna $file_choices.exclude_seq</token>
     <token name="@EXCLUDES_GENE@">$exclude_gene $exclude_protein $exclude_rna</token>
     <token name="@EXCLUDES_VIRUS_PROTEIN@">$exclude_protein $exclude_pdb $exclude_gpff $exclude_cds</token>
     <token name="@EXCLUDES_VIRUS_GENOME@">$exclude_seq @EXCLUDES_VIRUS_PROTEIN@</token>
-    <xml name="include" token_include_what="gbff" token_include_label="Include GenBank flat file sequence and annotation, if available">
-        <param argument="--include-@INCLUDE_WHAT@" type="boolean" truevalue="--include-@INCLUDE_WHAT@" falsevalue="" label="@INCLUDE_LABEL@" />
-    </xml>
-    <xml name="includes_genome">
-        <expand macro="include" include_what="gbff" include_label="Include GenBank flat file sequence and annotation, if available"/>
-        <expand macro="include" include_what="gtf" include_label="Include gtf annotation file, if available"/>
-    </xml>
     <xml name="includes_virus_genome">
         <expand macro="include" include_what="gbff" include_label="Include GenBank flat file sequence and annotation"/>
     </xml>
-    <token name="@INCLUDES_GENOME@">$include_gbff $include_gtf</token>
+    <token name="@INCLUDES_GENOME@">$file_choices.include_gbff $file_choices.include_gtf</token>
     <token name="@INCLUDES_VIRUS_GENOME@">$include_gbff</token>
     <xml name="released_options" token_released_what="genomes" token_before_or_after="before">
         <param argument="--released-@BEFORE_OR_AFTER@" type="text" optional="true" label="Only include @RELEASED_WHAT@ that have been released @BEFORE_OR_AFTER@ a specified date (MM/DD/YYYY)"></param>
     </xml>
-    <token name="@RELEASED_BEFORE@">#if $released_before:
---released-before '$released_before'
+    <token name="@RELEASED_BEFORE@">#if $filters.released_before:
+--released-before '$filters.released_before'
 #end if
     </token>
-    <token name="@RELEASED_SINCE@">#if $released_since:
---released-since '$released_since'
+    <token name="@RELEASED_SINCE@">#if $filters.released_since:
+--released-since '$filters.released_since'
 #end if
     </token>
-</macros>
\ No newline at end of file
+</macros>