--- a/csp2_snp.xml	Thu Dec 19 12:31:39 2024 -0500
+++ b/csp2_snp.xml	Thu Dec 19 13:02:58 2024 -0500
@@ -15,33 +15,44 @@
 #set ref_reads_forward=""
 #set ref_reads_reverse=""
 
-#if "$query_fasta.query_fasta_select" == 'collection'
+export QUERY_FASTA_SELECT="$query_fasta.query_fasta_select"
+export QUERY_READS_SELECT="$query_reads.query_reads_select"
+export REF_FASTA_SELECT="$ref_fasta.ref_fasta_select"
+export REF_READS_SELECT="$ref_reads.ref_reads_select"
+
+if [[ "\$QUERY_FASTA_SELECT" == 'collection' ]]; then
     #set query_fasta_input=$query_fasta.coll.elements
-#elseif "$query_fasta.query_fasta_select" == 'history'
+elif [[ "\$QUERY_FASTA_SELECT" == 'history' ]]; then
     #set query_fasta_input=$query_fasta.list
-#end if
+fi;
 
-#if "$ref_fasta.ref_fasta_select" == 'collection'
+if [[ "\$REF_FASTA_SELECT" == 'collection' ]]; then
     #set ref_fasta_input=$ref_fasta.coll.elements
-#elseif "$ref_fasta.ref_fasta_select" == 'history'
+elif [[ "\$REF_FASTA_SELECT" == 'history' ]]; then
     #set ref_fasta_input=$ref_fasta.list
-#end if
+fi;
 
-#if "$query_reads.query_reads_select" == 'collection'
+if [[ "\$QUERY_READS_SELECT" == 'collection' ]]; then
     #set query_reads_forward=$query_reads.coll.forward
     #set query_reads_reverse=$query_reads.coll.reverse
-#elseif "$query_reads.query_reads_select" == 'history'
+elif [[ "\$QUERY_READS_SELECT" == 'history' ]]; then
     #set query_reads_forward=$query_reads.list
-#end if
+fi;
 
-#if "$ref_reads.ref_reads_select" == 'collection'
+if [[ "\$REF_READS_SELECT" == 'collection' ]]; then
     #set ref_reads_forward=$ref_reads.coll.forward
     #set ref_reads_reverse=$ref_reads.coll.reverse
-#elseif "$ref_reads.ref_reads_select" == 'history'
+elif [[ "\$REF_READS_SELECT" =='history' ]]; then
     #set ref_reads_forward=$ref_reads.list
-#end if
+fi;
 
-if [[ "$query_fasta.query_fasta_select" == "none" ]]; then
+echo "Query Fasta: \$QUERY_FASTA_SELECT";
+echo "Ref Fasta: \$REF_FASTA_SELECT";
+
+echo "Query Reads: \$QUERY_READS_SELECT";
+echo "Ref Reads: \$REF_READS_SELECT";
+
+if [[ "\$QUERY_FASTA_SELECT" == 'none']]; then
         export QUERY_FASTA_ARG="";
 else
         #for query in $query_fasta_input: