--- a/csp2_snp.xml	Thu Dec 19 10:56:32 2024 -0500
+++ b/csp2_snp.xml	Thu Dec 19 11:22:22 2024 -0500
@@ -8,9 +8,14 @@
         <command detect_errors="aggressive"><![CDATA[
 mkdir ./queries ./references;
 
-if [[ "$query_fasta.query_fasta_select" == "none" ]]; then
+export QUERY_FASTA_SELECT="${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="${ref_reads.ref_reads_select}"
+
+if [[ "\$QUERY_FASTA_SELECT" == "none" ]]; then
         export QUERY_FASTA_ARG="";
-elif [[ "$query_fasta.query_fasta_select" == "history" ]]; then
+elif [[ "\$QUERY_FASTA_SELECT" == "history" ]]; then
         #for query in $query_fasta.list:
                 ln -sf ${query} ./queries/${query.element_identifier};
         #end for
@@ -22,9 +27,9 @@
         export QUERY_FASTA_ARG="--fasta ./queries";
 fi;
 
-if [[ "$ref_fasta.ref_fasta_select" == "none" ]]; then
+if [[ "\$REF_FASTA_SELECT" == "none" ]]; then
         export REF_FASTA_ARG="";
-elif [[ "$ref_fasta.ref_fasta_select" == "history" ]]; then
+elif [[ "\$REF_FASTA_SELECT" == "history" ]]; then
         #for ref in $ref_fasta.list:
                 ln -sf ${ref} ./references/${ref.element_identifier};
         #end for
@@ -36,9 +41,9 @@
         export REF_FASTA_ARG="--ref_fasta ./references";
 fi;
 
-if [[ "$query_reads.query_reads_select" == "none" ]]; then
+if [[ "\$QUERY_READS_SELECT" == "none" ]]; then
         export QUERY_READS_ARG="";
-elif [[ "$query_reads.query_reads_select" == "history" ]]; then
+elif [[ "\$QUERY_READS_SELECT" == "history" ]]; then
         #for query in $query_reads.list:
                 ln -sf ${query} ./queries/${query.element_identifier};
         #end for
@@ -53,9 +58,9 @@
         export QUERY_READS_ARG="--reads ./queries";
 fi;
 
-if [[ "$ref_reads.ref_reads_select" == "none" ]]; then
+if [[ "\$REF_READS_SELECT" == "none" ]]; then
         export REF_READS_ARG="";
-elif [[ "$ref_reads.ref_reads_select" == "history" ]]; then
+elif [[ "\$REF_READS_SELECT" == "history" ]]; then
         #for ref in $ref_reads.list:
                 ln -sf ${ref} ./references/${ref.element_identifier};
         #end for