--- a/csp2_snp.xml	Thu Dec 19 11:22:22 2024 -0500
+++ b/csp2_snp.xml	Thu Dec 19 12:19:14 2024 -0500
@@ -8,71 +8,75 @@
         <command detect_errors="aggressive"><![CDATA[
 mkdir ./queries ./references;
 
-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
+#set query_fasta_input=""
+#if $query_fasta.query_fasta_select == 'collection'
+    #set query_fasta_input=$query_fasta.coll.elements
+#elseif $query_fasta.query_fasta_select == 'history'
+    #set query_fasta_input=$query_fasta.list
+#end if
+
+if [[ "$query_fasta.query_fasta_select" == "none" ]]; then
         export QUERY_FASTA_ARG="";
-elif [[ "\$QUERY_FASTA_SELECT" == "history" ]]; then
-        #for query in $query_fasta.list:
-                ln -sf ${query} ./queries/${query.element_identifier};
-        #end for
-        export QUERY_FASTA_ARG="--fasta ./queries";
 else
-        #for query in $query_fasta.coll.elements:
+        #for query in $query_fasta_input:
                 ln -sf ${query} ./queries/${query.element_identifier};
         #end for
         export QUERY_FASTA_ARG="--fasta ./queries";
 fi;
 
-if [[ "\$REF_FASTA_SELECT" == "none" ]]; then
+#set ref_fasta_input=""
+#if $ref_fasta.ref_fasta_select == 'collection'
+    #set ref_fasta_input=$ref_fasta.coll.elements
+#elseif $ref_fasta.ref_fasta_select == 'history'
+    #set ref_fasta_input=$ref_fasta.list
+#end if
+
+if [[ "$ref_fasta.ref_fasta_select" == "none" ]]; then
         export REF_FASTA_ARG="";
-elif [[ "\$REF_FASTA_SELECT" == "history" ]]; then
-        #for ref in $ref_fasta.list:
+else
+        #for ref in $ref_fasta_input:
                 ln -sf ${ref} ./references/${ref.element_identifier};
         #end for
-        export REF_FASTA_ARG="--ref_fasta ./references";
-else
-        #for ref in $ref_fasta.coll.elements:
-                ln -sf ${ref} ./references/${ref.element_identifier};
-        #end for
-        export REF_FASTA_ARG="--ref_fasta ./references";
+        export REF_FASTA_ARG="--fasta ./references";
 fi;
 
-if [[ "\$QUERY_READS_SELECT" == "none" ]]; then
+#set query_reads_forward=""
+#set query_reads_reverse=""
+#if $query_reads.query_reads_select == 'collection'
+    #set query_reads_forward=$query_reads.coll.forward
+    #set query_reads_reverse=$query_reads.coll.revese
+#elseif $query_reads.query_reads_select == 'history'
+    #set query_reads_forward=$query_reads.list
+    #set query_reads_reverse=""
+#end if
+
+if [[ "$query_reads.query_reads_select" == "none" ]]; then
         export QUERY_READS_ARG="";
-elif [[ "\$QUERY_READS_SELECT" == "history" ]]; then
-        #for query in $query_reads.list:
-                ln -sf ${query} ./queries/${query.element_identifier};
-        #end for
-        export QUERY_READS_ARG="--reads ./queries";
 else
-        #for query in $query_reads.coll.forward:
-                ln -sf ${query} ./queries/${query.element_identifier};
-        #end for
-        #for query in $query_reads.coll.reverse:
+        #for query in $query_reads_forward $query_reads_reverse:
                 ln -sf ${query} ./queries/${query.element_identifier};
         #end for
         export QUERY_READS_ARG="--reads ./queries";
 fi;
 
-if [[ "\$REF_READS_SELECT" == "none" ]]; then
-        export REF_READS_ARG="";
-elif [[ "\$REF_READS_SELECT" == "history" ]]; then
-        #for ref in $ref_reads.list:
+#set ref_reads_forward=""
+#set ref_reads_reverse=""
+#if $ref_reads.ref_reads_select == 'collection'
+    #set ref_reads_forward=$ref_reads.coll.forward
+    #set ref_reads_reverse=$ref_reads.coll.revese
+#elseif $ref_reads.ref_reads_select == 'history'
+    #set ref_reads_forward=$ref_reads.list
+    #set ref_reads_reverse=""
+#end if
+
+if [[ "$ref_reads.ref_reads_select" == "none" ]]; then
+        export QUERY_READS_ARG="";
+else
+        #for ref in $ref_reads_forward $ref_reads_reverse:
                 ln -sf ${ref} ./references/${ref.element_identifier};
         #end for
-        export REF_READS_ARG="--ref_reads ./references";
-else
-        #for ref in $ref_reads.coll.forward:
-                ln -sf ${ref} ./references/${ref.element_identifier};
-        #end for
-        #for ref in $ref_reads.coll.reverse:
-                ln -sf ${ref} ./references/${ref.element_identifier};
-        #end for
-        export REF_READS_ARG="--ref_reads ./references";
+        export QUERY_READS_ARG="--reads ./queries";
 fi;
 
 if [[ "$trim_name" != "DUMMYCSP2TRIM" ]]; then