--- a/csp2_snp.xml	Thu Dec 19 12:19:14 2024 -0500
+++ b/csp2_snp.xml	Thu Dec 19 12:29:18 2024 -0500
@@ -8,14 +8,41 @@
         <command detect_errors="aggressive"><![CDATA[
 mkdir ./queries ./references;
 
+#set query_fasta_input=""
+#set ref_fasta_input=""
+#set query_reads_forward=""
+#set query_reads_reverse=""
+#set ref_reads_forward=""
+#set ref_reads_reverse=""
 
-#set query_fasta_input=""
-#if $query_fasta.query_fasta_select == 'collection'
+#if "$query_fasta.query_fasta_select" == 'collection'
     #set query_fasta_input=$query_fasta.coll.elements
-#elseif $query_fasta.query_fasta_select == 'history'
+#elseif "$query_fasta.query_fasta_select" == 'history'
     #set query_fasta_input=$query_fasta.list
 #end if
 
+#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 "$query_reads.query_reads_select" == 'collection'
+    #set query_reads_forward=$query_reads.coll.forward
+    #set query_reads_reverse=$query_reads.coll.reverse
+#elseif "$query_reads.query_reads_select" == 'history'
+    #set query_reads_forward=$query_reads.list
+    #set query_reads_reverse=""
+#end if
+
+#if "$ref_reads.ref_reads_select" == 'collection'
+    #set ref_reads_forward=$ref_reads.coll.forward
+    #set ref_reads_reverse=$ref_reads.coll.reverse
+#elseif "$ref_reads.ref_reads_select" == 'history'
+    #set ref_reads_forward=$ref_reads.list
+    #set ref_reads_reverse=""
+#end if
+
 if [[ "$query_fasta.query_fasta_select" == "none" ]]; then
         export QUERY_FASTA_ARG="";
 else
@@ -25,12 +52,6 @@
         export QUERY_FASTA_ARG="--fasta ./queries";
 fi;
 
-#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="";
@@ -41,16 +62,6 @@
         export REF_FASTA_ARG="--fasta ./references";
 fi;
 
-#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="";
 else
@@ -60,16 +71,6 @@
         export QUERY_READS_ARG="--reads ./queries";
 fi;
 
-#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
@@ -79,7 +80,7 @@
         export QUERY_READS_ARG="--reads ./queries";
 fi;
 
-if [[ "$trim_name" != "DUMMYCSP2TRIM" ]]; then
+if [ -n "$trim_name" ] && [ "$trim_name" != "None" ]; then
         export TRIM_ARG="--trim_name $trim_name";
 else
         export TRIM_ARG="";
@@ -172,7 +173,7 @@
                 <param name="readext" type="text" value="fastq.gz" label="Read extension format (e.g., fastq.gz)" optional="true" />
                 <param name="forward" type="text" value="_1.fastq.gz" label="Forward read suffix (e.g. _1.fastq.gz)" optional="true" />
                 <param name="reverse" type="text" value="_2.fastq.gz" label="Forward read suffix (e.g. _2.fastq.gz)" optional="true" />
-                <param name="trim_name" type="text" value="DUMMYCSP2TRIM" label="Text to remove from all file names (e.g., _contigs_skesa)" optional="true" />
+                <param name="trim_name" type="text" value="" label="Text to remove from all file names (e.g., _contigs_skesa)" optional="true" />
                 <param name="rescue" type="boolean" value="false" label="Enable SNP edge rescue mode" optional="true" />
                 <param name="max_missing" type="float" value="50" label="Maximum percent of isolates allowed to have missing data to retain a SNP" optional="true" />
                 <param name="n_ref" type="integer" value="1" label="Number of reference genomes to select" optional="true" />