--- a/csp2_snp.xml	Fri Dec 13 08:59:02 2024 -0500
+++ b/csp2_snp.xml	Thu Dec 19 08:53:33 2024 -0500
@@ -9,41 +9,62 @@
 mkdir ./queries ./references;
 
 if [ -n "$query_fasta" ] && [ "$query_fasta" != "None" ]; then
-        #for query in $query_fasta:
+        if [ -n "$query_fasta__collection_type" ]; then
+                #for query in $query_fasta_ELEMENTS:
                         ln -sf ${query} ./queries/${query.element_identifier};
-        #end for
+                #end for
+        else
+                #for query in $query_fasta:
+                        ln -sf ${query} ./queries/${query.element_identifier};
+                #end for
         export QUERY_FASTA_ARG="--fasta ./queries";
 else
         export QUERY_FASTA_ARG="";
 fi;
 
 if [ -n "$query_reads" ] && [ "$query_reads" != "None" ]; then
-        #for query in $query_reads:
-                ln -sf ${query} ./queries/${query.element_identifier};
-        #end for
-        export QUERY_READS_ARG="--reads ./queries";
+        if [ -n "$query_reads__collection_type" ]; then
+                #for query in $query_reads_ELEMENTS:
+                        ln -sf ${query} ./queries/${query.element_identifier};
+                #end for
+        else
+                #for query in $query_reads:
+                        ln -sf ${query} ./queries/${query.element_identifier};
+                #end for
+                export QUERY_READS_ARG="--reads ./queries";
 else
         export QUERY_READS_ARG="";
 fi;
 
 if [ -n "$ref_fasta" ] && [ "$ref_fasta" != "None" ]; then
-        #for ref in $ref_fasta:
-                ln -sf ${ref} ./references/${ref.element_identifier};
-        #end for
+        if [ -n "$ref_fasta__collection_type" ]; then
+                #for ref in $ref_fasta_ELEMENTS:
+                        ln -sf ${ref} ./references/${ref.element_identifier};
+                #end for
+        else
+                #for ref in $ref_fasta:
+                        ln -sf ${ref} ./references/${ref.element_identifier};
+                #end for
         export REF_FASTA_ARG="--ref_fasta ./references";
 else
         export REF_FASTA_ARG="";
 fi;
 
 if [ -n "$ref_reads" ] && [ "$ref_reads" != "None" ]; then
-        #for ref in $ref_reads:
-                ln -sf ${ref} ./references/${ref.element_identifier};
-        #end for
+        if [ -n "$ref_reads__collection_type" ]; then
+                #for ref in $ref_reads_ELEMENTS:
+                        ln -sf ${ref} ./references/${ref.element_identifier};
+                #end for
+        else
+                #for ref in $ref_reads:
+                        ln -sf ${ref} ./references/${ref.element_identifier};
+                #end for
         export REF_READS_ARG="--ref_reads ./references";
 else
         export REF_READS_ARG="";
 fi;
 
+
 if [ -n "$trim_name" ] && [ "$trim_name" != "None" ]; then
         export TRIM_ARG="--trim_name $trim_name";
 else
@@ -57,7 +78,6 @@
 fi;
 
 nextflow run ${__tool_directory__}/CSP2/CSP2.nf -profile csp2_galaxy --runmode snp \$QUERY_FASTA_ARG \$REF_FASTA_ARG \$QUERY_READS_ARG \$REF_READS_ARG \$TRIM_ARG \$RESCUE_ARG --readext $readext --forward $forward --reverse $reverse --ref_readext $readext --ref_forward $forward --ref_reverse $reverse --min_cov $min_cov --min_iden $min_iden --min_len $min_len --ref_edge $ref_edge --query_edge $query_edge --dwin $dwin --wsnps $wsnps --max_missing $max_missing --n_ref $n_ref --out ./CSP2_SNP_Output > Nextflow_Log.txt 2>&1 &&
-ls -la CSP2_SNP_Output/SNP_Analysis/* &&
 mkdir CSP2_Output &&
 cat CSP2_SNP_Output/logs/Reference_IDs.txt | while read line; do cp 'CSP2_SNP_Output/SNP_Analysis/'\$line'/CSP2_SNP_Pipeline.log' 'CSP2_Output/'\$line'_CSP2_SNP_Pipeline.log'; cp 'CSP2_SNP_Output/SNP_Analysis/'\$line'/Reference_Screening.tsv' 'CSP2_Output/'\$line'_Reference_Screening.tsv';  cp 'CSP2_SNP_Output/SNP_Analysis/'\$line'/snp_distance_matrix_preserved.tsv' 'CSP2_Output/'\$line'_snp_distance_matrix_preserved.tsv'; cp 'CSP2_SNP_Output/SNP_Analysis/'\$line'/snp_distance_pairwise_preserved.tsv' 'CSP2_Output/'\$line'_snp_distance_pairwise_preserved.tsv'; cp 'CSP2_SNP_Output/SNP_Analysis/'\$line'/snpma_preserved.fasta' 'CSP2_Output/'\$line'_snpma_preserved.fasta';done &&
 ls -la CSP2_Output;