--- a/csp2_snp.xml	Thu Dec 19 09:14:29 2024 -0500
+++ b/csp2_snp.xml	Thu Dec 19 10:43:45 2024 -0500
@@ -8,64 +8,69 @@
         <command detect_errors="aggressive"><![CDATA[
 mkdir ./queries ./references;
 
-if [ -n "$query_fasta" ] && [ "$query_fasta" != "None" ]; then
-        if [ -n "$use_query_fasta_collection" == "true" ]; then
-                #for query in $query_fasta_ELEMENTS:
-                        ln -sf ${query} ./queries/${query.element_identifier};
-                #end for
-        else
-                #for query in $query_fasta:
-                        ln -sf ${query} ./queries/${query.element_identifier};
-                #end for
+if [[ "$query_fasta.query_fasta_select" == "none" ]]; then
+        export QUERY_FASTA_ARG="";
+elif [[ "$query_fasta.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
-        export QUERY_FASTA_ARG="";
+        #for query in $query_fasta.elements:
+                ln -sf ${query} ./queries/${query.element_identifier};
+        #end for
+        export QUERY_FASTA_ARG="--fasta ./queries";
 fi;
 
-if [ -n "$query_reads" ] && [ "$query_reads" != "None" ]; then
-        if [ -n "$use_query_reads_collection" == "true" ]; 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";
+if [[ "$ref_fasta.ref_fasta_select" == "none" ]]; then
+        export REF_FASTA_ARG="";
+elif [[ "$ref_fasta.ref_fasta_select" == "history" ]]; then
+        #for ref in $ref_fasta.list:
+                ln -sf ${ref} ./references/${ref.element_identifier};
+        #end for
+        export REF_FASTA_ARG="--ref_fasta ./references";
 else
-        export QUERY_READS_ARG="";
+        #for ref in $ref_fasta.elements:
+                ln -sf ${ref} ./references/${ref.element_identifier};
+        #end for
+        export REF_FASTA_ARG="--ref_fasta ./references";
 fi;
 
-if [ -n "$ref_fasta" ] && [ "$ref_fasta" != "None" ]; then
-        if [ -n "$use_ref_fasta_collection" == "true" ]; 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";
+if [[ "$query_reads.query_reads_select" == "none" ]]; then
+        export QUERY_READS_ARG="";
+elif [[ "$query_reads.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
-        export REF_FASTA_ARG="";
+        #for query in $query_reads.coll.forward:
+                ln -sf ${query} ./queries/${query.element_identifier};
+        #end for
+        #for query in $query_reads.coll.reverse:
+                ln -sf ${query} ./queries/${query.element_identifier};
+        #end for
+        export QUERY_READS_ARG="--reads ./queries";
 fi;
 
-if [ -n "$ref_reads" ] && [ "$ref_reads" != "None" ]; then
-        if [ -n "$use_ref_reads_collection" == "true" ]; 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
+if [[ "$ref_reads.ref_reads_select" == "none" ]]; then
+        export REF_READS_ARG="";
+elif [[ "$ref_reads.ref_reads_select" == "history" ]]; then
+        #for ref in $ref_reads.list:
+                ln -sf ${ref} ./references/${ref.element_identifier};
+        #end for
         export REF_READS_ARG="--ref_reads ./references";
 else
-        export REF_READS_ARG="";
+        #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";
 fi;
 
-
-if [ -n "$trim_name" ] && [ "$trim_name" != "None" ]; then
+if [[ "$trim_name" != "DUMMYCSP2TRIM" ]]; then
         export TRIM_ARG="--trim_name $trim_name";
 else
         export TRIM_ARG="";
@@ -85,14 +90,69 @@
 ]]>
         </command>
         <inputs>
-                <param name="query_fasta" type="data" format="fasta" value="" label="Query assemblies" multiple="true" optional="true" />
-                <param name="use_query_fasta_collection" type="boolean" value="false" label="Use a collection for query assemblies?" optional="true" />
-                <param name="ref_fasta" type="data" format="fasta" value="" label="Reference assemblies" multiple="true" optional="true" />
-                <param name="use_ref_fasta_collection" type="boolean" value="false" label="Use a collection for reference assemblies?" optional="true" />
-                <param name="query_reads" type="data" format="fastq,fastq.gz" value="" label="Query reads" multiple="true" optional="true" />
-                <param name="use_ref_reads_collection" type="boolean" value="false" label="Use a collection for query reads?" optional="true" />
-                <param name="ref_reads" type="data" format="fastq,fastq.gz" value="" label="Reference reads" multiple="true" optional="true" />
-                <param name="use_ref_reads_collection" type="boolean" value="false" label="Use a collection for reference reads?" optional="true" />
+                <conditional name="query_fasta">
+                <param name="query_fasta_select" type="select" label="Get query assemblies from a collection or your history">
+                        <option value="none" selected="true">Do not provide query assemblies</option>
+                        <option value="collection">Query assemblies from a collection_type</option>
+                        <option value="history">Query assemblies from your history</option>
+                </param>
+                <when value="none">
+                </when>
+                <when value="collection">
+                        <param label="Query Assembly Collection" name="coll" type="data_collection" format="fasta" collection_type="list" />
+                </when>
+                <when value="history">
+                        <param label="Query Assembly List" type="data" name="list" format="fasta"  multiple="true" />
+                </when>
+                </conditional>
+
+                <conditional name="ref_fasta">
+                <param name="ref_fasta_select" type="select" label="Get reference assemblies from a collection or your history">
+                        <option value="none" selected="true">Do not provide reference assemblies</option>
+                        <option value="collection">Reference assemblies from a collection_type</option>
+                        <option value="history">Reference assemblies from your history</option>
+                </param>
+                <when value="none">
+                </when>
+                <when value="collection">
+                        <param label="Reference Assembly Collection" name="coll" type="data_collection" format="fasta" collection_type="list" />
+                </when>
+                <when value="history">
+                        <param label="Reference Assembly List" type="data" name="list" format="fasta"  multiple="true" />
+                </when>
+                </conditional>   
+                <conditional name="query_reads">
+                <param name="query_reads_select" type="select" label="Get query reads from a paired-end collection or your history">
+                        <option value="none" selected="true">Do not provide query reads</option>
+                        <option value="collection">Query reads from a collection_type</option>
+                        <option value="history">Query reads from your history</option>
+                </param>
+                <when value="none">
+                </when>
+                <when value="collection">
+                        <param label="Query Reads Collection" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="paired" />
+                </when>
+                <when value="history">
+                        <param label="Query Reads List" type="data" name="list" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2"  multiple="true" />
+                </when>
+                </conditional>
+
+                <conditional name="ref_reads">
+                <param name="ref_reads_select" type="select" label="Get reference reads from a paired-end collection or your history">
+                        <option value="none" selected="true">Do not provide reference reads</option>
+                        <option value="collection">Refrence reads from a collection_type</option>
+                        <option value="history">Refrence reads from your history</option>
+                </param>
+                <when value="none">
+                </when>
+                <when value="collection">
+                        <param label="Refrence Reads Collection" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="paired" />
+                </when>
+                <when value="history">
+                        <param label="Refrence Reads List" type="data" name="list" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2"  multiple="true" />
+                </when>
+                </conditional>             
+                
                 <param name="min_cov" type="float" value="85" label="Minimum reference genome coverage to proceed with distance estimation" optional="true" />
                 <param name="min_iden" type="float" value="99" label="Minimum alignment percent identity to detect SNPs" optional="true" />
                 <param name="min_len" type="integer" value="500" label="Minimum alignment length to detect SNPs" optional="true" />
@@ -103,7 +163,7 @@
                 <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="" label="Text to remove from all file names (e.g., _contigs_skesa)" 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="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" />