--- a/csp2_snp.xml	Thu Dec 19 15:55:32 2024 -0500
+++ b/csp2_snp.xml	Thu Dec 19 18:42:33 2024 -0500
@@ -89,7 +89,7 @@
                 <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="collection">Query assemblies from a FASTA collection</option>
                         <option value="history">Query assemblies from your history</option>
                 </param>
                 <when value="none">
@@ -105,7 +105,7 @@
                 <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="collection">Reference assemblies from a FASTA collection</option>
                         <option value="history">Reference assemblies from your history</option>
                 </param>
                 <when value="none">
@@ -120,7 +120,7 @@
                 <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="collection">Paired-end query reads from a collection</option>
                         <option value="history">Query reads from your history</option>
                 </param>
                 <when value="none">
@@ -136,8 +136,8 @@
                 <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>
+                        <option value="collection">Paired-end reference reads from a collection_type</option>
+                        <option value="history">Reference reads from your history</option>
                 </param>
                 <when value="none">
                 </when>
@@ -156,13 +156,13 @@
                 <param name="query_edge" type="integer" value="150" label="Prune SNPs within this many bases of query contig edge" optional="true" />
                 <param name="dwin" type="text" value="1000,125,15" label="Comma-separated set of window sizes for SNP density filtration (Set to 0 to disable density filtration)" optional="true" />
                 <param name="wsnps" type="text" value="3,2,1" label="Comma-separated list of maximum SNP counts per density window" optional="true" />
-                <param name="readext" type="text" value="fq.gz" label="Read extension format (e.g., fastq.gz)" optional="true" />
-                <param name="forward" type="text" value="_1.fq.gz" label="Forward read suffix (e.g. _1.fastq.gz)" optional="true" />
-                <param name="reverse" type="text" value="_2.fq.gz" label="Forward read suffix (e.g. _2.fastq.gz)" optional="true" />
+                <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="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" />
+                <param name="n_ref" type="integer" value="1" label="Number of reference genomes to select (disabled if reference reads/assemblies are provided)" optional="true" />
 
         </inputs>
         <outputs>