# HG changeset patch
# User rliterman
# Date 1734617669 18000
# Node ID d0a7dd5c900ebe58880b4385e5e5458300c36d6d
# Parent  a21f63856acf8e56bdeb8f2a1346d863e9ce84d6
"planemo upload"

diff -r a21f63856acf -r d0a7dd5c900e csp2_snp.xml
--- a/csp2_snp.xml	Thu Dec 19 08:53:33 2024 -0500
+++ b/csp2_snp.xml	Thu Dec 19 09:14:29 2024 -0500
@@ -9,7 +9,7 @@
 mkdir ./queries ./references;
 
 if [ -n "$query_fasta" ] && [ "$query_fasta" != "None" ]; then
-        if [ -n "$query_fasta__collection_type" ]; then
+        if [ -n "$use_query_fasta_collection" == "true" ]; then
                 #for query in $query_fasta_ELEMENTS:
                         ln -sf ${query} ./queries/${query.element_identifier};
                 #end for
@@ -23,7 +23,7 @@
 fi;
 
 if [ -n "$query_reads" ] && [ "$query_reads" != "None" ]; then
-        if [ -n "$query_reads__collection_type" ]; then
+        if [ -n "$use_query_reads_collection" == "true" ]; then
                 #for query in $query_reads_ELEMENTS:
                         ln -sf ${query} ./queries/${query.element_identifier};
                 #end for
@@ -37,7 +37,7 @@
 fi;
 
 if [ -n "$ref_fasta" ] && [ "$ref_fasta" != "None" ]; then
-        if [ -n "$ref_fasta__collection_type" ]; then
+        if [ -n "$use_ref_fasta_collection" == "true" ]; then
                 #for ref in $ref_fasta_ELEMENTS:
                         ln -sf ${ref} ./references/${ref.element_identifier};
                 #end for
@@ -51,7 +51,7 @@
 fi;
 
 if [ -n "$ref_reads" ] && [ "$ref_reads" != "None" ]; then
-        if [ -n "$ref_reads__collection_type" ]; then
+        if [ -n "$use_ref_reads_collection" == "true" ]; then
                 #for ref in $ref_reads_ELEMENTS:
                         ln -sf ${ref} ./references/${ref.element_identifier};
                 #end for
@@ -86,9 +86,13 @@
         </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" />
                 <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" />