--- a/cfsan_bettercallsal.xml	Thu Jun 15 11:16:45 2023 -0400
+++ b/cfsan_bettercallsal.xml	Tue Sep 05 11:51:40 2023 -0400
@@ -1,7 +1,7 @@
-<tool id="cfsan_bettercallsal" name="bettercallsal" version="0.2.0+galaxy0">
+<tool id="cfsan_bettercallsal" name="bettercallsal" version="0.6.1">
     <description>An automated workflow to assign Salmonella serotype based on NCBI Pathogen Detection Project for Salmonella.</description>
     <requirements>
-	<requirement type="package" version="22.10">nextflow</requirement>
+	<requirement type="package" version="23.04">nextflow</requirement>
     <requirement type="package" version="1.0.0">micromamba</requirement>
 	<requirement type="package">graphviz</requirement>
     </requirements>    
@@ -35,7 +35,7 @@
 	        ln -sf '$pair.reverse' './cpipes-input/$read_R2';
 	    #end for
     #end if
-	$__tool_directory__/0.5.0/cpipes
+	$__tool_directory__/0.6.1/cpipes
     --pipeline bettercallsal
     --input \${pwd_path}/cpipes-input
 	--output \${pwd_path}/cpipes-output
@@ -49,6 +49,7 @@
     #if ($sourmash_cond.run == "true"):
         --sfhpy_fcv $sourmash_cond.sfhpy_fcv
     #end if
+    --bcs_db_mode $bcs_db_mode
     --bcs_thresholds $bcs_thresholds
 	--fq_filename_delim '${fq_filename_delim}'
 	--fq_filename_delim_idx $fq_filename_delim_idx
@@ -76,6 +77,11 @@
                     help="For any data sets downloaded from NCBI into Galaxy, change this to _reverse.fastq.gz suffix."/>
             </when>
         </conditional>
+        <param name="bcs_db_mode" type="select" label="Select the database mode with bettercallsal"
+            help="Refer to `Database generation` section in our manuscript: https://doi.org/10.3389/fmicb.2023.1200983">
+            <option value="snp" selected="true">per_snp_cluster</option>
+            <option value="comp">per_computed_type</option>
+        </param>
         <param name="tuspy_n" optional="true" value="10" type="integer" label="Enter the number of top unique serotypes to retain after initial MASH screen step"
             help="The default value of 10 is suitable for almost all scenarios."/>
         <param name="bcs_thresholds" type="select" label="Enter the type of base quality thresholds to be set with bettercallsal"
@@ -173,13 +179,14 @@
   ]]></help>
     <citations>
         <citation type="bibtex">
-            @misc{bettercallsal,
+            @article{bettercallsal,
             author = {Konganti, Kranti},
             year = {2023},
+            month = {August},
             title = {bettercallsal: better calling of Salmonella serotypes from enrichment cultures using shotgun metagenomic profiling and its application in an outbreak setting},
-            publisher = {Cold Spring Harbor Laboratory},
-            journal = {bioRxiv},
-            url = {https://www.biorxiv.org/content/10.1101/2023.04.06.535929v1.full}}
+            journal = {Frontiers in Microbiology},
+            doi = {10.3389/fmicb.2023.1200983},
+            url = {https://www.frontiersin.org/articles/10.3389/fmicb.2023.1200983/full}}
         </citation>
     </citations>
 </tool>