# HG changeset patch
# User rliterman
# Date 1733261735 18000
# Node ID 6f85641ecd4807129ace746a7091603d22d8c59f
# Parent  5c609acba34e1330a4392d01c13b590208477fcc
"planemo upload"

diff -r 5c609acba34e -r 6f85641ecd48 csp_screen.xml
--- a/csp_screen.xml	Tue Dec 03 15:56:32 2024 -0500
+++ b/csp_screen.xml	Tue Dec 03 16:35:35 2024 -0500
@@ -57,10 +57,10 @@
 		export REF_ID_ARG="";
 fi;
 
-		nextflow run ${__tool_directory__}/CSP2/CSP2.nf -profile csp2_galaxy --runmode screen \$QUERY_FASTA_ARG \$REF_FASTA_ARG \$QUERY_READS_ARG \$REF_READS_ARG \$REF_ID_ARG \$TRIM_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 --cores 8 --out \$CSP2_DIR/CSP2_Screen_Output > Nextflow_Log.txt 2>&1;
+		nextflow run ${__tool_directory__}/CSP2/CSP2.nf -profile csp2_galaxy --cores $cores --runmode screen \$QUERY_FASTA_ARG \$REF_FASTA_ARG \$QUERY_READS_ARG \$REF_READS_ARG \$REF_ID_ARG \$TRIM_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 --cores 8 --out \$CSP2_DIR/CSP2_Screen_Output > Nextflow_Log.txt 2>&1;
 
-		zip -r work.zip work
-		zip -r csp2.zip CSP2_Screen_Output
+		zip -r work.zip work;
+		zip -r csp2.zip CSP2_Screen_Output;
 	]]>
 	</command>
 	<inputs>
@@ -73,6 +73,7 @@
 		<param name="min_len" type="integer" value="500" label="Minimum alignment length to detect SNPs" optional="true" />
 		<param name="ref_edge" type="integer" value="150" label="Prune SNPs within this many bases of reference contig edge" optional="true" />
 		<param name="query_edge" type="integer" value="150" label="Prune SNPs within this many bases of query contig edge" optional="true" />
+                <param name="cores" type="integer" value="2" label="Available cores per node" 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="fastq.gz" label="Read extension format (e.g., fastq.gz)" optional="true" />