# HG changeset patch
# User rliterman
# Date 1733434258 18000
# Node ID 106d28c851fa39fd5b37d82d611cae635e1248c3
# Parent  499342837ad784115fa36b97fd25f8f8c2656731
"planemo upload"

diff -r 499342837ad7 -r 106d28c851fa csp2_snp.xml
--- a/csp2_snp.xml	Thu Dec 05 15:38:54 2024 -0500
+++ b/csp2_snp.xml	Thu Dec 05 16:30:58 2024 -0500
@@ -59,7 +59,7 @@
 
 nextflow run ${__tool_directory__}/CSP2/CSP2.nf -profile csp2_galaxy1 --runmode snp \$QUERY_FASTA_ARG \$REF_FASTA_ARG \$QUERY_READS_ARG \$REF_READS_ARG \$TRIM_ARG \$RESCUE_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 --max_missing $max_missing --out \$CSP2_DIR/CSP2_SNP_Output > Nextflow_Log.txt 2>&1;
 
-mkdir -p Output; for file in CSP2_SNP_Output/SNP_Analysis/*/*; do ln -sf "\$file" Output/; done
+mkdir -p Output; for file in CSP2_SNP_Output/SNP_Analysis/*/*; do ln -sf "\$file" Output/; done;
 zip -r CSP2_Output.zip CSP2_SNP_Output;
 ]]>
         </command>