# HG changeset patch
# User rliterman
# Date 1733179076 18000
# Node ID 2ab525820ff25922615748989c14111a6243045c
# Parent  89d3f54fc370b126b0d3a89a94d0fbfd6996b747
"planemo upload"

diff -r 89d3f54fc370 -r 2ab525820ff2 csp2_screen.xml
--- a/csp2_screen.xml	Mon Dec 02 17:31:42 2024 -0500
+++ b/csp2_screen.xml	Mon Dec 02 17:37:56 2024 -0500
@@ -57,7 +57,7 @@
                 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 > \$CSP2_DIR/CSP2_Screen_Output/Nextflow_Log.txt 2>&1;
+			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;
         ]]>
 		</command>
 		<inputs>
@@ -81,7 +81,7 @@
 		<outputs>
 				<data name="screening_results" format="tabular" label="Screening Results" from_work_dir="CSP2_Screen_Output/Screening_Results.tsv" />
 				<data name="isolate_data" format="tabular" label="Isolate Data" from_work_dir="CSP2_Screen_Output/Isolate_Data.tsv" />
-				<data name="nextflow_log" format="txt" label="Nextflow Log" from_work_dir="CSP2_Screen_Output/Nextflow_Log.txt" />
+				<data name="nextflow_log" format="txt" label="Nextflow Log" from_work_dir="Nextflow_Log.txt" />
 		</outputs>
 		<tests>
 			<test>