# HG changeset patch
# User rliterman
# Date 1733242173 18000
# Node ID 074a2dc26b691dbb9921cc128eb532697560ab1c
# Parent  c3a0820082d11ee7795ba00085152f47d39823e7
"planemo upload"

diff -r c3a0820082d1 -r 074a2dc26b69 csp_screen.xml
--- a/csp_screen.xml	Tue Dec 03 10:43:25 2024 -0500
+++ b/csp_screen.xml	Tue Dec 03 11:09:33 2024 -0500
@@ -57,7 +57,9 @@
 		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 --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
 	]]>
 	</command>
 	<inputs>
@@ -82,7 +84,9 @@
 		<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="Nextflow_Log.txt" />
-		<data name="CSP2_Params" format="txt" label="Passed params" from_work_dir="CSP2_Screen_Output/logs/CSP2_Params.txt" />
+                <data name="CSP2_Params" format="txt" label="Passed params" from_work_dir="CSP2_Screen_Output/logs/CSP2_Params.txt" />
+                <data name="Ref_IDs" format="txt" label="Reference IDs" from_work_dir="CSP2_Screen_Output/logs/Reference_IDs.txt" />
+		<data name="Work_ZIP" format="zip" label="work" from_work_dir="work.zip" />
 	</outputs>
 	<tests>
 		<test>