# HG changeset patch
# User rliterman
# Date 1734031801 18000
# Node ID 1a38b6829885ea6784cda24a9688c53b8974229f
# Parent  32ee1ce2041138913b32ec3391359a45249e4b4c
"planemo upload"

diff -r 32ee1ce20411 -r 1a38b6829885 csp2_screen.xml
--- a/csp2_screen.xml	Thu Dec 12 14:22:33 2024 -0500
+++ b/csp2_screen.xml	Thu Dec 12 14:30:01 2024 -0500
@@ -7,7 +7,7 @@
         <version_command>nextflow -version</version_command>
         <command detect_errors="aggressive"><![CDATA[
 
-mkdir -p ./queries ./references &&
+mkdir ./queries ./references;
 
 if [ -n "$query_fasta" ] && [ "$query_fasta" != "None" ]; then
         #for query in $query_fasta:
@@ -20,27 +20,27 @@
 
 if [ -n "$query_reads" ] && [ "$query_reads" != "None" ]; then
         #for query in $query_reads:
-                ln -sf ${query} \$CSP2_DIR/queries/${query.element_identifier} &&
+                ln -sf ${query} ./queries/${query.element_identifier} &&
         #end for
-        export QUERY_READS_ARG="--reads \$CSP2_DIR/queries" &&
+        export QUERY_READS_ARG="--reads ./queries" &&
 else
         export QUERY_READS_ARG="" &&
 fi;
 
 if [ -n "$ref_fasta" ] && [ "$ref_fasta" != "None" ]; then
         #for ref in $ref_fasta:
-                ln -sf ${ref} \$CSP2_DIR/references/${ref.element_identifier} &&
+                ln -sf ${ref} ./references/${ref.element_identifier} &&
         #end for
-        export REF_FASTA_ARG="--ref_fasta \$CSP2_DIR/references" &&
+        export REF_FASTA_ARG="--ref_fasta ./references" &&
 else
         export REF_FASTA_ARG="" &&
 fi;
 
 if [ -n "$ref_reads" ] && [ "$ref_reads" != "None" ]; then
         #for ref in $ref_reads:
-                ln -sf ${ref} \$CSP2_DIR/references/${ref.element_identifier} &&
+                ln -sf ${ref} ./references/${ref.element_identifier} &&
         #end for
-        export REF_READS_ARG="--ref_reads \$CSP2_DIR/references" &&
+        export REF_READS_ARG="--ref_reads ./references" &&
 else
         export REF_READS_ARG="" &&
 fi;
@@ -57,8 +57,8 @@
         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 --out ./CSP2_Screen_Output > Nextflow_Log.txt 2>&1 &&
-cat Nextflow_Log.txt &&
+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 --out ./CSP2_Screen_Output > Nextflow_Log.txt 2>&1;
+cat Nextflow_Log.txt;
 ]]>
         </command>
         <inputs>