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changeset 52:44cbdce84814

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"planemo upload"
author rliterman
date Fri, 13 Dec 2024 08:59:02 -0500
parents 2a36d0ebb408
children a21f63856acf
files csp2_snp.xml
diffstat 1 files changed, 3 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/csp2_snp.xml	Fri Dec 13 08:49:33 2024 -0500
+++ b/csp2_snp.xml	Fri Dec 13 08:59:02 2024 -0500
@@ -56,7 +56,7 @@
         export RESCUE_ARG="";
 fi;
 
-nextflow run ${__tool_directory__}/CSP2/CSP2.nf -profile csp2_galaxy --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_SNP_Output > Nextflow_Log.txt 2>&1 &&
+nextflow run ${__tool_directory__}/CSP2/CSP2.nf -profile csp2_galaxy --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 --n_ref $n_ref --out ./CSP2_SNP_Output > Nextflow_Log.txt 2>&1 &&
 ls -la CSP2_SNP_Output/SNP_Analysis/* &&
 mkdir CSP2_Output &&
 cat CSP2_SNP_Output/logs/Reference_IDs.txt | while read line; do cp 'CSP2_SNP_Output/SNP_Analysis/'\$line'/CSP2_SNP_Pipeline.log' 'CSP2_Output/'\$line'_CSP2_SNP_Pipeline.log'; cp 'CSP2_SNP_Output/SNP_Analysis/'\$line'/Reference_Screening.tsv' 'CSP2_Output/'\$line'_Reference_Screening.tsv';  cp 'CSP2_SNP_Output/SNP_Analysis/'\$line'/snp_distance_matrix_preserved.tsv' 'CSP2_Output/'\$line'_snp_distance_matrix_preserved.tsv'; cp 'CSP2_SNP_Output/SNP_Analysis/'\$line'/snp_distance_pairwise_preserved.tsv' 'CSP2_Output/'\$line'_snp_distance_pairwise_preserved.tsv'; cp 'CSP2_SNP_Output/SNP_Analysis/'\$line'/snpma_preserved.fasta' 'CSP2_Output/'\$line'_snpma_preserved.fasta';done &&
@@ -82,6 +82,8 @@
                 <param name="trim_name" type="text" value="" label="Text to remove from all file names (e.g., _contigs_skesa)" optional="true" />
                 <param name="rescue" type="boolean" value="false" label="Enable SNP edge rescue mode" optional="true" />
                 <param name="max_missing" type="float" value="50" label="Maximum percent of isolates allowed to have missing data to retain a SNP" optional="true" />
+                <param name="n_ref" type="integer" value="1" label="Number of reference genomes to select" optional="true" />
+
         </inputs>
         <outputs>
                 <data name="isolate_data" format="tabular" label="Isolate Data" from_work_dir="CSP2_SNP_Output/Isolate_Data.tsv" />