Mercurial > repos > rliterman > csp2

comparison csp2_snp.xml @ 36:f6cd698b6f62

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"planemo upload"
author rliterman
date Thu, 05 Dec 2024 18:09:26 -0500
parents 106d28c851fa
children f62b9bcf7cf3
comparison
equal deleted inserted replaced
35:106d28c851fa 36:f6cd698b6f62
55 export RESCUE_ARG="--rescue"; 55 export RESCUE_ARG="--rescue";
56 else 56 else
57 export RESCUE_ARG=""; 57 export RESCUE_ARG="";
58 fi; 58 fi;
59 59
60 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; 60 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_DIR/CSP2_SNP_Output > Nextflow_Log.txt 2>&1;
61 61
62 mkdir -p Output; for file in CSP2_SNP_Output/SNP_Analysis/*/*; do ln -sf "\$file" Output/; done; 62 mkdir -p Output; for file in CSP2_SNP_Output/SNP_Analysis/*/*; do ln -sf "\$file" Output/; done;
63 zip -r CSP2_Output.zip CSP2_SNP_Output; 63 zip -r CSP2_Output.zip CSP2_SNP_Output;
64 ]]> 64 ]]>
65 </command> 65 </command>