Mercurial > repos > rliterman > csp2

comparison csp2_screen.xml @ 49:6aea52d80ab9

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"planemo upload"
author rliterman
date Thu, 12 Dec 2024 16:06:13 -0500
parents 90b09ae7e4ed
children 16b103443761
comparison
equal deleted inserted replaced
48:90b09ae7e4ed 49:6aea52d80ab9
55 export REF_ID_ARG="--ref_id $ref_id"; 55 export REF_ID_ARG="--ref_id $ref_id";
56 else 56 else
57 export REF_ID_ARG=""; 57 export REF_ID_ARG="";
58 fi; 58 fi;
59 59
60 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; 60 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 &&
61 ls -la CSP2_Screen_Output &&
62 sleep 5 &&
63 ls -la CSP2_Screen_Output &&
61 cp CSP2_Screen_Output/Screening_Results.tsv CSP2_Screen_Output/Raw_MUMmer_Summary.tsv CSP2_Screen_Output/Isolate_Data.tsv output/; 64 cp CSP2_Screen_Output/Screening_Results.tsv CSP2_Screen_Output/Raw_MUMmer_Summary.tsv CSP2_Screen_Output/Isolate_Data.tsv output/;
62 ]]> 65 ]]>
63 </command> 66 </command>
64 <inputs> 67 <inputs>
65 <param name="query_fasta" type="data" format="fasta" value="" label="Query assemblies" multiple="true" optional="true" /> 68 <param name="query_fasta" type="data" format="fasta" value="" label="Query assemblies" multiple="true" optional="true" />