| Previous changeset 25:5c609acba34e (2024-12-03) Next changeset 27:792274118b2e (2024-12-04) |
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Commit message:
"planemo upload" |
|
modified:
csp_screen.xml |
| csp_screen.xml |
| diff -r 5c609acba34e -r 6f85641ecd48 csp_screen.xml |
| csp_screen.xml |
| --- a/csp_screen.xml Tue Dec 03 15:56:32 2024 -0500 +++ b/csp_screen.xml Tue Dec 03 16:35:35 2024 -0500 @@ -57,10 +57,10 @@ 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 --cores $cores --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 - zip -r csp2.zip CSP2_Screen_Output + zip -r work.zip work; + zip -r csp2.zip CSP2_Screen_Output; ]]> </command> <inputs> @@ -73,6 +73,7 @@ <param name="min_len" type="integer" value="500" label="Minimum alignment length to detect SNPs" optional="true" /> <param name="ref_edge" type="integer" value="150" label="Prune SNPs within this many bases of reference contig edge" optional="true" /> <param name="query_edge" type="integer" value="150" label="Prune SNPs within this many bases of query contig edge" optional="true" /> + <param name="cores" type="integer" value="2" label="Available cores per node" optional="true" /> <param name="dwin" type="text" value="1000,125,15" label="Comma-separated set of window sizes for SNP density filtration (Set to 0 to disable density filtration)" optional="true" /> <param name="wsnps" type="text" value="3,2,1" label="Comma-separated list of maximum SNP counts per density window" optional="true" /> <param name="readext" type="text" value="fastq.gz" label="Read extension format (e.g., fastq.gz)" optional="true" /> |