Mercurial > repos > rliterman > csp2

comparison csp_screen.xml @ 26:6f85641ecd48

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload"
author rliterman
date Tue, 03 Dec 2024 16:35:35 -0500
parents 5c609acba34e
children 792274118b2e
comparison
equal deleted inserted replaced
25:5c609acba34e 26:6f85641ecd48
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 --cores 8 --out \$CSP2_DIR/CSP2_Screen_Output > Nextflow_Log.txt 2>&1; 60 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;
61 61
62 zip -r work.zip work 62 zip -r work.zip work;
63 zip -r csp2.zip CSP2_Screen_Output 63 zip -r csp2.zip CSP2_Screen_Output;
64 ]]> 64 ]]>
65 </command> 65 </command>
66 <inputs> 66 <inputs>
67 <param name="query_fasta" type="data" format="fasta" value="" label="Query assemblies" multiple="true" optional="true" /> 67 <param name="query_fasta" type="data" format="fasta" value="" label="Query assemblies" multiple="true" optional="true" />
68 <param name="ref_fasta" type="data" format="fasta" value="" label="Reference assemblies" multiple="true" optional="true" /> 68 <param name="ref_fasta" type="data" format="fasta" value="" label="Reference assemblies" multiple="true" optional="true" />
71 <param name="min_cov" type="float" value="85" label="Minimum reference genome coverage to proceed with distance estimation" optional="true" /> 71 <param name="min_cov" type="float" value="85" label="Minimum reference genome coverage to proceed with distance estimation" optional="true" />
72 <param name="min_iden" type="float" value="99" label="Minimum alignment percent identity to detect SNPs" optional="true" /> 72 <param name="min_iden" type="float" value="99" label="Minimum alignment percent identity to detect SNPs" optional="true" />
73 <param name="min_len" type="integer" value="500" label="Minimum alignment length to detect SNPs" optional="true" /> 73 <param name="min_len" type="integer" value="500" label="Minimum alignment length to detect SNPs" optional="true" />
74 <param name="ref_edge" type="integer" value="150" label="Prune SNPs within this many bases of reference contig edge" optional="true" /> 74 <param name="ref_edge" type="integer" value="150" label="Prune SNPs within this many bases of reference contig edge" optional="true" />
75 <param name="query_edge" type="integer" value="150" label="Prune SNPs within this many bases of query contig edge" optional="true" /> 75 <param name="query_edge" type="integer" value="150" label="Prune SNPs within this many bases of query contig edge" optional="true" />
76 <param name="cores" type="integer" value="2" label="Available cores per node" optional="true" />
76 <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" /> 77 <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" />
77 <param name="wsnps" type="text" value="3,2,1" label="Comma-separated list of maximum SNP counts per density window" optional="true" /> 78 <param name="wsnps" type="text" value="3,2,1" label="Comma-separated list of maximum SNP counts per density window" optional="true" />
78 <param name="readext" type="text" value="fastq.gz" label="Read extension format (e.g., fastq.gz)" optional="true" /> 79 <param name="readext" type="text" value="fastq.gz" label="Read extension format (e.g., fastq.gz)" optional="true" />
79 <param name="forward" type="text" value="_1.fastq.gz" label="Forward read suffix (e.g. _1.fastq.gz)" optional="true" /> 80 <param name="forward" type="text" value="_1.fastq.gz" label="Forward read suffix (e.g. _1.fastq.gz)" optional="true" />
80 <param name="reverse" type="text" value="_2.fastq.gz" label="Forward read suffix (e.g. _2.fastq.gz)" optional="true" /> 81 <param name="reverse" type="text" value="_2.fastq.gz" label="Forward read suffix (e.g. _2.fastq.gz)" optional="true" />