Mercurial > repos > rliterman > csp2

comparison csp2_snp.xml @ 52:44cbdce84814

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload"
author rliterman
date Fri, 13 Dec 2024 08:59:02 -0500
parents 2a36d0ebb408
children a21f63856acf
comparison
equal deleted inserted replaced
51:2a36d0ebb408 52:44cbdce84814
54 export RESCUE_ARG="--rescue"; 54 export RESCUE_ARG="--rescue";
55 else 55 else
56 export RESCUE_ARG=""; 56 export RESCUE_ARG="";
57 fi; 57 fi;
58 58
59 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 && 59 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 &&
60 ls -la CSP2_SNP_Output/SNP_Analysis/* && 60 ls -la CSP2_SNP_Output/SNP_Analysis/* &&
61 mkdir CSP2_Output && 61 mkdir CSP2_Output &&
62 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 && 62 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 &&
63 ls -la CSP2_Output; 63 ls -la CSP2_Output;
64 64
80 <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" />
81 <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" />
82 <param name="trim_name" type="text" value="" label="Text to remove from all file names (e.g., _contigs_skesa)" optional="true" /> 82 <param name="trim_name" type="text" value="" label="Text to remove from all file names (e.g., _contigs_skesa)" optional="true" />
83 <param name="rescue" type="boolean" value="false" label="Enable SNP edge rescue mode" optional="true" /> 83 <param name="rescue" type="boolean" value="false" label="Enable SNP edge rescue mode" optional="true" />
84 <param name="max_missing" type="float" value="50" label="Maximum percent of isolates allowed to have missing data to retain a SNP" optional="true" /> 84 <param name="max_missing" type="float" value="50" label="Maximum percent of isolates allowed to have missing data to retain a SNP" optional="true" />
85 <param name="n_ref" type="integer" value="1" label="Number of reference genomes to select" optional="true" />
86
85 </inputs> 87 </inputs>
86 <outputs> 88 <outputs>
87 <data name="isolate_data" format="tabular" label="Isolate Data" from_work_dir="CSP2_SNP_Output/Isolate_Data.tsv" /> 89 <data name="isolate_data" format="tabular" label="Isolate Data" from_work_dir="CSP2_SNP_Output/Isolate_Data.tsv" />
88 <data name="raw_mummer" format="tabular" label="Raw MUMmer Output" from_work_dir="CSP2_SNP_Output/Raw_MUMmer_Summary.tsv" /> 90 <data name="raw_mummer" format="tabular" label="Raw MUMmer Output" from_work_dir="CSP2_SNP_Output/Raw_MUMmer_Summary.tsv" />
89 91