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comparison csp2_snp.xml @ 30:1fe21a8717d4

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"planemo upload"
author rliterman
date Wed, 04 Dec 2024 17:06:15 -0500
parents b6ec322b1f05
children a12953834916
comparison
equal deleted inserted replaced
29:b6ec322b1f05 30:1fe21a8717d4
61 export RESCUE_ARG="--rescue"; 61 export RESCUE_ARG="--rescue";
62 else 62 else
63 export RESCUE_ARG=""; 63 export RESCUE_ARG="";
64 fi; 64 fi;
65 65
66 nextflow run ${__tool_directory__}/CSP2/CSP2.nf -profile csp2_galaxy --cores 1 --runmode snp \$QUERY_FASTA_ARG \$REF_FASTA_ARG \$QUERY_READS_ARG \$REF_READS_ARG \$REF_ID_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_DIR/CSP2_SNP_Output > Nextflow_Log.txt 2>&1; 66 nextflow run ${__tool_directory__}/CSP2/CSP2.nf -profile csp2_galaxy --cores 2 --runmode snp \$QUERY_FASTA_ARG \$REF_FASTA_ARG \$QUERY_READS_ARG \$REF_READS_ARG \$REF_ID_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_DIR/CSP2_SNP_Output > Nextflow_Log.txt 2>&1;
67 sleep 1; 67 zip -r CSP2_Output.zip CSP2_SNP_Output;
68 ]]> 68 ]]>
69 </command> 69 </command>
70 <inputs> 70 <inputs>
71 <param name="query_fasta" type="data" format="fasta" value="" label="Query assemblies" multiple="true" optional="true" /> 71 <param name="query_fasta" type="data" format="fasta" value="" label="Query assemblies" multiple="true" optional="true" />
72 <param name="ref_fasta" type="data" format="fasta" value="" label="Reference assemblies" multiple="true" optional="true" /> 72 <param name="ref_fasta" type="data" format="fasta" value="" label="Reference assemblies" multiple="true" optional="true" />
91 </inputs> 91 </inputs>
92 <outputs> 92 <outputs>
93 <data name="raw_mummer" format="tabular" label="Raw MUMmer Output" from_work_dir="CSP2_SNP_Output/Raw_MUMmer_Summary.tsv" /> 93 <data name="raw_mummer" format="tabular" label="Raw MUMmer Output" from_work_dir="CSP2_SNP_Output/Raw_MUMmer_Summary.tsv" />
94 <data name="isolate_data" format="tabular" label="Isolate Data" from_work_dir="CSP2_SNP_Output/Isolate_Data.tsv" /> 94 <data name="isolate_data" format="tabular" label="Isolate Data" from_work_dir="CSP2_SNP_Output/Isolate_Data.tsv" />
95 <data name="nextflow_log" format="txt" label="Nextflow Log" from_work_dir="Nextflow_Log.txt" /> 95 <data name="nextflow_log" format="txt" label="Nextflow Log" from_work_dir="Nextflow_Log.txt" />
96 96 <data name="csp2_zip" format="zip" label="Zipped Output" from_work_dir="CSP2_Output.zip" />
97
97 <collection name="snp_analysis_results" type="list:dataset" label="SNP Analysis Results by Reference ID"> 98 <collection name="snp_analysis_results" type="list:dataset" label="SNP Analysis Results by Reference ID">
98 <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/CSP2_SNP_Pipeline.log" format="txt" /> 99 <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/CSP2_SNP_Pipeline.log" format="txt" />
99 <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snplist.txt" format="txt" /> 100 <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snplist.txt" format="txt" />
100 <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snplist_preserved.txt" format="txt" /> 101 <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snplist_preserved.txt" format="txt" />
101 <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/Reference_Screening.tsv" format="tabular" /> 102 <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/Reference_Screening.tsv" format="tabular" />
102 <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/Locus_Categories.tsv" format="tabular" /> 103 <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/Locus_Categories.tsv" format="tabular" />
103 <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/Query_Coverage.tsv" format="tabular" /> 104 <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/Query_Coverage.tsv" format="tabular" />
104 <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snp_distance_matrix_preserved.tsv" format="tabular" /> 105 <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snp_distance_matrix_preserved.tsv" format="tabular" />
105 <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snp_distance_matrix.tsv" format="tabular" /> 106 <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snp_distance_matrix.tsv" format="tabular" />
106 <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snp_distance_pairwise_preserved.tsv" format="tabular" /> 107 <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snp_distance_pairwise_preserved.tsv" format="tabular" />
107 <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snp_distance_pairwise.tsv" format="tabular" /> 108 <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snp_distance_pairwise.tsv" format="tabular" />
108 <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snpma_preserved.fasta" format="fasta" /> 109 <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snpma_preserved.fasta" format="fasta" />
109 <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snpma.fasta" format="fasta" /> 110 <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snpma.fasta" format="fasta" />
110 </collection> 111 </collection>
111 </outputs> 112 </outputs>
112 <tests> 113 <tests>
113 <test> 114 <test>