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comparison csp2_snp.xml @ 37:f62b9bcf7cf3

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"planemo upload"
author rliterman
date Fri, 06 Dec 2024 08:08:22 -0500
parents f6cd698b6f62
children 2a36d0ebb408
comparison
equal deleted inserted replaced
36:f6cd698b6f62 37:f62b9bcf7cf3
57 export RESCUE_ARG=""; 57 export RESCUE_ARG="";
58 fi; 58 fi;
59 59
60 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_DIR/CSP2_SNP_Output > Nextflow_Log.txt 2>&1; 60 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_DIR/CSP2_SNP_Output > Nextflow_Log.txt 2>&1;
61 61
62 mkdir -p Output; for file in CSP2_SNP_Output/SNP_Analysis/*/*; do ln -sf "\$file" Output/; done;
63 zip -r CSP2_Output.zip CSP2_SNP_Output; 62 zip -r CSP2_Output.zip CSP2_SNP_Output;
64 ]]> 63 ]]>
65 </command> 64 </command>
66 <inputs> 65 <inputs>
67 <param name="query_fasta" type="data" format="fasta" value="" label="Query assemblies" multiple="true" optional="true" /> 66 <param name="query_fasta" type="data" format="fasta" value="" label="Query assemblies" multiple="true" optional="true" />
84 </inputs> 83 </inputs>
85 <outputs> 84 <outputs>
86 <data name="nextflow_log" format="txt" label="Nextflow Log" from_work_dir="Nextflow_Log.txt" /> 85 <data name="nextflow_log" format="txt" label="Nextflow Log" from_work_dir="Nextflow_Log.txt" />
87 <data name="isolate_data" format="tabular" label="Isolate Data" from_work_dir="CSP2_SNP_Output/Isolate_Data.tsv" /> 86 <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" /> 87 <data name="raw_mummer" format="tabular" label="Raw MUMmer Output" from_work_dir="CSP2_SNP_Output/Raw_MUMmer_Summary.tsv" />
89 <data name="reference_screening" format="tabular" label="Reference Screening Data" from_work_dir="Output/Reference_Screening.tsv" />
90 <data name="csp2_log" format="txt" label="CSP2 Log" from_work_dir="Output/CSP2_SNP_Pipeline.log" />
91 <data name="snp_matrix" format="tabular" label="Preserved SNP Matrix" from_work_dir="Output/snp_distance_matrix_preserved.tsv" />
92 <data name="snp_pairwise" format="tabular" label="Preserved SNP Pairwise Distances" from_work_dir="Output/snp_distance_pairwise_preserved.tsv" />
93 <data name="snp_alignment" format="fasta" label="Preserved SNP Alignment" from_work_dir="Output/snpma_preserved.fasta" />
94 <data name="csp2_zip" format="zip" label="Zipped Output" from_work_dir="CSP2_Output.zip" /> 88 <data name="csp2_zip" format="zip" label="Zipped Output" from_work_dir="CSP2_Output.zip" />
89 <collection name="reference_results" type="list:list">
90 <discover_datasets pattern="*/CSP2_SNP_Pipeline.log" format="txt" visible="true" directory="./CSP2_SNP_Output/SNP_Analysis" />
91 <discover_datasets pattern="*/Reference_Screening.tsv" format="tabular" visible="true" directory="./CSP2_SNP_Output/SNP_Analysis" />
92 <discover_datasets pattern="*/snp_distance_matrix_preserved.tsv" format="tabular" visible="true" directory="./CSP2_SNP_Output/SNP_Analysis" />
93 <discover_datasets pattern="*/snp_distance_pairwise_preserved.tsv" format="tabular" visible="true" directory="./CSP2_SNP_Output/SNP_Analysis" />
94 <discover_datasets pattern="*/snpma_preserved.fasta" format="fasta" visible="true" directory="./CSP2_SNP_Output/SNP_Analysis" />
95 </collection>
95 </outputs> 96 </outputs>
96 <tests> 97 <tests>
97 <test> 98 <test>
98 <param name="query_fasta"> 99 <param name="query_fasta">
99 <collection type="list"> 100 <collection type="list">