Mercurial > repos > rliterman > csp2
changeset 30:1fe21a8717d4
"planemo upload"
| author | rliterman |
|---|---|
| date | Wed, 04 Dec 2024 17:06:15 -0500 |
| parents | b6ec322b1f05 |
| children | 1117def5cd24 |
| files | csp2_screen.xml csp2_snp.xml |
| diffstat | 2 files changed, 12 insertions(+), 10 deletions(-) [+] |
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--- a/csp2_screen.xml Wed Dec 04 16:02:07 2024 -0500 +++ b/csp2_screen.xml Wed Dec 04 17:06:15 2024 -0500 @@ -57,9 +57,9 @@ export REF_ID_ARG=""; fi; -nextflow run ${__tool_directory__}/CSP2/CSP2.nf -profile csp2_galaxy --cores 1 --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 --out \$CSP2_DIR/CSP2_Screen_Output > Nextflow_Log.txt 2>&1; -sleep 1; - ]]> +nextflow run ${__tool_directory__}/CSP2/CSP2.nf -profile csp2_galaxy --cores 2 --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 --out \$CSP2_DIR/CSP2_Screen_Output > Nextflow_Log.txt 2>&1; +zip -r CSP2_Output.zip CSP2_Screen_Output; +]]> </command> <inputs> <param name="query_fasta" type="data" format="fasta" value="" label="Query assemblies" multiple="true" optional="true" /> @@ -80,10 +80,11 @@ <param name="ref_id" type="text" value="" label="Comma-separated list of desired Reference IDs (e.g., Sample_A,Sample_B)" optional="true" /> </inputs> <outputs> - <data name="screening_results" format="tabular" label="Screening Results" from_work_dir="CSP2_Screen_Output/Screening_Results.tsv" /> <data name="raw_mummer" format="tabular" label="Raw MUMmer Output" from_work_dir="CSP2_Screen_Output/Raw_MUMmer_Summary.tsv" /> <data name="isolate_data" format="tabular" label="Isolate Data" from_work_dir="CSP2_Screen_Output/Isolate_Data.tsv" /> + <data name="screening_results" format="tabular" label="Screening Results" from_work_dir="CSP2_Screen_Output/Screening_Results.tsv" /> <data name="nextflow_log" format="txt" label="Nextflow Log" from_work_dir="Nextflow_Log.txt" /> + <data name="csp2_zip" format="zip" label="Zipped Output" from_work_dir="CSP2_Output.zip" /> </outputs> <tests> <test>
--- a/csp2_snp.xml Wed Dec 04 16:02:07 2024 -0500 +++ b/csp2_snp.xml Wed Dec 04 17:06:15 2024 -0500 @@ -63,8 +63,8 @@ export RESCUE_ARG=""; fi; -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; -sleep 1; +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; +zip -r CSP2_Output.zip CSP2_SNP_Output; ]]> </command> <inputs> @@ -93,19 +93,20 @@ <data name="raw_mummer" format="tabular" label="Raw MUMmer Output" from_work_dir="CSP2_SNP_Output/Raw_MUMmer_Summary.tsv" /> <data name="isolate_data" format="tabular" label="Isolate Data" from_work_dir="CSP2_SNP_Output/Isolate_Data.tsv" /> <data name="nextflow_log" format="txt" label="Nextflow Log" from_work_dir="Nextflow_Log.txt" /> - + <data name="csp2_zip" format="zip" label="Zipped Output" from_work_dir="CSP2_Output.zip" /> + <collection name="snp_analysis_results" type="list:dataset" label="SNP Analysis Results by Reference ID"> - <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/CSP2_SNP_Pipeline.log" format="txt" /> + <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/CSP2_SNP_Pipeline.log" format="txt" /> <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snplist.txt" format="txt" /> <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snplist_preserved.txt" format="txt" /> <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/Reference_Screening.tsv" format="tabular" /> - <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/Locus_Categories.tsv" format="tabular" /> + <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/Locus_Categories.tsv" format="tabular" /> <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/Query_Coverage.tsv" format="tabular" /> <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snp_distance_matrix_preserved.tsv" format="tabular" /> <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snp_distance_matrix.tsv" format="tabular" /> <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snp_distance_pairwise_preserved.tsv" format="tabular" /> <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snp_distance_pairwise.tsv" format="tabular" /> - <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snpma_preserved.fasta" format="fasta" /> + <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snpma_preserved.fasta" format="fasta" /> <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snpma.fasta" format="fasta" /> </collection> </outputs>