| Previous changeset 13:c3a0820082d1 (2024-12-03) Next changeset 15:0d775868ee62 (2024-12-03) |
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Commit message:
"planemo upload" |
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modified:
csp_screen.xml |
| csp_screen.xml |
| diff -r c3a0820082d1 -r 074a2dc26b69 csp_screen.xml |
| csp_screen.xml |
| --- a/csp_screen.xml Tue Dec 03 10:43:25 2024 -0500 +++ b/csp_screen.xml Tue Dec 03 11:09:33 2024 -0500 @@ -57,7 +57,9 @@ export REF_ID_ARG=""; fi; -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; + 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; + + zip -r work.zip work ]]> </command> <inputs> @@ -82,7 +84,9 @@ <data name="screening_results" format="tabular" label="Screening Results" from_work_dir="CSP2_Screen_Output/Screening_Results.tsv" /> <data name="isolate_data" format="tabular" label="Isolate Data" from_work_dir="CSP2_Screen_Output/Isolate_Data.tsv" /> <data name="nextflow_log" format="txt" label="Nextflow Log" from_work_dir="Nextflow_Log.txt" /> - <data name="CSP2_Params" format="txt" label="Passed params" from_work_dir="CSP2_Screen_Output/logs/CSP2_Params.txt" /> + <data name="CSP2_Params" format="txt" label="Passed params" from_work_dir="CSP2_Screen_Output/logs/CSP2_Params.txt" /> + <data name="Ref_IDs" format="txt" label="Reference IDs" from_work_dir="CSP2_Screen_Output/logs/Reference_IDs.txt" /> + <data name="Work_ZIP" format="zip" label="work" from_work_dir="work.zip" /> </outputs> <tests> <test> |