Mercurial > repos > rliterman > csp2

comparison csp2_screen.xml @ 7:89d3f54fc370

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"planemo upload"
author rliterman
date Mon, 02 Dec 2024 17:31:42 -0500
parents 6e0ca63be26f
children 2ab525820ff2
comparison
equal deleted inserted replaced
6:6e0ca63be26f 7:89d3f54fc370
55 export REF_ID_ARG="--ref_id $ref_id"; 55 export REF_ID_ARG="--ref_id $ref_id";
56 else 56 else
57 export REF_ID_ARG=""; 57 export REF_ID_ARG="";
58 fi; 58 fi;
59 59
60 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 > \$CSP2_DIR/CSP2_Screen_Output/.nextflow.log 2>&1; 60 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 > \$CSP2_DIR/CSP2_Screen_Output/Nextflow_Log.txt 2>&1;
61 ]]> 61 ]]>
62 </command> 62 </command>
63 <inputs> 63 <inputs>
64 <param name="query_fasta" type="data" format="fasta" value="" label="Query assemblies" multiple="true" optional="true" /> 64 <param name="query_fasta" type="data" format="fasta" value="" label="Query assemblies" multiple="true" optional="true" />
65 <param name="ref_fasta" type="data" format="fasta" value="" label="Reference assemblies" multiple="true" optional="true" /> 65 <param name="ref_fasta" type="data" format="fasta" value="" label="Reference assemblies" multiple="true" optional="true" />
79 <param name="ref_id" type="text" value="" label="Comma-separated list of desired Reference IDs (e.g., Sample_A,Sample_B)" optional="true" /> 79 <param name="ref_id" type="text" value="" label="Comma-separated list of desired Reference IDs (e.g., Sample_A,Sample_B)" optional="true" />
80 </inputs> 80 </inputs>
81 <outputs> 81 <outputs>
82 <data name="screening_results" format="tabular" label="Screening Results" from_work_dir="CSP2_Screen_Output/Screening_Results.tsv" /> 82 <data name="screening_results" format="tabular" label="Screening Results" from_work_dir="CSP2_Screen_Output/Screening_Results.tsv" />
83 <data name="isolate_data" format="tabular" label="Isolate Data" from_work_dir="CSP2_Screen_Output/Isolate_Data.tsv" /> 83 <data name="isolate_data" format="tabular" label="Isolate Data" from_work_dir="CSP2_Screen_Output/Isolate_Data.tsv" />
84 <data name="nextflow_log" format="tabular" label="Nextflow Log" from_work_dir="CSP2_Screen_Output/.nextflow.log" /> 84 <data name="nextflow_log" format="txt" label="Nextflow Log" from_work_dir="CSP2_Screen_Output/Nextflow_Log.txt" />
85 </outputs> 85 </outputs>
86 <tests> 86 <tests>
87 <test> 87 <test>
88 <param name="query_fasta"> 88 <param name="query_fasta">
89 <collection type="list"> 89 <collection type="list">