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comparison csp2_snp.xml @ 33:6f4e6377ba64

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"planemo upload"
author rliterman
date Thu, 05 Dec 2024 12:32:42 -0500
parents a12953834916
children 499342837ad7
comparison
equal deleted inserted replaced
32:a12953834916 33:6f4e6377ba64
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 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 $n_ref --out \$CSP2_DIR/CSP2_SNP_Output > Nextflow_Log.txt 2>&1; 66 if [[ "$ondemand" == "true" ]]; then
67 export PROFILE_ARG="-profile csp2_galaxy1";
68 else
69 export PROFILE_ARG="-profile csp2_galaxy2";
70 fi;
71
72 nextflow run ${__tool_directory__}/CSP2/CSP2.nf \$PROFILE_ARG --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 zip -r CSP2_Output.zip CSP2_SNP_Output; 73 zip -r CSP2_Output.zip CSP2_SNP_Output;
68 ]]> 74 ]]>
69 </command> 75 </command>
70 <inputs> 76 <inputs>
71 <param name="query_fasta" type="data" format="fasta" value="" label="Query assemblies" multiple="true" optional="true" /> 77 <param name="query_fasta" type="data" format="fasta" value="" label="Query assemblies" multiple="true" optional="true" />
85 <param name="trim_name" type="text" value="" label="Text to remove from all file names (e.g., _contigs_skesa)" optional="true" /> 91 <param name="trim_name" type="text" value="" label="Text to remove from all file names (e.g., _contigs_skesa)" optional="true" />
86 <param name="ref_id" type="text" value="" label="Comma-separated list of desired Reference IDs (e.g., Sample_A,Sample_B)" optional="true" /> 92 <param name="ref_id" type="text" value="" label="Comma-separated list of desired Reference IDs (e.g., Sample_A,Sample_B)" optional="true" />
87 <param name="rescue" type="boolean" value="false" label="Enable SNP edge rescue mode" optional="true" /> 93 <param name="rescue" type="boolean" value="false" label="Enable SNP edge rescue mode" optional="true" />
88 <param name="max_missing" type="float" value="50" label="Maximum percent of isolates allowed to have missing data to retain a SNP" optional="true" /> 94 <param name="max_missing" type="float" value="50" label="Maximum percent of isolates allowed to have missing data to retain a SNP" optional="true" />
89 <param name="n_ref" type="integer" value="1" label="Number of reference isolates for CSP2 to select" optional="true" /> 95 <param name="n_ref" type="integer" value="1" label="Number of reference isolates for CSP2 to select" optional="true" />
90 96 <param name="ondemand" type="boolean" value="true" label="Use -profile csp2_galaxy1 (ondemand-small queue; set to false to use csp2_galaxy2 q8cpu)" optional="true" />
91 </inputs> 97 </inputs>
92 <outputs> 98 <outputs>
93 <data name="raw_mummer" format="tabular" label="Raw MUMmer Output" from_work_dir="CSP2_SNP_Output/Raw_MUMmer_Summary.tsv" /> 99 <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" /> 100 <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" /> 101 <data name="nextflow_log" format="txt" label="Nextflow Log" from_work_dir="Nextflow_Log.txt" />