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comparison csp2_screen.xml @ 30:1fe21a8717d4

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"planemo upload"
author rliterman
date Wed, 04 Dec 2024 17:06:15 -0500
parents b6ec322b1f05
children 6f4e6377ba64
comparison
equal deleted inserted replaced
29:b6ec322b1f05 30:1fe21a8717d4
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 --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; 60 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;
61 sleep 1; 61 zip -r CSP2_Output.zip CSP2_Screen_Output;
62 ]]> 62 ]]>
63 </command> 63 </command>
64 <inputs> 64 <inputs>
65 <param name="query_fasta" type="data" format="fasta" value="" label="Query assemblies" multiple="true" optional="true" /> 65 <param name="query_fasta" type="data" format="fasta" value="" label="Query assemblies" multiple="true" optional="true" />
66 <param name="ref_fasta" type="data" format="fasta" value="" label="Reference assemblies" multiple="true" optional="true" /> 66 <param name="ref_fasta" type="data" format="fasta" value="" label="Reference assemblies" multiple="true" optional="true" />
67 <param name="query_reads" type="data" format="fastq,fastq.gz" value="" label="Query reads" multiple="true" optional="true" /> 67 <param name="query_reads" type="data" format="fastq,fastq.gz" value="" label="Query reads" multiple="true" optional="true" />
78 <param name="reverse" type="text" value="_2.fastq.gz" label="Forward read suffix (e.g. _2.fastq.gz)" optional="true" /> 78 <param name="reverse" type="text" value="_2.fastq.gz" label="Forward read suffix (e.g. _2.fastq.gz)" optional="true" />
79 <param name="trim_name" type="text" value="" label="Text to remove from all file names (e.g., _contigs_skesa)" optional="true" /> 79 <param name="trim_name" type="text" value="" label="Text to remove from all file names (e.g., _contigs_skesa)" optional="true" />
80 <param name="ref_id" type="text" value="" label="Comma-separated list of desired Reference IDs (e.g., Sample_A,Sample_B)" optional="true" /> 80 <param name="ref_id" type="text" value="" label="Comma-separated list of desired Reference IDs (e.g., Sample_A,Sample_B)" optional="true" />
81 </inputs> 81 </inputs>
82 <outputs> 82 <outputs>
83 <data name="screening_results" format="tabular" label="Screening Results" from_work_dir="CSP2_Screen_Output/Screening_Results.tsv" />
84 <data name="raw_mummer" format="tabular" label="Raw MUMmer Output" from_work_dir="CSP2_Screen_Output/Raw_MUMmer_Summary.tsv" /> 83 <data name="raw_mummer" format="tabular" label="Raw MUMmer Output" from_work_dir="CSP2_Screen_Output/Raw_MUMmer_Summary.tsv" />
85 <data name="isolate_data" format="tabular" label="Isolate Data" from_work_dir="CSP2_Screen_Output/Isolate_Data.tsv" /> 84 <data name="isolate_data" format="tabular" label="Isolate Data" from_work_dir="CSP2_Screen_Output/Isolate_Data.tsv" />
85 <data name="screening_results" format="tabular" label="Screening Results" from_work_dir="CSP2_Screen_Output/Screening_Results.tsv" />
86 <data name="nextflow_log" format="txt" label="Nextflow Log" from_work_dir="Nextflow_Log.txt" /> 86 <data name="nextflow_log" format="txt" label="Nextflow Log" from_work_dir="Nextflow_Log.txt" />
87 <data name="csp2_zip" format="zip" label="Zipped Output" from_work_dir="CSP2_Output.zip" />
87 </outputs> 88 </outputs>
88 <tests> 89 <tests>
89 <test> 90 <test>
90 <param name="query_fasta"> 91 <param name="query_fasta">
91 <collection type="list"> 92 <collection type="list">