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59 lines
1.7 KiB
YAML
59 lines
1.7 KiB
YAML
name: "plasmidfinder"
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description: Identify plasmids in bacterial sequences and assemblies
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keywords:
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- fasta
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- fastq
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- plasmid
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tools:
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- "plasmidfinder":
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description: "PlasmidFinder allows identification of plasmids in total or partial sequenced isolates of bacteria."
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homepage: "https://cge.cbs.dtu.dk/services/PlasmidFinder/"
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documentation: "https://bitbucket.org/genomicepidemiology/plasmidfinder"
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tool_dev_url: "https://bitbucket.org/genomicepidemiology/plasmidfinder"
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doi: "10.1128/AAC.02412-14"
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licence: "['Apache-2.0']"
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- seqs:
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type: file
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description: Input FASTA or FASTQ formatted genome sequences
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pattern: "*.{fastq.gz,fq.gz,fastq.gz,fna.gz,fa.gz}"
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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- json:
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type: file
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description: The results from analysis in JSON format
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pattern: "*.json"
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- txt:
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type: file
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description: The summary of results from analysis
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pattern: "*.txt"
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- tsv:
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type: file
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description: The results from analysis in TSV format
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pattern: "*.tsv"
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- genome_seq:
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type: file
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description: FASTA of sequences in the input with a hit
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pattern: "*-hit_in_genome_seq.fsa"
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- plasmid_seq:
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type: file
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description: FASTA of plasmid sequences with a hit against the input
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pattern: "*-plasmid_seqs.fsa"
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authors:
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- "@rpetit3"
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