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58 lines
1.6 KiB
YAML
58 lines
1.6 KiB
YAML
name: abacas
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description: contiguate draft genome assembly
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keywords:
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- genome
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- assembly
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- contiguate
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tools:
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- abacas:
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description: |
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ABACAS is intended to rapidly contiguate (align, order, orientate),
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visualize and design primers to close gaps on shotgun assembled
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contigs based on a reference sequence.
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homepage: http://abacas.sourceforge.net/documentation.html
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documentation: http://abacas.sourceforge.net/documentation.html
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tool_dev_url: None
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doi: "10.1093/bioinformatics/btp347"
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licence: ['GPL v2-or-later']
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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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- scaffold:
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type: file
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description: Fasta file containing scaffold
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pattern: "*.{fasta,fa}"
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- fasta:
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type: file
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description: FASTA reference file
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pattern: "*.{fasta,fa}"
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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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- results:
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type: files
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description: |
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List containing abacas output files
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[ 'test.abacas.bin', 'test.abacas.fasta', 'test.abacas.gaps',
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'test.abacas.gaps.tab', 'test.abacas.nucmer.delta',
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'test.abacas.nucmer.filtered.delta', 'test.abacas.nucmer.tiling',
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'test.abacas.tab', 'test.abacas.unused.contigs.out',
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'test.abacas.MULTIFASTA.fa' ]
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pattern: "*.{abacas}*"
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- version:
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type: file
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description: File containing software version
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pattern: "*.{version.txt}"
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authors:
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- "@joseespinosa"
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- "@drpatelh"
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