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* Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
56 lines
2 KiB
YAML
56 lines
2 KiB
YAML
name: muscle
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description: MUSCLE is a program for creating multiple alignments of amino acid or nucleotide sequences. A range of options are provided that give you the choice of optimizing accuracy, speed, or some compromise between the two
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keywords:
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- msa
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- multiple sequence alignment
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tools:
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- muscle:
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description: MUSCLE is a multiple sequence alignment tool with high accuracy and throughput
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homepage: https://www.drive5.com/muscle
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documentation: http://www.drive5.com/muscle/muscle.html#_Toc81224840
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doi: "https://pubmed.ncbi.nlm.nih.gov/15034147/"
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licence: ['http://www.drive5.com/muscle/manual/license.html']
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input:
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- fasta:
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type: file
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description: Input sequences for alignment must be in FASTA format
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pattern: "*.{fasta,fa,fna}"
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output:
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- aligned_fasta:
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type: file
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description: Multiple sequence alignment produced in FASTA format
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pattern: "*.{afa}"
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- msf:
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type: file
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description: GCG Multiple Sequence File (MSF) alignment format (similar to CLUSTALW)
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pattern: "*.{msf}"
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- clustalw:
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type: file
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description: Multiple sequence alignment produced in ClustalW format without base/residue numbering
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pattern: "*.{clw}"
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- phyi:
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type: file
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description: Multiple sequence alignment produced in PHYLIP interleaved format
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pattern: "*.{phyi}"
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- phys:
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type: file
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description: Multiple sequence alignment produced in PHYLIP sequential format
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pattern: "*.{phys}"
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- html:
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type: file
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description: Multiple sequence alignment produced in HTML format
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pattern: "*.{html}"
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- tree:
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type: file
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description: NJ or UPGMA tree in Newick format produced from a multiple sequence alignment
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pattern: "*.{tree}"
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- log:
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type: file
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description: Log file of MUSCLE run
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pattern: "*{.log}"
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- version:
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type: file
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description: File containing MUSCLE software version
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pattern: "*.{version.txt}"
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authors:
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- "@MGordon"
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