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https://github.com/MillironX/nf-core_modules.git
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b5e3d16d80
* Created hmmer/eslalimask from template * esl-alimask module with --rf-is-mask test case * Add optional file output * Add hmmer to test name * Move from process_single to process_low * Test for versions.yml, plus content * Prettier * Avoid gzipping input alignment * meta.id to prefix * Fix version string so it's from *this* tool
105 lines
2.6 KiB
YAML
105 lines
2.6 KiB
YAML
name: "hmmer_eslalimask"
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description: Mask multiple sequence alignments
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keywords:
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- hmmer
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- alignment
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- mask
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tools:
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- "hmmer":
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description: "Biosequence analysis using profile hidden Markov models"
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homepage: http://hmmer.org/
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documentation: http://hmmer.org/documentation.html
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tool_dev_url: None
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doi: "http://dx.doi.org/10.1371/journal.pcbi.1002195"
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licence: ["BSD-3-Clause"]
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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' ]
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- unmaskedaln:
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type: file
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description: multiple sequence alignment, Stockholm or other formats
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pattern: "*"
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- fmask_rf:
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type: val
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description: Flag to output optional file with final mask of non-gap RF len
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- fmask_all:
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type: val
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description: Flag to output optional file with final mask of full aln len
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- gmask_rf:
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type: val
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description: Flag to output optional file gap-based 0/1 mask of non-gap RF len
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- gmask_all:
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type: val
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description: Flag to output optional file gap-based 0/1 mask of full aln len
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- pmask_rf:
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type: val
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description: Flag to output optional file with PP-based 0/1 mask of non-gap RF len
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- pmask_all:
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type: val
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description: Flag to output optional file with PP-based 0/1 mask of full aln len
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- maskfile:
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type: file
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description: mask file, see program documentation
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pattern: "*"
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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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- maskedaln:
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type: file
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description: Masked alignment in gzipped Stockholm format
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pattern: "*.sthlm.gz"
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- fmask_rf:
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type: file
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description: File with final mask of non-gap RF len
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pattern: "*.fmask-rf.gz"
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- fmask_all:
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type: file
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description: File with final mask of full aln len
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pattern: "*.fmask-all.gz"
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- gmask_rf:
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type: file
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description: File with gap-based 0/1 mask of non-gap RF len
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pattern: "*.gmask-rf.gz"
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- gmask_all:
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type: file
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description: File with gap-based 0/1 mask of full aln len
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pattern: "*.gmask-all.gz"
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- pmask_rf:
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type: file
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description: File with PP-based 0/1 mask of non-gap RF len
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pattern: "*.pmask-rf.gz"
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- pmask_all:
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type: file
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description: File with PP-based 0/1 mask of full aln len
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pattern: "*.pmask-all.gz"
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authors:
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- "@erikrikarddaniel"
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