181 lines
3.6 KiB
YAML
Executable File
181 lines
3.6 KiB
YAML
Executable File
tools:
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hmmsearch:
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id: "hmmsearch"
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name: "HMMER hmmsearch"
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category: "identification"
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executable: "hmmsearch"
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docker_image: "biocontainers/hmmer:v3.3.2_cv1"
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inputs:
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- name: "query"
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type: "hmm"
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required: true
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- name: "target"
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type: "fasta"
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required: true
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outputs:
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- name: "tblout"
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type: "tblout"
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- name: "domtblout"
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type: "domtblout"
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parameters:
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e_value:
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type: "float"
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default: 1e-5
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min: 1e-100
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max: 1.0
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coverage:
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type: "float"
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default: 0.5
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min: 0.1
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max: 1.0
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cpu:
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type: "int"
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default: 4
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timeout: 7200
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blastp:
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id: "blastp"
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name: "BLASTP"
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category: "identification"
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executable: "blastp"
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docker_image: "biocontainers/blast:v2.13.0_cv1"
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inputs:
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- name: "query"
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type: "fasta"
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required: true
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- name: "db"
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type: "blastdb"
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required: true
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outputs:
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- name: "results"
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type: "blast_out"
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parameters:
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e_value:
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type: "float"
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default: 1e-5
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max_target_seqs:
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type: "int"
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default: 500
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outfmt:
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type: "int"
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default: 6
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timeout: 3600
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mafft:
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id: "mafft"
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name: "MAFFT"
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category: "alignment"
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executable: "mafft"
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inputs:
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- name: "sequences"
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type: "fasta"
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required: true
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outputs:
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- name: "alignment"
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type: "fasta"
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parameters:
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strategy:
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type: "enum"
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default: "auto"
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values: ["auto", "linsi", "ginsi", "einsi", "fftns"]
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maxiterate:
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type: "int"
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default: 1000
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timeout: 7200
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iqtree:
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id: "iqtree"
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name: "IQ-TREE"
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category: "phylogeny"
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executable: "iqtree2"
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docker_image: "biocontainers/iqtree:v2.2.0_cv1"
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inputs:
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- name: "alignment"
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type: "fasta"
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required: true
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outputs:
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- name: "tree"
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type: "newick"
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- name: "log"
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type: "log"
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parameters:
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model:
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type: "enum"
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default: "MFP"
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values: ["MFP", "LG", "WAG", "JTT"]
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bootstrap:
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type: "int"
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default: 1000
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threads:
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type: "int"
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default: 4
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timeout: 14400
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mcscanx:
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id: "mcscanx"
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name: "MCScanX"
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category: "comparative"
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executable: "MCScanX"
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inputs:
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- name: "gff"
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type: "gff"
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required: true
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- name: "blast"
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type: "blast_out"
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required: true
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outputs:
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- name: "collinearity"
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type: "collinearity"
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- name: "tandem"
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type: "tandem"
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parameters:
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match_score:
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type: "int"
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default: 50
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gap_penalty:
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type: "int"
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default: -1
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timeout: 3600
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meme:
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id: "meme"
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name: "MEME"
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category: "annotation"
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executable: "meme"
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docker_image: "biocontainers/meme:v5.0.0_cv1"
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inputs:
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- name: "sequences"
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type: "fasta"
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required: true
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outputs:
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- name: "motifs"
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type: "xml"
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parameters:
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nmotifs:
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type: "int"
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default: 10
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min_width:
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type: "int"
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default: 6
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max_width:
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type: "int"
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default: 200
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timeout: 7200
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categories:
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identification:
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name: "Gene Identification"
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tools: ["hmmsearch", "blastp"]
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alignment:
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name: "Sequence Alignment"
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tools: ["mafft"]
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phylogeny:
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name: "Phylogenetic Analysis"
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tools: ["iqtree"]
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comparative:
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name: "Comparative Genomics"
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tools: ["mcscanx"]
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annotation:
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name: "Functional Annotation"
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tools: ["meme"]
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