@prefix CommandLineBinding: .
@prefix xsd: .
@prefix DockerRequirement: .
@prefix Workflow: .
@prefix sld: .
@prefix rdfs: .
@prefix CommandOutputBinding: .
@prefix SoftwarePackage: .
@prefix ns1: .
@prefix SoftwareRequirement: .
@prefix rdf: .
@prefix ScatterMethod: .
@prefix cwl: .
@prefix ExpressionTool: .
a cwl:ExpressionTool ;
ExpressionTool:expression "${ var proteins = [];\n var nucleotides = [];\n var names = [];\n inputs.clusters.listing.forEach(function (item) {\n if (item.class == \"Directory\") {\n names.push(item.basename);\n item.listing.forEach(function (item2) {\n if (item2.basename.startsWith(\"nt\")) {\n nucleotides.push(item2);\n } else if (item2.basename.startsWith(\"aa\")) {\n proteins.push(item2);\n };\n });\n };\n });\n return { \"proteins\": proteins,\n \"nucleotides\": nucleotides,\n \"names\": names };\n }\n" ;
cwl:inputs ;
cwl:outputs , , ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
rdfs:label "guide tree" ;
cwl:outputSource ;
sld:type cwl:File .
cwl:source .
cwl:source .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.0" ;
cwl:baseCommand ( "codeml" "paml0-3.ctl" ) ;
cwl:cwlVersion ;
cwl:hints [ a cwl:SoftwareRequirement ;
SoftwareRequirement:packages [ SoftwarePackage:package "paml" ;
SoftwarePackage:specs "https://identifiers.org/rrid/RRID:SCR_014932"
]
] ;
cwl:hints [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "seqfile = $(inputs.sequences.path)\ntreefile = $(inputs.tree.path)\noutfile = results0-3.txt * main result file name\nnoisy = 9 * 0,1,2,3,9: how much rubbish on the screen\nverbose = 1 * 1:detailed output\nrunmode = 0 * 0:user defined tree\nseqtype = 1 * 1:codons\nCodonFreq = 2 * 0:equal, 1:F1X4, 2:F3X4, 3:F61\nmodel = 0 * 0:one omega ratio for all branches\n * 1:separate omega for each branch\n * 2:user specified dN/dS ratios for branches\nNSsites = 0 3 \nicode = 0 * 0:universal code\nfix_kappa = 0 * 1:kappa fixed, 0:kappa to be estimated\nkappa = 4 * initial or fixed kappa\nfix_omega = 0 * 1:omega fixed, 0:omega to be estimated\nomega = 5 * initial omega\n * RateAncestor = 1\nncatG = 3 * num. of categories in the dG or AdG models of rates\ngetSE = 0 * 0: don't want them, 1: want S.E.s of estimates\n" ;
cwl:entryname "paml0-3.ctl"
]
] ;
cwl:hints [ a ] ;
cwl:hints [ a ] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/biocontainers/paml:4.9--1"
] ;
cwl:inputs , ;
cwl:outputs .
cwl:source .
rdfs:label "Multiple sequence alignment" ;
cwl:outputBinding [ CommandOutputBinding:glob
"60b927d59b81c1c48b20da30e2a9ee14e088023a" ] ;
sld:type cwl:File .
a cwl:Workflow ;
ns1:original_cwlVersion "v1.0" ;
Workflow:steps , ;
cwl:cwlVersion ;
cwl:hints [ a ] ;
cwl:hints [ a ] ;
cwl:inputs ;
cwl:outputs , ;
cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ;
cwl:requirements [ a cwl:ScatterFeatureRequirement ] .
cwl:outputSource ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
sld:type [ sld:items cwl:File ;
sld:type sld:array
] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
rdfs:label "Multiple sequence alignment" ;
cwl:outputBinding [ CommandOutputBinding:glob
"9f8315f080f2fbdc1f58607c6f734b28cee77736" ] ;
sld:type cwl:File .
cwl:source .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:prefix "-output" ;
cwl:valueFrom "paml"
]
"$(inputs.protein_alignment.path)" "$(inputs.nucleotides.path)"
) ;
cwl:baseCommand ( "pal2nal.pl" ) ;
cwl:cwlVersion ;
cwl:hints [ a ] ;
cwl:hints [ a cwl:SoftwareRequirement ;
SoftwareRequirement:packages [ SoftwarePackage:package "pal2nal" ;
SoftwarePackage:specs "https://doi.org/10.1093/nar/gkl315"
]
] ;
cwl:hints [ a ] ;
cwl:inputs , ;
cwl:outputs ;
cwl:stdout "9f8315f080f2fbdc1f58607c6f734b28cee77736" .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
sld:type cwl:Directory .
cwl:in ;
cwl:out , ;
cwl:run .
cwl:outputBinding [ CommandOutputBinding:glob
"results0-3.txt" ] ;
sld:type cwl:File .
a cwl:Workflow ;
ns1:original_cwlVersion "v1.0" ;
Workflow:steps , , ;
cwl:cwlVersion ;
cwl:hints [ a ] ;
cwl:hints [ a ] ;
cwl:inputs , ;
cwl:outputs , , , .
sld:type cwl:File .
sld:type [ sld:items cwl:File ;
sld:type sld:array
] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
rdfs:label "dN/dS results" ;
cwl:outputSource ;
sld:type cwl:File .
cwl:source .
cwl:in , ;
cwl:out ;
cwl:run .
cwl:source .
cwl:source .
cwl:in , ;
cwl:out ;
cwl:run .
rdfs:comment "Each sub-directory should contain a single protein (aa.fa) and a single\nnucleotide sequence (nt.fa) file. The name of the sub-directory will be\npreserved.\n" ;
rdfs:label "A directory of directories" ;
sld:type cwl:Directory .
rdfs:label "nucleotides alignment" ;
cwl:outputSource ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.multi_sequence.nameroot).ph" ] ;
sld:type cwl:File .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "-i" "$(inputs.multi_sequence.path)" "--guidetree-out" "$(inputs.multi_sequence.nameroot).ph" "--threads" "$(runtime.cores)" ) ;
cwl:baseCommand ( "clustalo" ) ;
cwl:cwlVersion ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "biocontainers/clustal-omega"
] ;
cwl:hints [ a cwl:SoftwareRequirement ;
SoftwareRequirement:packages [ SoftwarePackage:package "clustalo" ;
SoftwarePackage:specs "https://identifiers.org/rrid/RRID:SCR_001591"
]
] ;
cwl:hints [ a ] ;
cwl:hints [ a ] ;
cwl:inputs ;
cwl:outputs , ;
cwl:stdout "60b927d59b81c1c48b20da30e2a9ee14e088023a" .
rdfs:label "nucleotide sequence" ;
sld:type cwl:File .
sld:type cwl:File .
rdfs:label "Multiple sequence alignment" ;
sld:type cwl:File .
cwl:in , ;
cwl:out ;
cwl:run ;
cwl:scatter ( ) ;
cwl:scatterMethod ScatterMethod:dotproduct .
rdfs:label "proteins alignment" ;
cwl:outputSource ;
sld:type cwl:File .
rdfs:label "proteins" ;
sld:type cwl:File .
sld:type cwl:File .
cwl:source .
sld:type cwl:File .
cwl:in ;
cwl:out , , ;
cwl:run .
cwl:outputSource ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .