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FragGeneScan1_20.cwl
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FragGeneScan1_20.cwl
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cwlVersion: v1.0
class: CommandLineTool
label: "FragGeneScan: find (fragmented) genes in short reads"
doc: |
FragGeneScan is an application for finding (fragmented) genes in short
reads. It can also be applied to predict prokaryotic genes in incomplete
assemblies or complete genomes.
FragGeneScan was first released through omics website (http://omics.informatics.indiana.edu/FragGeneScan/)
in March 2010, where you can find its old releases. FragGeneScan migrated to SourceForge in October, 2013
(https://sourceforge.net/projects/fraggenescan/).
Version 1.20 can be downloaded here:
https://sourceforge.net/projects/fraggenescan/files/
baseCommand: [] # FragGeneScan
requirements:
SchemaDefRequirement:
types:
- $import: FragGeneScan-model.yaml
InlineJavascriptRequirement: {}
ShellCommandRequirement: {}
hints:
SoftwareRequirement:
packages:
fraggenescan:
specs: [ "https://identifiers.org/rrid/RRID:SCR_011929" ]
version: [ "1.20" ]
inputs:
sequence:
type: File
format: edam:format_1929 # FASTA
inputBinding:
prefix: -s
completeSeq:
doc: |
True if the sequence file has complete genomic sequences
False if the sequence file has short sequence reads
type: boolean
inputBinding:
valueFrom: |
${ if (self) {
return [ "-w", "1" ];
} else {
return [ "-w", "0" ];
}
}
model: FragGeneScan-model.yaml#model
threadNumber:
type: int?
inputBinding:
prefix: -p
arguments:
- mkdir
- train
- ;
- ln
- -s
- $(inputs.model.main.path)
- train/
- ;
- ln
- -s
- $(inputs.model.prob_forward.path)
- train/gene
- ;
- ln
- -s
- $(inputs.model.prob_backward.path)
- train/rgene
- ;
- ln
- -s
- $(inputs.model.prob_noncoding.path)
- train/noncoding
- ;
- ln
- -s
- $(inputs.model.prob_start.path)
- train/start
- ;
- ln
- -s
- $(inputs.model.prob_stop.path)
- train/stop
- ;
- ln
- -s
- $(inputs.model.prob_start1.path)
- train/start1
- ;
- ln
- -s
- $(inputs.model.prob_stop1.path)
- train/stop1
- ;
- ln
- -s
- $(inputs.model.pwm_dist.path)
- train/pwm
- ;
- FragGeneScan
- -o
- $(runtime.outdir)/predicted_cds
- -t
- train/$(inputs.model.main.basename)
# TODO: when Toil supports the InitialWorkDirRequirement, use that instead of
# this ShellCommandRequirement hack/workaround
outputs:
predictedCDS:
type: File
format: edam:format_1929 # FASTA
outputBinding:
glob: predicted_cds.faa
$namespaces: { edam: "http://edamontology.org/" }
$schemas: [ "http://edamontology.org/EDAM_1.16.owl" ]