/
protein_extract.cwl
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/
protein_extract.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
label: "protein_extract"
class: Workflow
inputs:
input: File
nogenbank: boolean
oproteins: string?
olds2: string?
oseqids: string?
outputs:
proteins:
type: File
outputSource: protein_extract/proteins
lds2:
type: File
outputSource: lds2_fix/lds2
seqids:
type: File
outputSource: protein_extract/seqids
steps:
protein_extract:
in:
input: input
nogenbank: nogenbank
oproteins: oproteins
olds2: olds2
oseqids: oseqids
out: [ proteins, lds2, seqids ]
run:
class: CommandLineTool
#protein_extract -input-manifest models.mft -o proteins.asn -olds2 LDS2 -oseqids proteins.seq_ids -nogenbank
baseCommand: protein_extract
inputs:
input:
type: File
inputBinding:
prefix: -input
nogenbank:
type: boolean
inputBinding:
prefix: -nogenbank
oproteins:
type: string?
default: "proteins.asn"
inputBinding:
prefix: -o
olds2:
type: string?
default: "LDS2"
inputBinding:
prefix: -olds2
oseqids:
type: string?
default: "proteins.seq_ids"
inputBinding:
prefix: -oseqids
outputs:
proteins:
type: File
outputBinding:
glob: $(inputs.oproteins)
lds2:
type: File
outputBinding:
glob: $(inputs.olds2)
seqids:
type: File
outputBinding:
glob: $(inputs.oseqids)
lds2_fix:
in:
in_lds2: protein_extract/lds2
out: [lds2]
run:
class: CommandLineTool
requirements:
InitialWorkDirRequirement:
listing:
- entry: $(inputs.in_lds2)
writable: true
baseCommand: sqlite3
inputs:
in_lds2:
type: File
inputBinding:
position: 1
sql:
type: string?
default: "update file set file_name=replace(file_name, rtrim(file_name, replace(file_name, '/', '')), '');"
inputBinding:
position: 2
outputs:
lds2:
type: File
outputBinding:
glob: $(inputs.in_lds2.basename)