/
optimal-pipeline-xml.cwl
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optimal-pipeline-xml.cwl
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class: Workflow
cwlVersion: v1.0
id: optimal_pipeline
label: optimal-pipeline
$namespaces:
sbg: 'https://www.sevenbridges.com/'
inputs:
- id: coding
type: 'string[]'
'sbg:x': -257.91571044921875
'sbg:y': 192.51539611816406
- id: abs_path
type: string
'sbg:x': -242.37277221679688
'sbg:y': 353.3030700683594
- id: drugbank_mapping
type: string
'sbg:x': -264.2220458984375
'sbg:y': -110
- id: api_key
type: string
'sbg:x': -258.5850830078125
'sbg:y': -241.3938446044922
- id: xml_path
type: Directory
'sbg:x': -271.93145751953125
'sbg:y': 61.290611267089844
outputs:
- id: annotated_with_doid
outputSource:
- annotate_druglabels/output
type: File
'sbg:x': 1039.222412109375
'sbg:y': 103.11963653564453
- id: cleaned_data
outputSource:
- clean_text/output
type: File
'sbg:x': 1034.700927734375
'sbg:y': 377.3329162597656
- id: labels_withDBID
outputSource:
- map2drugbank/output
type: File
'sbg:x': 1002.2223510742188
'sbg:y': -120.88036346435547
steps:
- id: extract_xml
in:
- id: coding
source:
- coding
- id: xml_path
source: xml_path
- id: abs_path
source: abs_path
out:
- id: output
run: steps/extract-xml.cwl
label: extract-xml
'sbg:x': 191.941650390625
'sbg:y': 190.73094177246094
- id: clean_text
in:
- id: xml_product
source: extract_xml/output
- id: abs_path
source: abs_path
out:
- id: output
run: steps/clean-text.cwl
label: clean-text
'sbg:x': 378.58953857421875
'sbg:y': 248.26510620117188
- id: map2drugbank
in:
- id: drugbank_mapping
source: drugbank_mapping
- id: xml_product_cleaned
source: clean_text/output
- id: abs_path
source: abs_path
out:
- id: output
run: steps/map2drugbank.cwl
label: map2DrugBank
'sbg:x': 537.8374633789062
'sbg:y': -90.61640930175781
- id: annotate_druglabels
in:
- id: xml_product_dbid
source: map2drugbank/output
- id: abs_path
source: abs_path
- id: api_key
source: api_key
out:
- id: output
run: steps/annotate-druglabels.cwl
label: annotate-druglabels
'sbg:x': 784.881591796875
'sbg:y': 100
requirements: []