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maw_single.cwl
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cwlVersion: v1.0
class: Workflow
inputs:
python_script:
type: File
default:
class: File
path: Workflow_Python_Script_all.py
r_script:
type: File
default:
class: File
path: Workflow_R_Script_all.r
mzml_file:
type: File
gnps_file:
type: File
hmdb_file:
type: File
mbank_file:
type: File
ppmx:
type: int
collision_info:
type: boolean
db_name:
type: string
db_path:
type: File
# isotope:
# type: boolean
# default: False
steps:
dereplication:
run: maw-r.cwl
in:
workflow_script: r_script
mzml_file: mzml_file
gnps_file: gnps_file
hmdb_file: hmdb_file
mbank_file: mbank_file
ppmx: ppmx
collision_info: collision_info
db_name: db_name
db_path: db_path
out:
# - ms_files
- results
- peaks_and_parameters
- msp_file
- ms1data
- gnps_dir
- hmdb_dir
- mbank_dir
metfrag:
run: maw-metfrag.cwl
scatter:
- PeakList
- IonizedPrecursorMass
- PrecursorIonMode
- SampleName
scatterMethod: dotproduct
in:
PeakList:
source: dereplication/peaks_and_parameters
valueFrom: $(self.PeakList)
IonizedPrecursorMass:
source: dereplication/peaks_and_parameters
valueFrom: $(self.IonizedPrecursorMass)
PrecursorIonMode:
source: dereplication/peaks_and_parameters
valueFrom: $(self.PrecursorIonMode)
SampleName:
source: dereplication/peaks_and_parameters
valueFrom: $(self.SampleName)
LocalDatabasePath: db_path
out: [metfrag_candidate_list]
#out: metfrag_candidate_list
# sirius_isotope:
# run: sirius-new.cwl
# in:
# spectrum: dereplication/ms_files
# isotope:
# default: False
# #parameter: dereplication/parameters
# scatter:
# - spectrum
# #- parameter
# out: [results]
# sirius_no_isotope:
# run: sirius-new.cwl
# in:
# spectrum: dereplication/ms_files
# isotope:
# default: True
# #parameter: dereplication/parameters
# scatter:
# - spectrum
# #- parameter
# out: [results]
cheminformatics:
run: maw-py.cwl
in:
workflow_script: python_script
msp_file: dereplication/msp_file
gnps_dir: dereplication/gnps_dir
hmdb_dir: dereplication/hmdb_dir
mbank_dir: dereplication/mbank_dir
# sirius_results:
# source: [sirius_no_isotope/results, sirius_isotope/results]
# linkMerge: True
metfrag_candidate_list: metfrag/metfrag_candidate_list
ms1data: dereplication/ms1data
#out: [results, provenance]
out:
# - msp_file_df
# - ms1data_df
- candidate_files
- result
outputs:
candidate_files:
type: File[]
outputSource: cheminformatics/candidate_files
result:
type: File
outputSource: cheminformatics/result
requirements:
ScatterFeatureRequirement: {}
StepInputExpressionRequirement: {}
InlineJavascriptRequirement: {}