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knime-labelfree-quantification.red.yml
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knime-labelfree-quantification.red.yml
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cli:
baseCommand: run-knime
class: CommandLineTool
cwlVersion: v1.0
doc: KNIME Labelfree Quantification.
inputs:
database_name:
doc: Name of database file located in databases subdirectory.
inputBinding: {position: 1}
type: string
input_dir:
doc: Input directory containing datasets and databases subdirectories.
inputBinding: {position: 0}
type: Directory
outputs:
execute_log:
outputBinding: {glob: execute.log}
type: File
peptide_background_quantification:
outputBinding: {glob: peptide_background_quantification.csv}
type: File
peptide_quantification:
outputBinding: {glob: peptide_quantification.csv}
type: File
protein_background_quantification:
outputBinding: {glob: protein_background_quantification.csv}
type: File
protein_quantification:
outputBinding: {glob: protein_quantification.csv}
type: File
container:
engine: docker
settings:
image: {url: 'docker.io/deepprojects/knime-labelfree-quantification:0.3'}
execution:
engine: ccfaice
settings: {}
inputs:
database_name: s_pyo_sf370_potato_human_target_decoy_with_contaminants.fasta
input_dir:
class: Directory
connector:
access: {archiveFormat: gztar, url: 'https://s3.denbi.uni-tuebingen.de/fb-test/demo_container/cibi_user_meeting_2018/labelfree_example.tar.gz'}
command: red-connector-http-archive
listing:
- basename: datasets
class: Directory
listing:
- {basename: lfq_spikein_dilution_1.mzML, class: File}
- {basename: lfq_spikein_dilution_2.mzML, class: File}
- {basename: lfq_spikein_dilution_3.mzML, class: File}
- basename: databases
class: Directory
listing:
- {basename: s_pyo_sf370_potato_human_target_decoy_with_contaminants.fasta,
class: File}
- {basename: s_pyo_sf370_potato_human_target_decoy_with_contaminants.fasta.phr,
class: File}
- {basename: s_pyo_sf370_potato_human_target_decoy_with_contaminants.fasta.pin,
class: File}
- {basename: s_pyo_sf370_potato_human_target_decoy_with_contaminants.fasta.psq,
class: File}
- {basename: uniprot-s-pyogenes-sf370-plus-potato-and-human-spike-ins.fasta,
class: File}
- {basename: uniprot-s-pyogenes-sf370-plus-potato-and-human-spike-ins.fasta.phr,
class: File}
- {basename: uniprot-s-pyogenes-sf370-plus-potato-and-human-spike-ins.fasta.pin,
class: File}
- {basename: uniprot-s-pyogenes-sf370-plus-potato-and-human-spike-ins.fasta.psq,
class: File}
redVersion: '8'