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Dockstore.cwl
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Dockstore.cwl
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#!/usr/bin/env cwl-runner
#
# Authors: Andrew Lamb
cwlVersion: v1.0
class: CommandLineTool
baseCommand: [Rscript, /usr/local/bin/cibersort_wrapper.R]
doc: "run CIBERSORT"
requirements:
- class: InlineJavascriptRequirement
hints:
DockerRequirement:
dockerPull: quay.io/cri-iatlas/iatlas-tool-cibersort
inputs:
sig_matrix_file:
type: File
inputBinding:
prefix: --sig_matrix_file
doc: Path to reference matrix.
mixture_file:
type: File
inputBinding:
prefix: --mixture_file
doc: Path to mixture matrix.
output_file_string:
type: string
default: "./output_file.tsv"
inputBinding:
prefix: --output_file
doc: Path to write output file
perm:
type: ["null", int]
inputBinding:
prefix: --perm
doc: No. permutations; set to >=100 to calculate p-values (default = 0)
QN:
type: ["null", boolean]
inputBinding:
prefix: --QN
doc: "Quantile normalization of input mixture (default = TRUE)"
absolute:
type: ["null", boolean]
inputBinding:
prefix: --absolute
doc: Run CIBERSORT in absolute mode (default = FALSE).
abs_method:
type: ["null", string]
inputBinding:
prefix: --abs_method
doc: If absolute is set to TRUE, choose method 'no.sumto1' or 'sig.score'
outputs:
output_file:
type: File
outputBinding:
glob: $(inputs.output_file_string)
doc: see output_string