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mutex.cwl
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mutex.cwl
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cwlVersion: v1.0
class: CommandLineTool
label: mutex
requirements:
DockerRequirement:
dockerPull: "opengenomics/mutex:v2.0.2"
baseCommand: ["mutex.py"]
inputs:
data_file:
type: File
doc: Name of the data file. Mandatory.
inputBinding:
prefix: --data-file
network_file:
type: File
doc: To customize the signaling network, users can use this parameter. The tab-delimited network file should contain 3 columns (Gene Symbol 1, interaction-type, Gene Symbol 2). Mandatory.
inputBinding:
prefix: --network-file
max_group_size:
type: int
default: 5
doc: The maximum size of a result mutex group. Integer value. Default is 5.
inputBinding:
prefix: --max-group-size
first_level_random_iteration:
type: int
default: 10000
doc: Number of randomization to estimate null distribution of member p-values in mutex groups. Integer. Default is 10000.
inputBinding:
prefix: --first-level-random-iteration
second_level_random_iteration:
type: int
default: 100
doc: Number of runs to estimate the null distribution of final scores. Integer. Default is 100. If FDR control on results is not required and only the ranking of the result groups is sufficient, set this parameter to 0.
inputBinding:
prefix: --second-level-random-iteration
fdr_cutoff:
type: float?
doc: Users can select a specific FDR cutoff. When not provided, or when set to a negative value, the FDR cutoff that maximizes the expected value of true positives - false positives is used.
inputBinding:
prefix: --fdr-cutoff
score_cutoff:
type: float?
inputBinding:
prefix: --score-cutoff
search_on_signaling_network:
type: string
default: "true"
doc: Whether to reduce the search space using the signaling network. "true" or "false". Default is "true".
inputBinding:
prefix: --search-on-signaling-network
genes_file:
type: File?
doc: This parameter can be used to limit the search to a subset of genes. The file should contain a gene symbol per line.
inputBinding:
prefix: --genes-file
gene_ranking_file:
type: File?
inputBinding:
prefix: --gene-ranking-file
sample_to_tissue_mapping_file:
type: File?
inputBinding:
prefix: --sample-to-tissue-mapping-file
gene_limit:
type: int?
inputBinding:
prefix: --gene-limit
minimum_alteration_count_threshold:
type: int?
inputBinding:
prefix: --minimum-alteration-count-threshold
random:
type: boolean
default: false
inputBinding:
prefix: --random
outputs:
ranked_groups:
type: File
outputBinding:
glob: ./*/ranked-groups.txt
fdr_guide:
type: File
outputBinding:
glob: ./*/fdr-guide.txt
result_groups:
type: File
outputBinding:
glob: ./*/result-groups.cus
merged_network:
type: File
outputBinding:
glob: ./*/merged-network.sif