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example syntax for restrictions #350

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example syntax for restrictions #350

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25 changes: 25 additions & 0 deletions workflow/cwl/raptor-build.cwl
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Original file line number Diff line number Diff line change
Expand Up @@ -47,6 +47,14 @@ inputs:
inputBinding:
prefix: --output

false_positive_rate:
type: double?
label: The false positive rate used for building the index.
doc: |
Default: 0.05. Value must be in range [0,1]
inputBinding:
prefix: --fpr

hints:
SoftwareRequirement:
packages:
Expand All @@ -55,6 +63,20 @@ hints:
version: [ "2.0.0"]
DockerRequirement:
dockerPull: quay.io/biocontainers/raptor:2.0.0--h19e8d03_1
cwltool:ParameterRestrictions:
restrictions:
kmer_size:
- class: intInterval
low: 0
high: 32 # inclusive by default
index_size:
- class: regex
pattern: "\d*[kmgt]"
false_positive_rate:
- class: interval
low: 0
high: 1
high_inclusive: false
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The fpr could be 1, though it wouldn't make sense


requirements:
EnvVarRequirement:
Expand Down Expand Up @@ -89,3 +111,6 @@ outputs:
type: File
outputBinding:
glob: $(inputs.output_name)

$namespaces:
cwltool: "http://commonwl.org/cwltool#"
20 changes: 12 additions & 8 deletions workflow/cwl/raptor-search.cwl
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Expand Up @@ -18,13 +18,6 @@ inputs:
format:
- edam:format_1929 # FASTA
- edam:format_1930 # FASTQ
false_positive_rate:
type: double?
label: The false positive rate used for building the index.
doc: |
Default: 0.05. Value must be in range [0,1]
inputBinding:
prefix: --fpr
error_tolerance:
type: int?
label: The number of errors to tolerate
Expand All @@ -39,7 +32,7 @@ inputs:
inputBinding:
prefix: --output
p_max:
type: double
type: double?
label: Used in the dynamic thresholding
doc: |
The higher p_max, the lower the threshold. Default: 0.15. Value must be in
Expand All @@ -52,6 +45,16 @@ hints:
packages:
raptor:
specs: [ https://bio.tools/raptor ]
cwltool:ParameterRestrictions:
restrictions:
error_tolerance:
- class: intInterval
low: 0
# high default value is positive infinity
p_max:
- class: interval
low: 0
high: 1

requirements:
EnvVarRequirement:
Expand All @@ -73,3 +76,4 @@ outputs:

$namespaces:
edam: http://edamontology.org/
cwltool: "http://commonwl.org/cwltool#"