From 2bb9d18d5a4889d4399acac163632d57bb45f516 Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Tue, 11 Jul 2023 13:49:41 +0200
Subject: [PATCH] example syntax for restrictions

---
 workflow/cwl/raptor-build.cwl  | 25 +++++++++++++++++++++++++
 workflow/cwl/raptor-search.cwl | 20 ++++++++++++--------
 2 files changed, 37 insertions(+), 8 deletions(-)

diff --git a/workflow/cwl/raptor-build.cwl b/workflow/cwl/raptor-build.cwl
index 77c5acdb..f6b49b6a 100644
--- a/workflow/cwl/raptor-build.cwl
+++ b/workflow/cwl/raptor-build.cwl
@@ -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:
@@ -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
 
 requirements:
   EnvVarRequirement:
@@ -89,3 +111,6 @@ outputs:
     type: File    
     outputBinding:
       glob: $(inputs.output_name)
+
+$namespaces:
+  cwltool: "http://commonwl.org/cwltool#"
diff --git a/workflow/cwl/raptor-search.cwl b/workflow/cwl/raptor-search.cwl
index 3102ad04..1461b8ee 100644
--- a/workflow/cwl/raptor-search.cwl
+++ b/workflow/cwl/raptor-search.cwl
@@ -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
@@ -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
@@ -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:
@@ -73,3 +76,4 @@ outputs:
 
 $namespaces:
   edam: http://edamontology.org/
+  cwltool: "http://commonwl.org/cwltool#"