Add simple parsing of integer, float, and string parameters to tool builder.

jmchilton · jmchilton · commit b0b867ed2401 · 2016-05-10T19:20:06.000-04:00
Works for CWL builder - but should be back ported to Galaxy is possible.
diff --git a/planemo/tool_builder.py b/planemo/tool_builder.py
@@ -4,6 +4,7 @@
 Galaxy and CWL tool descriptions.
 """
 from collections import namedtuple
+import re
 import shlex
 import subprocess
 
@@ -148,7 +149,7 @@
 inputs:
 {%- for input in inputs %}
   - id: {{ input.id }}
-    type: File
+    type: {{ input.type }}
     description: |
       TODO
     inputBinding:
@@ -388,6 +389,11 @@ def cwl_lex_list(self):
                 output_count += 1
                 output = CwlOutput("output%d" % output_count, position, prefix)
                 parse_list.append(output)
+            elif prefix:
+                param_id = prefix.prefix.lower().rstrip("=")
+                type_ = param_type(value)
+                input = CwlInput(param_id, position, prefix, type_=type_)
+                parse_list.append(input)
             else:
                 part = CwlCommandPart(value, position, prefix)
                 parse_list.append(part)
@@ -489,10 +495,11 @@ def is_token(self, value):
 
 class CwlInput(object):
 
-    def __init__(self, id, position, prefix):
+    def __init__(self, id, position, prefix, type_="File"):
         self.id = id
         self.position = position
         self.prefix = prefix
+        self.type = type_
 
     def is_token(self, value):
         return False
@@ -726,6 +733,15 @@ def __str__(self):
         return base.format(attrs, self.name)
 
 
+def param_type(value):
+    if re.match("^\d+$", value):
+        return "int"
+    elif re.match("^\d+?\.\d+?$", value):
+        return "float"
+    else:
+        return "string"
+
+
 class Container(object):
 
     def __init__(self, image_id):
diff --git a/tests/test_command_io.py b/tests/test_command_io.py
@@ -64,7 +64,11 @@ def test_example_cwl_simple_redirect():
 
 
 def test_prefixes_separated():
-    command_io = _example("seqtk convert -i '1.bed' --output '1.bam'", example_outputs=["1.bam"], example_inputs=["1.bed"])
+    command_io = _example(
+        "seqtk convert -i '1.bed' --output '1.bam'",
+        example_outputs=["1.bam"],
+        example_inputs=["1.bed"]
+    )
     cwl_properties = command_io.cwl_properties()
     _assert_eq(cwl_properties["base_command"], ["seqtk", "convert"])
     _assert_eq(cwl_properties["inputs"][0].position, 1)
@@ -78,7 +82,11 @@ def test_prefixes_separated():
 
 
 def test_prefixes_joined():
-    command_io = _example("seqtk convert INPUT=1.bed OUTPUT=1.bam", example_outputs=["1.bam"], example_inputs=["1.bed"])
+    command_io = _example(
+        "seqtk convert INPUT=1.bed OUTPUT=1.bam",
+        example_outputs=["1.bam"],
+        example_inputs=["1.bed"]
+    )
     cwl_properties = command_io.cwl_properties()
     _assert_eq(cwl_properties["base_command"], ["seqtk", "convert"])
     _assert_eq(cwl_properties["inputs"][0].position, 1)
@@ -91,6 +99,35 @@ def test_prefixes_joined():
     _assert_eq(cwl_properties["stdout"], None)
 
 
+def test_integer_parameters():
+    command_io = _example(
+        "seqtk convert --size 100 -i '1.bed' --threshold 2.0 --output_type bam > '1.bam'",
+        example_outputs=["1.bam"],
+        example_inputs=["1.bed"]
+    )
+    cwl_properties = command_io.cwl_properties()
+    _assert_eq(cwl_properties["base_command"], ["seqtk", "convert"])
+    _assert_eq(len(cwl_properties["inputs"]), 4)
+    _assert_eq(cwl_properties["inputs"][0].position, 1)
+    _assert_eq(cwl_properties["inputs"][0].type, "int")
+    _assert_eq(cwl_properties["inputs"][0].prefix.prefix, "--size")
+
+    _assert_eq(cwl_properties["inputs"][1].position, 2)
+    _assert_eq(cwl_properties["inputs"][1].type, "File")
+    _assert_eq(cwl_properties["inputs"][1].prefix.prefix, "-i")
+
+    _assert_eq(cwl_properties["inputs"][2].position, 3)
+    _assert_eq(cwl_properties["inputs"][2].type, "float")
+    _assert_eq(cwl_properties["inputs"][2].prefix.prefix, "--threshold")
+
+    _assert_eq(cwl_properties["inputs"][3].position, 4)
+    _assert_eq(cwl_properties["inputs"][3].type, "string")
+    _assert_eq(cwl_properties["inputs"][3].prefix.prefix, "--output_type")
+
+    _assert_eq(cwl_properties["outputs"][0].glob, "out")
+    _assert_eq(cwl_properties["stdout"], "out")
+
+
 def _example(example_command, example_outputs=[], example_inputs=[]):
     """Build a CommandIO object for test cases."""
     kwds = {}
