Implement cwl_script command.

Author: jmchilton

.gitmodules

@@ -1,3 +1,6 @@
 [submodule "planemo/xml/xsd/tool"]
 	path = planemo/xml/xsd/tool
 	url = https://github.com/JeanFred/Galaxy-XSD
+[submodule "planemo_ext/cwl2script"]
+	path = planemo_ext/cwl2script
+	url = https://github.com/common-workflow-language/cwl2script.git

planemo/commands/cmd_cwl_script.py

@@ -0,0 +1,76 @@
+"""
+"""
+from __future__ import print_function
+
+import copy
+import os
+
+import click
+
+import schema_salad
+import cwltool
+from cwltool.main import load_tool
+from cwltool.process import (
+    checkRequirements,
+    shortname,
+)
+from cwl2script.cwl2script import (
+    supportedProcessRequirements,
+    generateScriptForWorkflow,
+    generateScriptForTool,
+)
+
+from planemo.cli import pass_context
+from planemo import options
+
+
+@click.command("cwl_script")
+@options.required_tool_arg()
+@options.required_job_arg()
+@click.option('--no_container', is_flag=True, default=False)
+@click.option('outdir', '--output_dir', type=click.Path())
+@click.option('basedir', '--base_dir', type=click.Path(), default=".")
+@pass_context
+def cli(ctx, path, job_path, **kwds):
+    """This compiles simple common workflow language workflows to a shell
+    script.
+    """
+    uri = "file://" + os.path.abspath(job_path)
+
+    loader = schema_salad.ref_resolver.Loader({
+        "@base": uri,
+        "path": {
+            "@type": "@id"
+        }
+    })
+
+    job, _ = loader.resolve_ref(uri)
+
+    t = load_tool(path, False, False, cwltool.workflow.defaultMakeTool, True)
+
+    if type(t) == int:
+        return t
+
+    checkRequirements(t.tool, supportedProcessRequirements)
+
+    for inp in t.tool["inputs"]:
+        if shortname(inp["id"]) in job:
+            pass
+        elif shortname(inp["id"]) not in job and "default" in inp:
+            job[shortname(inp["id"])] = copy.copy(inp["default"])
+        elif shortname(inp["id"]) not in job and inp["type"][0] == "null":
+            pass
+        else:
+            raise Exception("Missing inputs `%s`" % shortname(inp["id"]))
+
+    if not kwds.get("basedir", None):
+        kwds["basedir"] = os.path.dirname(os.path.abspath(job_path))
+
+    outdir = kwds.get("outdir")
+
+    if t.tool["class"] == "Workflow":
+        print(generateScriptForWorkflow(t, job, outdir))
+    elif t.tool["class"] == "CommandLineTool":
+        print(generateScriptForTool(t, job, outdir))
+
+    return 0

planemo/options.py

@@ -99,6 +99,16 @@ def enable_cwl_option():
     )
 
 
+def cwl_conformance_test():
+    return click.option(
+        "--conformance-test",
+        is_flag=True,
+        help=("Generate CWL conformance test object describing job. "
+              "Required by CWL conformance test suite and implemented "
+              "by cwltool reference implementation."),
+    )
+
+
 def brew_dependency_resolution():
     return click.option(
         "--brew_dependency_resolution",
@@ -182,6 +192,19 @@ def required_tool_arg():
     return click.argument("path", metavar="TOOL_PATH", type=arg_type)
 
 
+def required_job_arg():
+    """ Decorate click method as requiring the path to a single tool.
+    """
+    arg_type = click.Path(
+        exists=True,
+        file_okay=True,
+        dir_okay=False,
+        readable=True,
+        resolve_path=True,
+    )
+    return click.argument("job_path", metavar="JOB_PATH", type=arg_type)
+
+
 def _optional_tools_default(ctx, param, value):
     if param.name == "paths" and len(value) == 0:
         return [os.path.abspath(os.getcwd())]

planemo_ext/cwl2script

@@ -23,6 +23,7 @@
     'PyGithub',
     'bioblend',
     'glob2',
+    'cwltool',
 ]
 
 # Latest stable bioblend does not support Python 3, setup dev dependency.
@@ -59,6 +60,7 @@
         'planemo.shed2tap',
         'planemo.xml',
         'planemo_ext',
+        'planemo_ext.cwl2script',
         'planemo_ext.galaxy',
         'planemo_ext.galaxy.eggs',
         'planemo_ext.galaxy.tools',