Better CWL 1.0 tool_init.

.gitignore

@@ -50,6 +50,7 @@ output/*/index.html
 docs/_build
 
 .venv
+.venv3
 
 tool_test_output.*
 

Makefile

@@ -6,10 +6,12 @@ ENV?=py27
 ARGS?=
 # Location of virtualenv used for development.
 VENV?=.venv
+VENV3?=.venv3
 # Open resource on Mac OS X or Linux
 OPEN_RESOURCE=bash -c 'open $$0 || xdg-open $$0'
 # Source virtualenv to execute command (flake8, sphinx, twine, etc...)
 IN_VENV=if [ -f $(VENV)/bin/activate ]; then . $(VENV)/bin/activate; fi;
+IN_VENV3=if [ -f $(VENV3)/bin/activate ]; then . $(VENV3)/bin/activate; fi;
 # TODO: add this upstream as a remote if it doesn't already exist.
 UPSTREAM?=galaxyproject
 SOURCE_DIR?=planemo
@@ -54,6 +56,10 @@ setup-venv: ## setup a development virutalenv in current directory
 	if [ ! -d $(VENV) ]; then virtualenv $(VENV); exit; fi;
 	$(IN_VENV) pip install --upgrade pip && pip install -r requirements.txt && pip install -r dev-requirements.txt
 
+setup-venv3: ## setup a development virutalenv in current directory
+	if [ ! -d $(VENV3) ]; then virtualenv -p python3 $(VENV3); exit; fi;
+	$(IN_VENV3) pip install --upgrade pip && pip install -r requirements.txt && pip install -r dev-requirements.txt
+
 setup-git-hook-lint: ## setup precommit hook for linting project
 	cp $(BUILD_SCRIPTS_DIR)/pre-commit-lint .git/hooks/pre-commit
 

planemo/tool_builder.py

@@ -135,12 +135,25 @@
 class: CommandLineTool
 id: "{{id}}"
 label: "{{label}}"
-{%- if containers %}
+{%- if containers or requirements %}
 hints:
 {%- for container in containers %}
-  - class: DockerRequirement
+  DockerRequirement:
     dockerPull: {{ container.image_id }}
 {%- endfor %}
+{%- if requirements %}
+  SoftwareRequirement:
+    packages:
+{%- for requirement in requirements %}
+    - package: {{ requirement.name }}
+{%- if requirement.version %}
+      version:
+      - "{{ requirement.version }}"
+{%- else %}
+      version: []
+{%- endif %}
+{%- endfor %}
+{%- endif %}
 {%- endif %}
 {%- if inputs or outputs %}
 inputs:
@@ -268,6 +281,7 @@ def _build_cwl(**kwds):
         "cwl_version": DEFAULT_CWL_VERSION,
         "help": kwds.get("help", ""),
         "containers": kwds.get("containers", []),
+        "requirements": kwds.get("requirements", []),
         "id": kwds.get("id"),
         "label": kwds.get("name"),
     }
@@ -641,7 +655,7 @@ def _handle_requirements(kwds):
     """
     requirements = kwds["requirement"]
     del kwds["requirement"]
-    requirements = map(Requirement, requirements or [])
+    requirements = list(map(Requirement, requirements or []))
 
     container = kwds["container"]
     del kwds["container"]