Implement a planemo tool_factory command to launch the tool factory.

Works with all the same options as planemo serve - for instance planemo --install_galaxy tool_factory will download the latest tip of Galaxy and serve the tool factory from that.

This commit includes the most recent tool factory 2 code base ripped from tools-iuc (https://github.com/galaxyproject/tools-iuc/tree/master/tools/tool_factory_2 with the modifications from galaxyproject/tools-iuc#48).

This is very experimental - I can get the tool factory to show and run - but my tests never seem to produce output.

Author: jmchilton

docs/commands.rst

@@ -21,5 +21,6 @@ documentation describes these commands.
 .. include:: commands/shed_upload.rst
 .. include:: commands/syntax.rst
 .. include:: commands/test.rst
+.. include:: commands/tool_factory.rst
 .. include:: commands/tool_init.rst
 .. include:: commands/travis_init.rst

docs/commands/tool_factory.rst

@@ -0,0 +1,40 @@
+
+``tool_factory`` command
+===============================
+
+This section is auto-generated from the help text for the planemo command
+``tool_factory``. This help message can be generated with ``planemo tool_factory
+--help``.
+
+**Usage**::
+
+    planemo tool_factory [OPTIONS]
+
+**Help**
+
+(Experimental) Launch Galaxy with the Tool Factory 2 available.
+
+For more information about the Galaxy Tool Factory see the publication
+Creating reusable tools from scripts: the Galaxy Tool Factory by Lazarus
+et. al. (10.1093/bioinformatics/bts573). Available at
+http://www.ncbi.nlm.nih.gov/pubmed/23024011.
+
+**Options**::
+
+
+      --galaxy_root DIRECTORY         Root of development galaxy directory to
+                                      execute command with.
+      --install_galaxy                Download and configure a disposable copy of
+                                      Galaxy from github.
+      --test_data DIRECTORY           test-data directory to for specified
+                                      tool(s).
+      --dependency_resolvers_config_file PATH
+                                      Dependency resolver configuration for Galaxy
+                                      to target.
+      --job_config_file PATH          Job configuration file for Galaxy to target.
+      --tool_dependency_dir DIRECTORY
+                                      Tool dependency dir for Galaxy to target.
+      --brew_dependency_resolution    Configure Galaxy to use plain brew
+                                      dependency resolution.
+      --help                          Show this message and exit.
+    

planemo/commands/cmd_tool_factory.py

@@ -0,0 +1,29 @@
+import os
+
+import click
+from planemo.cli import pass_context
+from planemo import options
+from planemo import galaxy_serve
+
+
+@click.command('tool_factory')
+@options.galaxy_root_option()
+@options.install_galaxy_option()
+@options.test_data_option()
+@options.dependency_resolvers_option()
+@options.job_config_option()
+@options.tool_dependency_dir_option()
+@options.brew_dependency_resolution()
+@pass_context
+def cli(ctx, **kwds):
+    """(Experimental) Launch Galaxy with the Tool Factory 2 available.
+
+    For more information about the Galaxy Tool Factory see the publication
+    Creating reusable tools from scripts: the Galaxy Tool Factory by Lazarus
+    et. al. (10.1093/bioinformatics/bts573). Available at
+    http://www.ncbi.nlm.nih.gov/pubmed/23024011.
+    """
+    # TODO: de-duplicate option handling with cmd_serve.
+    mod_dir = os.path.dirname(__file__)
+    tf_dir = os.path.join(mod_dir, '..', '..', 'tool_factory_2')
+    galaxy_serve.serve(ctx, os.path.abspath(tf_dir), **kwds)

planemo/galaxy_config.py

@@ -191,6 +191,7 @@ def config_join(*args):
         if preseeded_database:
             env["GALAXY_TEST_DB_TEMPLATE"] = os.path.abspath(database_location)
         env["GALAXY_TEST_UPLOAD_ASYNC"] = "false"
+        env["GALAXY_DEVELOPMENT_ENVIRONMENT"] = "1"
         web_config = __sub(WEB_SERVER_CONFIG_TEMPLATE, template_args)
         open(config_join("galaxy.ini"), "w").write(web_config)
         tool_conf_contents = __sub(TOOL_CONF_TEMPLATE, template_args)

setup.py

@@ -42,6 +42,9 @@
         'planemo_ext.galaxy.tools.deps.resolvers',
         'planemo_ext.galaxy.util',
     ],
+    data_files=[('tool_factory_2', ['tool_factory_2/rgToolFactory2.xml',
+                                    'tool_factory_2/rgToolFactory2.py',
+                                    'tool_factory_2/getlocalrpackages.py'])],
     entry_points='''
         [console_scripts]
         planemo=planemo.cli:planemo

tool_factory_2/LICENSE

@@ -0,0 +1,16 @@
+toolfactory_2
+=============
+
+This is an upgrade to the tool factory but with added parameters 
+(optionally editable in the generated tool form - otherwise fixed) and 
+multiple input files.
+
+Any number of  parameters up to the limit of your patience with repeat groups
+These are optionally editable by the user - names cannot be changed so 
+no overwriting $JAVA_HOME_DIR or else permanently fixed and not editable at run time.
+
+Any number of input files can be passed to your script, but of course it
+has to deal with them. Both path and metadata name are supplied either in the environment 
+(bash/sh) or as command line parameters (python,perl,rscript) that need to be parsed and
+dealt with in the script.
+