Merge pull request #1263 from Kulivox/auto-tool-gen

Implement automatic tool generation based on the source code of the tool

docs/_writing_argparse.rst

@@ -0,0 +1,30 @@
+Creating Galaxy tools from python scripts using argparse
+========================================================
+
+If a python script should be wrapped that creates its command line interface
+using the argparse library, then planemo can generate a good starting point.
+
+All you need to do is to pass the path to the python source file containing
+the argparse definition. Lets use ``tests/data/autopygen/autopygen_end_to_end_sub.py``
+from the planemo tests as an example:
+
+::
+
+    $ planemo tool_init -i e2e -n e2e
+                        --autopygen tests/data/autopygen/autopygen_end_to_end_sub.py
+                        -- tool tool.xml
+
+Here we only provided the ``id`` and ``name`` in addition to the python sources
+and planemo creates a pretty tool xml files that can serve as a good starting point
+to create a functional Galaxy tool in ``tool.xml``.
+Additional information, e.g. requirements, help, etc, can and should be given with
+additional parameters to planemo.
+
+There are a few points that need to be edited in any case.  Most importantly
+since in most cases ``argparse`` does not distinguish between input and output
+files all file parameters will be rendered as input parameters of the tool.
+
+Please open an issue if you have ideas on how to improve the generated tools:
+https://github.com/galaxyproject/planemo/issues
+
+

docs/commands/tool_init.rst

@@ -51,5 +51,9 @@ Generate tool outline from given arguments.
                                 'seqtk@1.68').
       --container TEXT          Add a Docker image identifier for this tool.
       --cwl                     Build a CWL tool instead of a Galaxy tool.
+      --autopygen TEXT          Option for automatic generation of tool file, from
+                                python source code that uses argparse. Parameter is
+                                a path to source file containing definition of the
+                                parser
       --help                    Show this message and exit.
     

docs/writing_standalone.rst

@@ -12,6 +12,7 @@ if you have not already installed it.
 .. include:: _writing_parameters.rst
 .. include:: _writing_scripts.rst
 .. include:: _writing_suites.rst
+.. include:: _writing_argparse.rst
 .. include:: _writing_conclusion.rst
 
 .. _Galaxy: http://galaxyproject.org/
@@ -21,3 +22,4 @@ if you have not already installed it.
 .. _linuxbrew: https://github.com/Homebrew/linuxbrew
 .. _Vagrant: https://www.vagrantup.com/
 .. _Planemo: http://planemo.readthedocs.org/
+