GitLocker: The Coding Marketplace

Description:

argparse2tool 0.4.9

This project aims to provide a drop-in replacement for argparse which allows
generating Galaxy XML and CWL Tools.
It is quite literally a drop-in replacement. You (or the upstream tool
author) can use argparse completely as normal
import argparse
When this package is installed and PYTHONPATH=$(argparse2tool) is set the
dropin replacement of argparse is used ahead of the
system argparse, argparse2tool will capture all argparse function
calls, and process them specially.
This information captured in this process is used to produce Galaxy
Tool XML when it’s requested
with the --generate_galaxy_xml flag, or CWL
Tools when
requested with the --generate_cwl_tool flag.
For our example python script you can see
the generated Galaxy XML and CWL
Tools.

Running
To generate XML or CWL, run your tool with the appropriate command line
flag
$ PYTHONPATH=$(argparse2tool) <tool command> --generate_galaxy_xml <other options> > tool.xml
$ PYTHONPATH=$(argparse2tool) <tool command> --generate_cwl_tool <other options> > tool.cwl
The project includes a sample example.py file which uses as many
argparse features as possible. CWL and Galaxy XML support different
portions feature sets which will be visible in the generated outputs.
$ PYTHONPATH=$(argparse2tool) python example.py --generate_galaxy_xml
$ PYTHONPATH=$(argparse2tool) python example.py --generate_cwl_tool

CWL Specific Functionality
Example for CNVkit toolkit
$ cnvkit.py batch --generate_cwl_tool -d ~/cnvkit-tools/ --generate_outputs
If there are subcommands in the provided command, all possible tools
will be generated, for instance, for CNVkit
$ cnvkit.py --generate_cwl_tool
will produce CWL tool descriptions for cnvkit.py batch,
cnvkit.py access, cnvkit.py export bed, cnvkit.py export cdt
and all other subcommands.
Other options (which work only with --generate_cwl_tool provided,
except for help message) are:

-o FILENAME, --output_section FILENAME: File with manually
filled output section which is put to a formed CWL tool.
argparse2tool is not very good at generating outputs, it
recognizes output files only if they have type
argparse.FileType('w'), so output section is often blank and
should be filled manually.
-go, --generate_outputs: flag for generating outputs not only
from arguments that are instances of argparse.FileType('w'), but
also from every argument which contains output keyword in its
name. For instance, argument --output-file with no type will also
be placed to output section. However, ‘–output-directory’ argument
will also be treated like File, so generated tools must be checked
carefully if when this option is selected.
-b, basecommand: command which appears in basecommand
field in a resulting tool. It is handy to use this option when you
run tool with shebang, but want python to be in basecommand
field and the file amidst arguments. Example:
$ .search.py --generate_cwl_tool -b python.

Basecommand of the formed tool will be ['python'], and search
will be a positional argument on position 0.

-d, --directory: directory for storing tool descriptions.
--help_arg2cwl: prints this help message.

How it works
Internally, argparse2tool, masquerading as argparse attempts to
find and import the real argparse. It then stores a reference to the
code module for the system argparse, and presents the user with all of
the functions that stdlib’s argparse provides. Every function call is
passed through the system argparse. However, argparse2tool captures the
details of those calls and when Tool XML or CWL is requested, it builds
up the tool definition and prints it out to standard output.

Examples
You can see the example.py file for an example with numerous types
of arguments and options that you might see in real tools. Accordingly
there is an example.xml file with the output.

It doesn’t work!!
If you are not able to use the
--generate_galaxy_xml/--generate_cwl_tool flags after
installing, it is probably because of module load order.
argparse2tool must precede argparse in the path.
To easily correct this, run the tool argparse2tool which
is installed as part of this package. Correctly functioning paths will
produce the following:
$ argparse2tool
PATH_TO_THE_DROPINS
while incorrectly ordered paths will produce a helpful error message:
$ argparse2tool
no dropins dir...
This is intended to be used inline:
user@host:$ PYTHONPATH=$(argparse2tool) python my_script.py --generate_galaxy_xml

Limitations
This code doesn’t cover the entirety of the argparse API yet, and
there are some bugs to work out on the XML generation side:

argparse

groups not supported (in galaxy, everything should still work in
argparse)
some features like templating of the version string (please submit
bugs)

galaxyxml

bugs in conditionals/whens (probably)

argparse2tool Galaxy XML Output

support declaring output files in an argparse-esque manner

argparse2tool CWL Output

Some of argparse features can not be ported to CWL.

nargs=N. Number of arguments can not be specified in CWL
(yet).
const argument of add_argument(). All constants must be
specified in job files.
Custom types and custom actions are not supported.
Argument groups don’t work in CWL as arguments are sorted with
a special
algorithm
Mutual exclusion is not supported.

License
Apache License, v2