Main program and default plugin parameters

usage: Command parser [-h] –path PATH –tool-name TOOL_NAME [–verbose] [–debug] [–plugins-path PLUGINS_PATH] [–dont-redirect-output] [–galaxy-profile GALAXY_PROFILE] –descr DESCR –requirements REQUIREMENTS

–tool-version TOOL_VERSION [–inputs INPUTS]

options:

-h, --help

show this help message and exit

Default program parameters:

--path PATH

Path to the source file

--tool-name TOOL_NAME

Name of the package for which you are creating the tool definition file

Logging arguments:

--verbose

Prints out info logs

--debug

Print out debug text

Plugin discovery:

--plugins-path PLUGINS_PATH

Path to directory containing plugins you want to use

Default plugin:

--dont-redirect-output

If this argument is present, tool will not redirect its output to output files during execution in galaxy

--galaxy-profile GALAXY_PROFILE

Version of galaxy profile

--descr DESCR

Description of the tool

--requirements REQUIREMENTS

Comma separated list of package:version pairs

--tool-version TOOL_VERSION

Version of the tool

--inputs INPUTS

Comma separated list of names and format types of program arguments that define inputs. (name:format,name:format) For example, if your program accepts path to vcf file in argument called input, enter ‘input:vcf’