Galaxy integration

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https://wiki.galaxyproject.org/Admin/Tools/AddToolTutorial
https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax

https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#Number_of_Output_datasets_cannot_be_determined_until_tool_run
https://web.science.mq.edu.au/~cassidy/2015/10/21/galaxy-tool-generating-datasets/

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Basic tool definition added in 5982c69.

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Still need error handling.

https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Cstdio.3E.2C_.3Cregex.3E.2C_and_.3Cexit_code.3E_tag_sets

How to pass log info about which alternate data source was used to Galaxy interface?

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Job output is visible to Galaxy administrators from Admin > Server > Manage Jobs

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Output is also visible to submitting user from View Details on an output dataset. The details page has links to the job's stdout and stderr.

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If a tool does not have any valid or <exit_code> tags, then Galaxy will use the previous technique for finding errors - any text on stderr indicates an error, and neither stdout nor the tool's exit code will be checked.

https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Cstdio.3E.2C_.3Cregex.3E.2C_and_.3Cexit_code.3E_tag_sets

Because logs are printed to stderr, this means the Galaxy tool will always report an error until these configuration elements are added.

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Basic exit code configuration added in f9db57d.

Use regex tag to warn user if files could not be verified?