ft_master/proto_v10_import#72

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sveinugu wants to merge 128 commits intohb_masterfrom

ft_master/proto_v10_import

Commits on Oct 23, 2017

Merge remote-tracking branch 'origin/proto_dev' into proto_master
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Commits on Jan 5, 2018

Commits on Jan 6, 2018

Commits on Jan 7, 2018

ProTo: removed logging
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ProTo: Unfinished update of core dev tools. Added directory listing and the possibility for explicit creation of new dirs. Some cleanup
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ProTo: Finished support for package selection via subdirectories in GenerateToolsTool. Added validation and some polishing. Renaming of some variables. Updated config paths.
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ProTo: Updated help text. Improved directory naming validation. Increased maximum number of directory levels.
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ProTo: Removed tool type selection box. Cleanup
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ProTo: small refactorings needed for HB subclassing
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ProTo: Made tool root configurable
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ProTo: refactored to allow HyperBrowser subclassing. Improved input validation. Now does not show hidden XML sections in options box. Removed unused config constant. Cleanup
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ProTo: Refactored ProtoToolRegister in order to handle equal classnames for classes in different modules correctly. Some cleanup and small fixes
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ProTo: Full refactor of ProtoToolRegister. Added tool for hiding modules in ExploreToolsTool. Added support for automatic hiding of non-tool classes in the webtool module in order to speed up Explo…
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ProTo: Added tool to debug exceptions in import of ProTo tools.
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ProTo: Added and edited tool descriptions
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ProTo: Reverted import in ToolTemplate. Relative import path to support HB subclassing
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ProTo: Fixed imports
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Now also excludes HB tool templates
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ProTo: except_classes -> installed_classes. Fixed logic for filling out nontool hidden modules.
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ProTo: rename tools
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Added initial "hidden nontool modules" config file
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ProTo: Removed GPL Copyright messages from code files
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Fixed bug in loading old HB analysis tool
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ProTo: Added standard excluded 'files' directory to gitignore
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ProTo: now does not print names instead of label='' in various box types.
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ProTo: Now sorts directory structure lists
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ProTo: Fixed rpy2 version dependency
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ProTo: Added html_title config. Pull request?
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Removed HyperBrowser-specific modules
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Added and reformatted license information for The Genomic HyperBrowser, Galaxy ProTo, and the Galaxy project.
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Removed HyperBrowser licenses and license info
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Moved FileImport hidden tool to ProTo
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Added new tools to tool_conf.xml sample files.
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Changed linebreaks to LF
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Commits on Jan 14, 2018

Commits on Jan 18, 2018

Commits on Jan 19, 2018

Commits on Jan 20, 2018

Added hidden element
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Commits on Jan 26, 2018

Commits on Jan 30, 2018

Commits on May 24, 2018