def getToolDescription():
from proto.HtmlCore import HtmlCore
core = HtmlCore()
core.smallHeader("General description")
core.paragraph("This tool is used to try out ProTo tools that have "
"not been installed as separate tools in the tool "
"menu. This is typically used for development "
"purposes, so that one can polish the tool until it "
"is finished for deployment in the tool menu. "
"When a tool is installed into the menu, the tool "
"disappears from the tool list in this tool."
"The logic for inclusion in the list is that there "
"exists a Python module with a class that inherits "
"from GeneralGuiTool, without there existing "
"a Galaxy xml file for the tool.")
core.paragraph(
"Note: when the list of tools is generated, modules "
"under the tool directory that does not contain "
"ProTo tool classes are stored and excluded from "
"subsequent runs. This is done to improve loading "
"times. The hidden tool modules are stored in the "
'"%s" ' % os.path.basename(HIDDEN_NONTOOL_MODULES_CONFIG_FN) +
'file in the "config" folder. This file can be manually edited if needed.'
)
return str(core)
def getToolDescription(cls):
from proto.HtmlCore import HtmlCore
core = HtmlCore()
core.smallHeader("General description")
core.paragraph(
"This tool is used to install ProTo tools into the tool menu. "
"The installation process creates a Galaxy tool XML file and "
"adds the tool to the tool menu (in the 'tool_conf.xml' file). "
"After execution, the XML file has been generated and added "
"to the tool configuration file, but Galaxy needs to reload "
"the tool menu for it to become visible. This is done by a "
"Galaxy administrator, either from the Admin menu, or from a "
"link in the output history element from this tool.")
core.paragraph("Note that the after this tool has been executed "
"but before a Galaxy administrator has reloaded the "
"tool menu, the tool is not available from neither "
"of the 'ProTo tool explorer' tool or from the "
"Galaxy menu.")
core.divider()
core.smallHeader("Parameters")
core.descriptionLine("Select tool", "The tool to install.",
emphasize=True)
core.descriptionLine("Tool ID",
"The Galaxy tool id for the new tool to be "
"created. This is the 'id' argument to the "
"<tool> tag in the tool XML file.",
emphasize=True)
core.descriptionLine("Tool name",
"The name of the tool as it will appear in the "
"tool menu. The tool name will appear as a HTML "
"link.", emphasize=True)
core.descriptionLine("Tool description",
"The description of the tool as it will appear "
"in the tool menu. The tool description will "
"appear directly after the tool name as "
"normal text.", emphasize=True)
core.descriptionLine("Tool XML file",
"The path (relative to '%s') and name " %
os.path.sep.join([''] + cls._getProtoRelToolDirs(fromBase=True)) +
"of the Galaxy tool XML file to be created. "
"The tool file can be named anything and be "
"placed anywhere (as the 'tool_conf.xml' file "
"contains the path to the tool XML file). "
"However, we encourage the practice of placing "
"the Galaxy tool XML file together with the "
"Python module, in the same directory and "
"with the same name as tool module (with e.g. "
"'ABCTool.xml' instead of 'AbcTool.py').",
emphasize=True)
core.descriptionLine("Select section in tool_conf.xml file",
"The section in the tool_conf.xml file where"
"the tool should be placed in the menu. "
"This corresponds to the first level in the"
"tool hierarchy.", emphasize=True)
return str(core)
def getToolDescription():
core = HtmlCore()
core.smallHeader("General description")
core.paragraph("This tool is used to dynamically generate a Python "
"module defining a new ProTo tool. After tool "
"execution, The tool will be available from the "
"'ProTo tool explorer' tool for development purposes.")
core.divider()
core.smallHeader("Parameters")
core.descriptionLine(
"Choose directory for new tool",
"Hierarchical selection of directory in which to "
"place the new tool. The directory structure defines "
"the Python package which is used if one needs to import "
"the tool. The package name is automatically shown in an info "
"box according to the selections. It is also possible "
"to create new directories. Note that the creation of "
"new directories happens at execution of this tool. ",
emphasize=True)
core.descriptionLine("Module/class name",
"The name of the Python module (filename) and "
"class for the new tool. For historical reasons, "
"ProTo uses 'MixedCase' naming for both the "
"module and the class. By convention, it is "
"advised (but not required) to end the name "
"with 'Tool', e.g. 'MyNewTool'. This will create "
"a Python module 'MyNewTool.py' with the class "
"'MyNewTool', inheriting from "
"'proto.GeneralGuiTool'.",
emphasize=True)
core.descriptionLine("Tool name",
"A string with the name or title of the tool. "
"This will appear on the top of the tool GUI "
"as well as being the default value for the "
"tool name in the menu (which can be changed "
"when installing).",
emphasize=True)
core.descriptionLine("Use template with inline documentation",
"The new Python module is based upon a template"
"file containing a simple example tool with "
"two option boxes (one selection box and one "
"text box). There are two such template files, "
"one that contains inline documentation of the "
"methods and possible choices, and one without "
"the documentation. Advanced users could select "
"the latter to make the tool code itself shorter "
"and more readable.",
emphasize=True)
return str(core)
def getToolDescription(cls):
from proto.HtmlCore import HtmlCore
core = HtmlCore()
core.smallHeader("General description")
core.paragraph(
"This tool is used for debugging when an uninstalled tool does not appear "
'in the "Explore ProTo tools" tool. This is typically due to an Python '
"exception being raised at the import the tool module. This tool "
"lists all modules under the tool directory that cannot be imported "
"due to an exception. When selecting the tool, a traceback of the "
'exception is shown. One can also click "Execute" to store the exception '
"within a history element (which will then become red). This is "
"useful if one wants to send a bug report for the exception, or if one "
"wants to keep a backlog of the error messages.")
return str(core)
def getToolDescription(cls):
from proto.HtmlCore import HtmlCore
core = HtmlCore()
core.smallHeader("General description")
core.paragraph(
"This tool is used to hide modules containing ProTo tools from "
'the "Explore ProTo tools" tool. This is both useful in order to '
"to reduce the list, and also to reduce the loading times of the "
"explore tool.")
core.paragraph(
"Hidden tool modules are stored in the "
'"%s" ' % os.path.basename(HIDDEN_MODULES_CONFIG_FN) +
'file in the "config" folder. This file can be manually edited if needed.'
)
return str(core)