Mercurial > repos > guerler > springsuite
comparison planemo/lib/python3.7/site-packages/bioblend/toolshed/__init__.py @ 0:d30785e31577 draft
"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
| author | guerler |
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| date | Fri, 31 Jul 2020 00:18:57 -0400 |
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| -1:000000000000 | 0:d30785e31577 |
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| 1 """ | |
| 2 A base representation of an instance of Tool Shed | |
| 3 """ | |
| 4 from bioblend.galaxyclient import GalaxyClient | |
| 5 from bioblend.toolshed import categories, repositories, tools | |
| 6 | |
| 7 | |
| 8 class ToolShedInstance(GalaxyClient): | |
| 9 def __init__(self, url, key=None, email=None, password=None, verify=True): | |
| 10 """ | |
| 11 A base representation of a connection to a ToolShed instance, identified | |
| 12 by the ToolShed URL and user credentials. | |
| 13 | |
| 14 After you have created a ``ToolShedInstance`` object, access various | |
| 15 modules via the class fields. For example, to work with repositories and | |
| 16 get a list of all public repositories, the following should be done:: | |
| 17 | |
| 18 from bioblend import toolshed | |
| 19 | |
| 20 ts = toolshed.ToolShedInstance(url='https://testtoolshed.g2.bx.psu.edu') | |
| 21 | |
| 22 rl = ts.repositories.get_repositories() | |
| 23 | |
| 24 tools = ts.tools.search_tools('fastq') | |
| 25 | |
| 26 :type url: str | |
| 27 :param url: A FQDN or IP for a given instance of ToolShed. For example: | |
| 28 https://testtoolshed.g2.bx.psu.edu . If a ToolShed instance | |
| 29 is served under a prefix (e.g. | |
| 30 http://127.0.0.1:8080/toolshed/), supply the entire URL | |
| 31 including the prefix (note that the prefix must end with a | |
| 32 slash). | |
| 33 | |
| 34 :type key: str | |
| 35 :param key: If required, user's API key for the given instance of ToolShed, | |
| 36 obtained from the user preferences. | |
| 37 | |
| 38 :type email: str | |
| 39 :param email: ToolShed e-mail address corresponding to the user. | |
| 40 Ignored if key is supplied directly. | |
| 41 | |
| 42 :type password: str | |
| 43 :param password: Password of ToolShed account corresponding to the above | |
| 44 e-mail address. Ignored if key is supplied directly. | |
| 45 | |
| 46 :param verify: Whether to verify the server's TLS certificate | |
| 47 :type verify: bool | |
| 48 """ | |
| 49 super().__init__(url, key, email, password, verify=verify) | |
| 50 self.categories = categories.ToolShedCategoryClient(self) | |
| 51 self.repositories = repositories.ToolShedRepositoryClient(self) | |
| 52 self.tools = tools.ToolShedToolClient(self) |