/usr/lib/python3/dist-packages/bioblend/toolshed/tools/__init__.py is in python3-bioblend 0.7.0-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 | """
Interaction with a Tool Shed instance tools
"""
from bioblend.galaxy.client import Client
class ToolShedClient(Client):
def __init__(self, toolshed_instance):
self.module = 'tools'
super(ToolShedClient, self).__init__(toolshed_instance)
def search_tools(self, q, page=1, page_size=10):
"""
Search for tools in a Galaxy Tool Shed
:type q: str
:param q: query string for searching purposes
:type page: int
:param page: page requested
:type page_size: int
:param page_size: page size requested
:rtype: dict
:return: dictionary containing search hits as well as metadata
for the search
example:
{
u'hits':
[
{
u'matched_terms': [],
u'score': 3.0,
u'tool': {
u'description': u'convert between various FASTQ quality formats',
u'id': u'69819b84d55f521efda001e0926e7233',
u'name': u'FASTQ Groomer',
u'repo_name': None,
u'repo_owner_username': u'devteam'
}
},
{
u'matched_terms': [],
u'score': 3.0,
u'tool': {
u'description': u'converts a bam file to fastq files.',
u'id': u'521e282770fd94537daff87adad2551b',
u'name': u'Defuse BamFastq',
u'repo_name': None,
u'repo_owner_username': u'jjohnson'
}
}
],
u'hostname': u'https://testtoolshed.g2.bx.psu.edu/',
u'page': u'1',
u'page_size': u'2',
u'total_results': u'118'
}
"""
params = dict(q=q, page=page, page_size=page_size)
return Client._get(self, params=params)
|