Mercurial > repos > fubar > toolfactory

comparison rgToolFactory.py @ 15:824d21b5c773 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author fubar
date Thu, 20 Mar 2014 06:09:56 -0400
parents 43ab59672f78
children 903e3748f735
comparison
equal deleted inserted replaced
14:43ab59672f78 15:824d21b5c773
88 myversion = 'V001.1 March 2014' 88 myversion = 'V001.1 March 2014'
89 verbose = False 89 verbose = False
90 debug = False 90 debug = False
91 toolFactoryURL = 'https://bitbucket.org/fubar/galaxytoolfactory' 91 toolFactoryURL = 'https://bitbucket.org/fubar/galaxytoolfactory'
92 92
93 # if we do html we need these dependencies 93 # if we do html we need these dependencies specified in a tool_dependencies.xml file and referred to in the generated
94 # tool xml
94 toolhtmldepskel = """<?xml version="1.0"?> 95 toolhtmldepskel = """<?xml version="1.0"?>
95 <tool_dependency> 96 <tool_dependency>
96 <package name="ghostscript" version="9.10"> 97 <package name="ghostscript" version="9.10">
97 <repository name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu/" /> 98 <repository name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu/" />
98 </package> 99 </package>
102 <readme> 103 <readme>
103 %s 104 %s
104 </readme> 105 </readme>
105 </tool_dependency> 106 </tool_dependency>
106 """ 107 """
108
109 protorequirements = """<requirements>
110 <requirement type="package" version="9.10">ghostscript</requirement>
111 <requirement type="package" version="1.3.18">graphicsmagick</requirement>
112 </requirements>"""
107 113
108 def timenow(): 114 def timenow():
109 """return current time as a string 115 """return current time as a string
110 """ 116 """
111 return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time())) 117 return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
231 </tool> 237 </tool>
232 238
233 """ 239 """
234 newXML="""<tool id="%(toolid)s" name="%(toolname)s" version="%(tool_version)s"> 240 newXML="""<tool id="%(toolid)s" name="%(toolname)s" version="%(tool_version)s">
235 %(tooldesc)s 241 %(tooldesc)s
242 %(requirements)s
236 %(command)s 243 %(command)s
237 <inputs> 244 <inputs>
238 %(inputs)s 245 %(inputs)s
239 </inputs> 246 </inputs>
240 <outputs> 247 <outputs>
273 <param name="runMe" value="$runMe"/> 280 <param name="runMe" value="$runMe"/>
274 <output name="tab_file" file="%(test1Output)s" ftype="tabular" /> 281 <output name="tab_file" file="%(test1Output)s" ftype="tabular" />
275 <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="10"/> 282 <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="10"/>
276 </test></tests>""" 283 </test></tests>"""
277 xdict = {} 284 xdict = {}
285 xdict['requirements'] = ''
286 if self.opts.make_HTML:
287 xdict['requirements'] = protorequirements
278 xdict['tool_version'] = self.opts.tool_version 288 xdict['tool_version'] = self.opts.tool_version
279 xdict['test1Input'] = self.test1Input 289 xdict['test1Input'] = self.test1Input
280 xdict['test1HTML'] = self.test1HTML 290 xdict['test1HTML'] = self.test1HTML
281 xdict['test1Output'] = self.test1Output 291 xdict['test1Output'] = self.test1Output
282 if self.opts.make_HTML and self.opts.output_tab <> 'None': 292 if self.opts.make_HTML and self.opts.output_tab <> 'None':