comparison rgToolFactory.py @ 41:8d28e32c71ff draft

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40:8603867451d8

# copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
# 
# all rights reserved
# Licensed under the LGPL
# suggestions for improvement and bug fixes welcome at https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
#
# march 2014
# had to remove dependencies because cross toolshed dependencies are not possible - can't pre-specify a toolshed url for graphicsmagick and ghostscript
# grrrrr - night before a demo
# added dependencies to a tool_dependencies.xml if html page generated so generated tool is properly portable

            a(self.sfile)
        else:
            a('-') # stdin
        a(opts.input_tab)
        a(opts.output_tab)
        self.outFormats = 'tabular' # TODO make this an option at tool generation time
        self.inputFormats = 'tabular,txt' # TODO make this an option at tool generation time
        self.test1Input = '%s_test1_input.xls' % self.toolname
        self.test1Output = '%s_test1_output.xls' % self.toolname
        self.test1HTML = '%s_test1_output.html' % self.toolname

    def makeXML(self):

            --tool_name "%(toolname)s" %(command_inputs)s %(command_outputs)s """
        # may NOT be an input or htmlout - appended later
        tooltestsTabOnly = """
        <tests>
        <test>
        <param name="input1" value="%(test1Input)s" ftype="tabular"/>
        <param name="job_name" value="test1"/>
        <param name="runMe" value="$runMe"/>
        <output name="tab_file" file="%(test1Output)s" ftype="tabular"/>
        </test>
        </tests>
        """
        tooltestsHTMLOnly = """
        <tests>
        <test>
        <param name="input1" value="%(test1Input)s" ftype="tabular"/>
        <param name="job_name" value="test1"/>
        <param name="runMe" value="$runMe"/>
        <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="5"/>
        </test>
        </tests>
        """
        tooltestsBoth = """<tests>
        <test>
        <param name="input1" value="%(test1Input)s" ftype="tabular"/>
        <param name="job_name" value="test1"/>
        <param name="runMe" value="$runMe"/>
        <output name="tab_file" file="%(test1Output)s" ftype="tabular" />
        <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="10"/>
        </test>
        </tests>
        """
        xdict = {}
        xdict['requirements'] = ''
        if self.opts.make_HTML:
            if self.opts.include_dependencies == "yes":
                xdict['requirements'] = protorequirements
        xdict['tool_version'] = self.opts.tool_version

            xdict['outputs'] +=  ' <data format="html" name="html_file" label="${job_name}.html"/>\n'
        else:
            xdict['command_outputs'] += ' --output_dir "./"' 
        if self.opts.output_tab <> 'None':
            xdict['command_outputs'] += ' --output_tab "$tab_file"'
            xdict['outputs'] += ' <data format="%s" name="tab_file" label="${job_name}"/>\n' % self.outFormats
        xdict['command'] = newCommand % xdict
        xmls = newXML % xdict
        xf = open(self.xmlfile,'w')
        xf.write(xmls)
        xf.write('\n')

    a('--tool_name',default=None)
    a('--interpreter',default=None)
    a('--output_dir',default='./')
    a('--output_html',default=None)
    a('--input_tab',default="None")
    a('--output_tab',default="None")
    a('--user_email',default='Unknown')
    a('--bad_user',default=None)
    a('--make_Tool',default=None)
    a('--make_HTML',default=None)
    a('--help_text',default=None)

41:8d28e32c71ff

# copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
# 
# all rights reserved
# Licensed under the LGPL
# suggestions for improvement and bug fixes welcome at https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
#
# August 2014 
# merged John Chilton's citation addition and ideas from Marius van den Beek to enable arbitrary
# data types for input and output - thanks!
#
# march 2014
# had to remove dependencies because cross toolshed dependencies are not possible - can't pre-specify a toolshed url for graphicsmagick and ghostscript
# grrrrr - night before a demo
# added dependencies to a tool_dependencies.xml if html page generated so generated tool is properly portable

            a(self.sfile)
        else:
            a('-') # stdin
        a(opts.input_tab)
        a(opts.output_tab)
        self.outputFormat = self.opts.output_format
        self.inputFormats = self.opts.input_formats 
        self.test1Input = '%s_test1_input.xls' % self.toolname
        self.test1Output = '%s_test1_output.xls' % self.toolname
        self.test1HTML = '%s_test1_output.html' % self.toolname

    def makeXML(self):

            --tool_name "%(toolname)s" %(command_inputs)s %(command_outputs)s """
        # may NOT be an input or htmlout - appended later
        tooltestsTabOnly = """
        <tests>
        <test>
        <param name="input1" value="%(test1Input)s" ftype="%(inputFormats)s"/>
        <param name="job_name" value="test1"/>
        <param name="runMe" value="$runMe"/>
        <output name="tab_file" file="%(test1Output)s" ftype="%(outputFormat)s"/>
        </test>
        </tests>
        """
        tooltestsHTMLOnly = """
        <tests>
        <test>
        <param name="input1" value="%(test1Input)s" ftype="%(inputFormats)s"/>
        <param name="job_name" value="test1"/>
        <param name="runMe" value="$runMe"/>
        <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="5"/>
        </test>
        </tests>
        """
        tooltestsBoth = """<tests>
        <test>
        <param name="input1" value="%(test1Input)s" ftype="%(inputFormats)s"/>
        <param name="job_name" value="test1"/>
        <param name="runMe" value="$runMe"/>
        <output name="tab_file" file="%(test1Output)s" ftype="%(outputFormat)s" />
        <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="10"/>
        </test>
        </tests>
        """
        xdict = {}
        xdict['outputFormat'] = self.outputFormat
        xdict['inputFormats'] = self.inputFormats
        xdict['requirements'] = ''
        if self.opts.make_HTML:
            if self.opts.include_dependencies == "yes":
                xdict['requirements'] = protorequirements
        xdict['tool_version'] = self.opts.tool_version

            xdict['outputs'] +=  ' <data format="html" name="html_file" label="${job_name}.html"/>\n'
        else:
            xdict['command_outputs'] += ' --output_dir "./"' 
        if self.opts.output_tab <> 'None':
            xdict['command_outputs'] += ' --output_tab "$tab_file"'
            xdict['outputs'] += ' <data format="%s" name="tab_file" label="${job_name}"/>\n' % self.outputFormat
        xdict['command'] = newCommand % xdict
        xmls = newXML % xdict
        xf = open(self.xmlfile,'w')
        xf.write(xmls)
        xf.write('\n')

    a('--tool_name',default=None)
    a('--interpreter',default=None)
    a('--output_dir',default='./')
    a('--output_html',default=None)
    a('--input_tab',default="None")
    a('--input_formats',default="tabular,text")
    a('--output_tab',default="None")
    a('--output_format',default="tabular")
    a('--user_email',default='Unknown')
    a('--bad_user',default=None)
    a('--make_Tool',default=None)
    a('--make_HTML',default=None)
    a('--help_text',default=None)