comparison rgToolFactory.py @ 13:7725e4ab27e1

Adding tests - problem to find the script - needs a fixed string somewhere. Updated readme

12:d12728e33c3d

    def makeXML(self):
        """
        Create a Galaxy xml tool wrapper for the new script as a string to write out
        fixme - use templating or something less fugly than this
        """    
        newXML="""<tool id="%(toolid)s" name="%(toolname)s" version="0.01">
            %(tooldesc)s
            %(command)s
            <inputs>

            <configfiles>
            <configfile name="runMe">
            %(script)s
            </configfile>
            </configfiles>
            </tool>""" # needs a dict with toolname, toolid, interpreter, scriptname, command, inputs as a multi line string ready to write, outputs ditto, help ditto
               
        newCommand="""<command interpreter="python">
            %(toolname)s.py --script_path "$runMe" --interpreter "%(interpreter)s" 
            --tool_name "%(toolname)s" %(command_inputs)s %(command_outputs)s 
            </command>""" # may NOT be an input or htmlout
            
        xdict = {}
        xdict['script'] = self.script # configfile is least painful way to embed script to avoid external dependencies
        if self.opts.help_text:
            xdict['help'] = open(self.opts.help_text,'r').read()
        else:

13:7725e4ab27e1

    def makeXML(self):
        """
        Create a Galaxy xml tool wrapper for the new script as a string to write out
        fixme - use templating or something less fugly than this.
        Here's an example of what we produce

        <tool id="reverse" name="reverse" version="0.01">
            <description>a tabular file</description>
            <command interpreter="python">
            reverse.py --script_path "$runMe" --interpreter "python" 
            --tool_name "reverse" --input_tab "$input1" --output_tab "$tab_file" 
            </command>
            <inputs>
            <param name="input1"  type="data" format="tabular" label="Select a suitable input file from your history"/><param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="reverse"/>

            </inputs>
            <outputs>
            <data format="tabular" name="tab_file" label="${job_name}"/>

            </outputs>
            <help>
            
**What it Does**

Reverse the columns in a tabular file

            </help>
            <configfiles>
            <configfile name="runMe">
            
# reverse order of columns in a tabular file
import sys
inp = sys.argv[1]
outp = sys.argv[2]
i = open(inp,'r')
o = open(outp,'w')
for row in i:
     rs = row.rstrip().split('\t')
     rs.reverse()
     o.write('\t'.join(rs))
     o.write('\n')
i.close()
o.close()
 

            </configfile>
            </configfiles>
            </tool>
        
        """    
        newXML="""<tool id="%(toolid)s" name="%(toolname)s" version="0.01">
            %(tooldesc)s
            %(command)s
            <inputs>

            <configfiles>
            <configfile name="runMe">
            %(script)s
            </configfile>
            </configfiles>
            %(tooltests)s
            </tool>""" # needs a dict with toolname, toolid, interpreter, scriptname, command, inputs as a multi line string ready to write, outputs ditto, help ditto
               
        newCommand="""<command interpreter="python">
            %(toolname)s.py --script_path "$runMe" --interpreter "%(interpreter)s" 
            --tool_name "%(toolname)s" %(command_inputs)s %(command_outputs)s 
            </command>""" # may NOT be an input or htmlout
        tooltests = """<tests><test>
        <param name="input1" value="%s" ftype="%s"/>
        <param name="job_name" value="test1"/>
        <param name="runMe" value="$runMe"/>
        </test><tests>"""
        xdict = {}
        xdict['script'] = self.script # configfile is least painful way to embed script to avoid external dependencies
        if self.opts.help_text:
            xdict['help'] = open(self.opts.help_text,'r').read()
        else: