comparison rgToolFactory2.py @ 3:d75fd880fce2 draft

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author fubar
date Sun, 11 Jan 2015 22:01:27 -0500
parents 6a3c292412fa
children b85a3b92e9f7
comparison
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2:6a3c292412fa 3:d75fd880fce2
309 309
310 <tool id="reverse" name="reverse" version="0.01"> 310 <tool id="reverse" name="reverse" version="0.01">
311 <description>a tabular file</description> 311 <description>a tabular file</description>
312 <command interpreter="python"> 312 <command interpreter="python">
313 reverse.py --script_path "$runMe" --interpreter "python" 313 reverse.py --script_path "$runMe" --interpreter "python"
314 --tool_name "reverse" --input_tab "$input1" --output_tab "$tab_file" 314 --tool_name "reverse" --input_tab "$input1" --output_tab "$output1"
315 </command> 315 </command>
316 <inputs> 316 <inputs>
317 <param name="input1" type="data" format="tabular" label="Select one or more input files from your history"/> 317 <param name="input1" type="data" format="tabular" label="Select one or more input files from your history"/>
318 <param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="reverse"/> 318 <param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="reverse"/>
319 </inputs> 319 </inputs>
320 <outputs> 320 <outputs>
321 <data format="tabular" name="tab_file" label="${job_name}"/> 321 <data format="tabular" name="output1q" label="${job_name}"/>
322 322
323 </outputs> 323 </outputs>
324 <help> 324 <help>
325 325
326 **What it Does** 326 **What it Does**
495 xdict['command_outputs'] += ' --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"' 495 xdict['command_outputs'] += ' --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"'
496 xdict['outputs'] += ' <data format="html" name="html_file" label="${job_name}.html"/>\n' 496 xdict['outputs'] += ' <data format="html" name="html_file" label="${job_name}.html"/>\n'
497 else: 497 else:
498 xdict['command_outputs'] += ' --output_dir "./"' 498 xdict['command_outputs'] += ' --output_dir "./"'
499 if self.opts.output_tab: 499 if self.opts.output_tab:
500 xdict['command_outputs'] += ' --output_tab "$tab_file"' 500 xdict['command_outputs'] += ' --output_tab "$output1"'
501 xdict['outputs'] += ' <data format="%s" name="output1" label="${job_name}"/>\n' % self.outFormats 501 xdict['outputs'] += ' <data format="%s" name="output1" label="${job_name}"/>\n' % self.outFormats
502 xdict['command'] = newCommand % xdict 502 xdict['command'] = newCommand % xdict
503 if self.opts.citations: 503 if self.opts.citations:
504 citationstext = open(self.opts.citations,'r').read() 504 citationstext = open(self.opts.citations,'r').read()
505 citation_tuples = parse_citations(citationstext) 505 citation_tuples = parse_citations(citationstext)