Mercurial > repos > fubar > tool_factory_2
comparison rgToolFactory2.py @ 3:d75fd880fce2 draft
Uploaded
author | fubar |
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date | Sun, 11 Jan 2015 22:01:27 -0500 |
parents | 6a3c292412fa |
children | b85a3b92e9f7 |
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2:6a3c292412fa | 3:d75fd880fce2 |
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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) |