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comparison toolfactory/test-data/input1_sample @ 1:0183cad9d13b draft

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planemo upload
author fubar
date Thu, 22 Feb 2024 10:48:01 +0000
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0:2beaae16651e 1:0183cad9d13b
1 #!/usr/bin/env python
2 # rgToolFactory.py
3 # see https://github.com/fubar2/toolfactory
4 #
5 # copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
6 #
7 # all rights reserved
8 # Licensed under the LGPL
9 # suggestions for improvement and bug fixes welcome at https://github.com/fubar2/toolfactory
10 #
11 # July 2020: BCC was fun and I feel like rip van winkle after 5 years.
12 # Decided to
13 # 1. Fix the toolfactory so it works - done for simplest case
14 # 2. Fix planemo so the toolfactory function works
15 # 3. Rewrite bits using galaxyxml functions where that makes sense - done
16 #
17 # removed all the old complications including making the new tool use this same script
18 # galaxyxml now generates the tool xml https://github.com/hexylena/galaxyxml
19 # No support for automatic HTML file creation from arbitrary outputs
20 # TODO: add option to run that code as a post execution hook
21 # TODO: add additional history input parameters - currently only one
22
23
24 import argparse
25 import logging
26 import os
27 import re
28 import shutil
29 import subprocess
30 import sys
31 import tarfile
32 import tempfile
33 import time
34
35 import galaxyxml.tool as gxt
36 import galaxyxml.tool.parameters as gxtp
37
38 import lxml
39
40 myversion = "V2.1 July 2020"
41 verbose = True
42 debug = True
43 toolFactoryURL = "https://github.com/fubar2/toolfactory"
44 ourdelim = "~~~"
45
46 # --input_files="$input_files~~~$CL~~~$input_formats~~~$input_label
47 # ~~~$input_help"
48 IPATHPOS = 0
49 ICLPOS = 1
50 IFMTPOS = 2
51 ILABPOS = 3
52 IHELPOS = 4
53 IOCLPOS = 5
54
55 # --output_files "$otab.history_name~~~$otab.history_format~~~$otab.CL
56 ONAMEPOS = 0
57 OFMTPOS = 1
58 OCLPOS = 2
59 OOCLPOS = 3
60
61 # --additional_parameters="$i.param_name~~~$i.param_value~~~
62 # $i.param_label~~~$i.param_help~~~$i.param_type~~~$i.CL~~~i$.param_CLoverride"
63 ANAMEPOS = 0
64 AVALPOS = 1
65 ALABPOS = 2
66 AHELPPOS = 3
67 ATYPEPOS = 4
68 ACLPOS = 5
69 AOVERPOS = 6
70 AOCLPOS = 7
71
72
73 foo = len(lxml.__version__)
74 # fug you, flake8. Say my name!
75
76 def timenow():
77 """return current time as a string
78 """
79 return time.strftime("%d/%m/%Y %H:%M:%S", time.localtime(time.time()))
80
81
82 def quote_non_numeric(s):
83 """return a prequoted string for non-numerics
84 useful for perl and Rscript parameter passing?
85 """
86 try:
87 _ = float(s)
88 return s
89 except ValueError:
90 return '"%s"' % s
91
92
93 html_escape_table = {"&": "&amp;", ">": "&gt;", "<": "&lt;", "$": r"\$"}
94
95
96 def html_escape(text):
97 """Produce entities within text."""
98 return "".join(html_escape_table.get(c, c) for c in text)
99
100
101 def html_unescape(text):
102 """Revert entities within text. Multiple character targets so use replace"""
103 t = text.replace("&amp;", "&")
104 t = t.replace("&gt;", ">")
105 t = t.replace("&lt;", "<")
106 t = t.replace("\\$", "$")
107 return t
108
109
110 def parse_citations(citations_text):
111 """
112 """
113 citations = [c for c in citations_text.split("**ENTRY**") if c.strip()]
114 citation_tuples = []
115 for citation in citations:
116 if citation.startswith("doi"):
117 citation_tuples.append(("doi", citation[len("doi") :].strip()))
118 else:
119 citation_tuples.append(
120 ("bibtex", citation[len("bibtex") :].strip())
121 )
122 return citation_tuples
123
124
125 class ScriptRunner:
126 """Wrapper for an arbitrary script
127 uses galaxyxml
128
129 """
130
131 def __init__(self, args=None):
132 """
133 prepare command line cl for running the tool here
134 and prepare elements needed for galaxyxml tool generation
135 """
136
137 self.infiles = [x.split(ourdelim) for x in args.input_files]
138 self.outfiles = [x.split(ourdelim) for x in args.output_files]
139 self.addpar = [x.split(ourdelim) for x in args.additional_parameters]
140 self.args = args
141 self.cleanuppar()
142 self.lastclredirect = None
143 self.lastxclredirect = None
144 self.cl = []
145 self.xmlcl = []
146 self.is_positional = self.args.parampass == "positional"
147 aCL = self.cl.append
148 assert args.parampass in [
149 "0",
150 "argparse",
151 "positional",
152 ], 'Parameter passing in args.parampass must be "0","positional" or "argparse"'
153 self.tool_name = re.sub("[^a-zA-Z0-9_]+", "", args.tool_name)
154 self.tool_id = self.tool_name
155 if self.args.interpreter_name:
156 exe = "$runMe"
157 else:
158 exe = self.args.exe_package
159 assert (
160 exe is not None
161 ), "No interpeter or executable passed in - nothing to run so cannot build"
162 self.tool = gxt.Tool(
163 self.args.tool_name,
164 self.tool_id,
165 self.args.tool_version,
166 self.args.tool_desc,
167 exe,
168 )
169 self.tinputs = gxtp.Inputs()
170 self.toutputs = gxtp.Outputs()
171 self.testparam = []
172 if (
173 self.args.runmode == "Executable" or self.args.runmode == "system"
174 ): # binary - no need
175 aCL(self.args.exe_package) # this little CL will just run
176 else:
177 self.prepScript()
178 self.elog = "%s_error_log.txt" % self.tool_name
179 self.tlog = "%s_runner_log.txt" % self.tool_name
180
181 if self.args.parampass == "0":
182 self.clsimple()
183 else:
184 clsuffix = []
185 xclsuffix = []
186 for i, p in enumerate(self.infiles):
187 if p[IOCLPOS] == "STDIN":
188 appendme = [
189 p[IOCLPOS],
190 p[ICLPOS],
191 p[IPATHPOS],
192 "< %s" % p[IPATHPOS],
193 ]
194 xappendme = [
195 p[IOCLPOS],
196 p[ICLPOS],
197 p[IPATHPOS],
198 "< $%s" % p[ICLPOS],
199 ]
200 else:
201 appendme = [p[IOCLPOS], p[ICLPOS], p[IPATHPOS], ""]
202 xappendme = [p[IOCLPOS], p[ICLPOS], "$%s" % p[ICLPOS], ""]
203 clsuffix.append(appendme)
204 xclsuffix.append(xappendme)
205 # print('##infile i=%d, appendme=%s' % (i,appendme))
206 for i, p in enumerate(self.outfiles):
207 if p[OOCLPOS] == "STDOUT":
208 self.lastclredirect = [">", p[ONAMEPOS]]
209 self.lastxclredirect = [">", "$%s" % p[OCLPOS]]
210 else:
211 clsuffix.append([p[OOCLPOS], p[OCLPOS], p[ONAMEPOS], ""])
212 xclsuffix.append(
213 [p[OOCLPOS], p[OCLPOS], "$%s" % p[ONAMEPOS], ""]
214 )
215 for p in self.addpar:
216 clsuffix.append(
217 [p[AOCLPOS], p[ACLPOS], p[AVALPOS], p[AOVERPOS]]
218 )
219 xclsuffix.append(
220 [p[AOCLPOS], p[ACLPOS], '"$%s"' % p[ANAMEPOS], p[AOVERPOS]]
221 )
222 clsuffix.sort()
223 xclsuffix.sort()
224 self.xclsuffix = xclsuffix
225 self.clsuffix = clsuffix
226 if self.args.parampass == "positional":
227 self.clpositional()
228 else:
229 self.clargparse()
230
231 def prepScript(self):
232 aCL = self.cl.append
233 rx = open(self.args.script_path, "r").readlines()
234 rx = [x.rstrip() for x in rx]
235 rxcheck = [x.strip() for x in rx if x.strip() > ""]
236 assert len(rxcheck) > 0, "Supplied script is empty. Cannot run"
237 self.script = "\n".join(rx)
238 fhandle, self.sfile = tempfile.mkstemp(
239 prefix=self.tool_name, suffix="_%s" % (self.args.interpreter_name)
240 )
241 tscript = open(self.sfile, "w")
242 tscript.write(self.script)
243 tscript.close()
244 self.indentedScript = " %s" % "\n".join(
245 [" %s" % html_escape(x) for x in rx]
246 )
247 self.escapedScript = "%s" % "\n".join(
248 [" %s" % html_escape(x) for x in rx]
249 )
250 art = "%s.%s" % (self.tool_name, self.args.interpreter_name)
251 artifact = open(art, "wb")
252 artifact.write(bytes(self.script, "utf8"))
253 artifact.close()
254 aCL(self.args.interpreter_name)
255 aCL(self.sfile)
256
257 def cleanuppar(self):
258 """ positional parameters are complicated by their numeric ordinal"""
259 for i, p in enumerate(self.infiles):
260 if self.args.parampass == "positional":
261 assert p[ICLPOS].isdigit(), (
262 "Positional parameters must be ordinal integers - got %s for %s"
263 % (p[ICLPOS], p[ILABPOS])
264 )
265 p.append(p[ICLPOS])
266 if p[ICLPOS].isdigit() or self.args.parampass == "0":
267 scl = "input%d" % (i + 1)
268 p[ICLPOS] = scl
269 self.infiles[i] = p
270 for i, p in enumerate(
271 self.outfiles
272 ): # trying to automagically gather using extensions
273 if self.args.parampass == "positional" and p[OCLPOS] != "STDOUT":
274 assert p[OCLPOS].isdigit(), (
275 "Positional parameters must be ordinal integers - got %s for %s"
276 % (p[OCLPOS], p[ONAMEPOS])
277 )
278 p.append(p[OCLPOS])
279 if p[OCLPOS].isdigit() or p[OCLPOS] == "STDOUT":
280 scl = p[ONAMEPOS]
281 p[OCLPOS] = scl
282 self.outfiles[i] = p
283 for i, p in enumerate(self.addpar):
284 if self.args.parampass == "positional":
285 assert p[ACLPOS].isdigit(), (
286 "Positional parameters must be ordinal integers - got %s for %s"
287 % (p[ACLPOS], p[ANAMEPOS])
288 )
289 p.append(p[ACLPOS])
290 if p[ACLPOS].isdigit():
291 scl = "input%s" % p[ACLPOS]
292 p[ACLPOS] = scl
293 self.addpar[i] = p
294
295 def clsimple(self):
296 """ no parameters - uses < and > for i/o
297 """
298 aCL = self.cl.append
299 aCL("<")
300 aCL(self.infiles[0][IPATHPOS])
301 aCL(">")
302 aCL(self.outfiles[0][OCLPOS])
303 aXCL = self.xmlcl.append
304 aXCL("<")
305 aXCL("$%s" % self.infiles[0][ICLPOS])
306 aXCL(">")
307 aXCL("$%s" % self.outfiles[0][ONAMEPOS])
308
309 def clpositional(self):
310 # inputs in order then params
311 aCL = self.cl.append
312 for (o_v, k, v, koverride) in self.clsuffix:
313 if " " in v:
314 aCL("%s" % v)
315 else:
316 aCL(v)
317 aXCL = self.xmlcl.append
318 for (o_v, k, v, koverride) in self.xclsuffix:
319 aXCL(v)
320 if self.lastxclredirect:
321 aXCL(self.lastxclredirect[0])
322 aXCL(self.lastxclredirect[1])
323
324 def clargparse(self):
325 """ argparse style
326 """
327 aCL = self.cl.append
328 aXCL = self.xmlcl.append
329 # inputs then params in argparse named form
330 for (o_v, k, v, koverride) in self.xclsuffix:
331 if koverride > "":
332 k = koverride
333 elif len(k.strip()) == 1:
334 k = "-%s" % k
335 else:
336 k = "--%s" % k
337 aXCL(k)
338 aXCL(v)
339 for (o_v, k, v, koverride) in self.clsuffix:
340 if koverride > "":
341 k = koverride
342 elif len(k.strip()) == 1:
343 k = "-%s" % k
344 else:
345 k = "--%s" % k
346 aCL(k)
347 aCL(v)
348
349 def getNdash(self, newname):
350 if self.is_positional:
351 ndash = 0
352 else:
353 ndash = 2
354 if len(newname) < 2:
355 ndash = 1
356 return ndash
357
358 def doXMLparam(self):
359 """flake8 made me do this..."""
360 for p in self.outfiles:
361 newname, newfmt, newcl, oldcl = p
362 ndash = self.getNdash(newcl)
363 aparm = gxtp.OutputData(newcl, format=newfmt, num_dashes=ndash)
364 aparm.positional = self.is_positional
365 if self.is_positional:
366 if oldcl == "STDOUT":
367 aparm.positional = 9999999
368 aparm.command_line_override = "> $%s" % newcl
369 else:
370 aparm.positional = int(oldcl)
371 aparm.command_line_override = "$%s" % newcl
372 self.toutputs.append(aparm)
373 tp = gxtp.TestOutput(
374 name=newcl, value="%s_sample" % newcl, format=newfmt
375 )
376 self.testparam.append(tp)
377 for p in self.infiles:
378 newname = p[ICLPOS]
379 newfmt = p[IFMTPOS]
380 ndash = self.getNdash(newname)
381 if not len(p[ILABPOS]) > 0:
382 alab = p[ICLPOS]
383 else:
384 alab = p[ILABPOS]
385 aninput = gxtp.DataParam(
386 newname,
387 optional=False,
388 label=alab,
389 help=p[IHELPOS],
390 format=newfmt,
391 multiple=False,
392 num_dashes=ndash,
393 )
394 aninput.positional = self.is_positional
395 self.tinputs.append(aninput)
396 tparm = gxtp.TestParam(name=newname, value="%s_sample" % newname)
397 self.testparam.append(tparm)
398 for p in self.addpar:
399 newname, newval, newlabel, newhelp, newtype, newcl, override, oldcl = p
400 if not len(newlabel) > 0:
401 newlabel = newname
402 ndash = self.getNdash(newname)
403 if newtype == "text":
404 aparm = gxtp.TextParam(
405 newname,
406 label=newlabel,
407 help=newhelp,
408 value=newval,
409 num_dashes=ndash,
410 )
411 elif newtype == "integer":
412 aparm = gxtp.IntegerParam(
413 newname,
414 label=newname,
415 help=newhelp,
416 value=newval,
417 num_dashes=ndash,
418 )
419 elif newtype == "float":
420 aparm = gxtp.FloatParam(
421 newname,
422 label=newname,
423 help=newhelp,
424 value=newval,
425 num_dashes=ndash,
426 )
427 else:
428 raise ValueError(
429 'Unrecognised parameter type "%s" for\
430 additional parameter %s in makeXML'
431 % (newtype, newname)
432 )
433 aparm.positional = self.is_positional
434 if self.is_positional:
435 aninput.positional = int(oldcl)
436 self.tinputs.append(aparm)
437 self.tparm = gxtp.TestParam(newname, value=newval)
438 self.testparam.append(tparm)
439
440 def doNoXMLparam(self):
441 alab = self.infiles[0][ILABPOS]
442 if len(alab) == 0:
443 alab = self.infiles[0][ICLPOS]
444 max1s = (
445 "Maximum one input if parampass is 0 - more than one input files supplied - %s"
446 % str(self.infiles)
447 )
448 assert len(self.infiles) == 1, max1s
449 newname = self.infiles[0][ICLPOS]
450 aninput = gxtp.DataParam(
451 newname,
452 optional=False,
453 label=alab,
454 help=self.infiles[0][IHELPOS],
455 format=self.infiles[0][IFMTPOS],
456 multiple=False,
457 num_dashes=0,
458 )
459 aninput.command_line_override = "< $%s" % newname
460 aninput.positional = self.is_positional
461 self.tinputs.append(aninput)
462 tp = gxtp.TestParam(name=newname, value="%s_sample" % newname)
463 self.testparam.append(tp)
464 newname = self.outfiles[0][OCLPOS]
465 newfmt = self.outfiles[0][OFMTPOS]
466 anout = gxtp.OutputData(newname, format=newfmt, num_dashes=0)
467 anout.command_line_override = "> $%s" % newname
468 anout.positional = self.is_positional
469 self.toutputs.append(anout)
470 tp = gxtp.TestOutput(
471 name=newname, value="%s_sample" % newname, format=newfmt
472 )
473 self.testparam.append(tp)
474
475 def makeXML(self):
476 """
477 Create a Galaxy xml tool wrapper for the new script
478 Uses galaxyhtml
479 Hmmm. How to get the command line into correct order...
480 """
481 self.tool.command_line_override = self.xmlcl
482 if self.args.interpreter_name:
483 self.tool.interpreter = self.args.interpreter_name
484 if self.args.help_text:
485 helptext = open(self.args.help_text, "r").readlines()
486 helptext = [html_escape(x) for x in helptext]
487 self.tool.help = "".join([x for x in helptext])
488 else:
489 self.tool.help = (
490 "Please ask the tool author (%s) for help \
491 as none was supplied at tool generation\n"
492 % (self.args.user_email)
493 )
494 self.tool.version_command = None # do not want
495 requirements = gxtp.Requirements()
496
497 if self.args.interpreter_name:
498 if self.args.interpreter_name == "python":
499 requirements.append(
500 gxtp.Requirement(
501 "package", "python", self.args.interpreter_version
502 )
503 )
504 elif self.args.interpreter_name not in ["bash", "sh"]:
505 requirements.append(
506 gxtp.Requirement(
507 "package",
508 self.args.interpreter_name,
509 self.args.interpreter_version,
510 )
511 )
512 else:
513 if self.args.exe_package and self.args.parampass != "system":
514 requirements.append(
515 gxtp.Requirement(
516 "package",
517 self.args.exe_package,
518 self.args.exe_package_version,
519 )
520 )
521 self.tool.requirements = requirements
522 if self.args.parampass == "0":
523 self.doNoXMLparam()
524 else:
525 self.doXMLparam()
526 self.tool.outputs = self.toutputs
527 self.tool.inputs = self.tinputs
528 if self.args.runmode not in ["Executable", "system"]:
529 configfiles = gxtp.Configfiles()
530 configfiles.append(gxtp.Configfile(name="runMe", text=self.script))
531 self.tool.configfiles = configfiles
532 tests = gxtp.Tests()
533 test_a = gxtp.Test()
534 for tp in self.testparam:
535 test_a.append(tp)
536 tests.append(test_a)
537 self.tool.tests = tests
538 self.tool.add_comment(
539 "Created by %s at %s using the Galaxy Tool Factory."
540 % (self.args.user_email, timenow())
541 )
542 self.tool.add_comment("Source in git at: %s" % (toolFactoryURL))
543 self.tool.add_comment(
544 "Cite: Creating re-usable tools from scripts doi: 10.1093/bioinformatics/bts573"
545 )
546 exml = self.tool.export()
547 xf = open('%s.xml' % self.tool_name, "w")
548 xf.write(exml)
549 xf.write("\n")
550 xf.close()
551 # ready for the tarball
552
553 def makeTooltar(self):
554 """
555 a tool is a gz tarball with eg
556 /toolname/tool.xml /toolname/tool.py /toolname/test-data/test1_in.foo ...
557 NOTE names for test inputs and outputs are munged here so must
558 correspond to actual input and output names used on the generated cl
559 """
560 retval = self.run()
561 if retval:
562 sys.stderr.write(
563 "## Run failed. Cannot build yet. Please fix and retry"
564 )
565 sys.exit(1)
566 tdir = "tfout"
567 if not os.path.exists(tdir):
568 os.mkdir(tdir)
569 self.makeXML()
570 testdir = os.path.join(tdir, "test-data")
571 if not os.path.exists(testdir):
572 os.mkdir(testdir) # make tests directory
573 for p in self.infiles:
574 pth = p[IPATHPOS]
575 dest = os.path.join(testdir, "%s_sample" % p[ICLPOS])
576 shutil.copyfile(pth, dest)
577 for p in self.outfiles:
578 pth = p[OCLPOS]
579 if p[OOCLPOS] == "STDOUT" or self.args.parampass == "0":
580 pth = p[ONAMEPOS]
581 dest = os.path.join(testdir, "%s_sample" % p[ONAMEPOS])
582 shutil.copyfile(pth, dest)
583 dest = os.path.join(tdir, p[ONAMEPOS])
584 shutil.copyfile(pth, dest)
585 else:
586 pth = p[OCLPOS]
587 dest = os.path.join(testdir, "%s_sample" % p[OCLPOS])
588 shutil.copyfile(pth, dest)
589 dest = os.path.join(tdir, p[OCLPOS])
590 shutil.copyfile(pth, dest)
591
592 if os.path.exists(self.tlog) and os.stat(self.tlog).st_size > 0:
593 shutil.copyfile(self.tlog, os.path.join(testdir, "test1_log_outfiletxt"))
594 if self.args.runmode not in ["Executable", "system"]:
595 stname = os.path.join(tdir, "%s" % (self.sfile))
596 if not os.path.exists(stname):
597 shutil.copyfile(self.sfile, stname)
598 xreal = '%s.xml' % self.tool_name
599 xout = os.path.join(tdir,xreal)
600 shutil.copyfile(xreal, xout)
601 tarpath = "toolfactory_%s.tgz" % self.tool_name
602 tf = tarfile.open(tarpath, "w:gz")
603 tf.add(name=tdir, arcname=self.tool_name)
604 tf.close()
605 shutil.copyfile(tarpath, self.args.new_tool)
606 shutil.copyfile(xreal,"tool_xml.txt")
607 repdir = "TF_run_report_tempdir"
608 if not os.path.exists(repdir):
609 os.mkdir(repdir)
610 repoutnames = [x[OCLPOS] for x in self.outfiles]
611 with os.scandir('.') as outs:
612 for entry in outs:
613 if entry.name.endswith('.tgz') or not entry.is_file():
614 continue
615 if entry.name in repoutnames:
616 shutil.copyfile(entry.name,os.path.join(repdir,entry.name))
617 elif entry.name == "%s.xml" % self.tool_name:
618 shutil.copyfile(entry.name,os.path.join(repdir,"new_tool_xml"))
619 return retval
620
621 def run(self):
622 """
623 Some devteam tools have this defensive stderr read so I'm keeping with the faith
624 Feel free to update.
625 """
626 s = "run cl=%s" % str(self.cl)
627
628 logging.debug(s)
629 scl = " ".join(self.cl)
630 err = None
631 if self.args.parampass != "0":
632 ste = open(self.elog, "wb")
633 if self.lastclredirect:
634 sto = open(
635 self.lastclredirect[1], "wb"
636 ) # is name of an output file
637 else:
638 sto = open(self.tlog, "wb")
639 sto.write(
640 bytes(
641 "## Executing Toolfactory generated command line = %s\n"
642 % scl,
643 "utf8",
644 )
645 )
646 sto.flush()
647 p = subprocess.run(self.cl, shell=False, stdout=sto, stderr=ste)
648 sto.close()
649 ste.close()
650 tmp_stderr = open(self.elog, "rb")
651 err = ""
652 buffsize = 1048576
653 try:
654 while True:
655 err += str(tmp_stderr.read(buffsize))
656 if not err or len(err) % buffsize != 0:
657 break
658 except OverflowError:
659 pass
660 tmp_stderr.close()
661 retval = p.returncode
662 else: # work around special case of simple scripts that take stdin and write to stdout
663 sti = open(self.infiles[0][IPATHPOS], "rb")
664 sto = open(self.outfiles[0][ONAMEPOS], "wb")
665 # must use shell to redirect
666 p = subprocess.run(self.cl, shell=False, stdout=sto, stdin=sti)
667 retval = p.returncode
668 sto.close()
669 sti.close()
670 if os.path.isfile(self.tlog) and os.stat(self.tlog).st_size == 0:
671 os.unlink(self.tlog)
672 if os.path.isfile(self.elog) and os.stat(self.elog).st_size == 0:
673 os.unlink(self.elog)
674 if p.returncode != 0 and err: # problem
675 sys.stderr.write(err)
676 logging.debug("run done")
677 return retval
678
679
680 def main():
681 """
682 This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as:
683 <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath" --tool_name "foo" --interpreter "Rscript"
684 </command>
685 """
686 parser = argparse.ArgumentParser()
687 a = parser.add_argument
688 a("--script_path", default="")
689 a("--tool_name", default=None)
690 a("--interpreter_name", default=None)
691 a("--interpreter_version", default=None)
692 a("--exe_package", default=None)
693 a("--exe_package_version", default=None)
694 a("--input_files", default=[], action="append")
695 a("--output_files", default=[], action="append")
696 a("--user_email", default="Unknown")
697 a("--bad_user", default=None)
698 a("--make_Tool", default=None)
699 a("--help_text", default=None)
700 a("--tool_desc", default=None)
701 a("--tool_version", default=None)
702 a("--citations", default=None)
703 a("--additional_parameters", action="append", default=[])
704 a("--edit_additional_parameters", action="store_true", default=False)
705 a("--parampass", default="positional")
706 a("--tfout", default="./tfout")
707 a("--new_tool", default="new_tool")
708 a("--runmode", default=None)
709 args = parser.parse_args()
710 assert not args.bad_user, (
711 'UNAUTHORISED: %s is NOT authorized to use this tool until Galaxy admin adds %s to "admin_users" in the Galaxy configuration file'
712 % (args.bad_user, args.bad_user)
713 )
714 assert (
715 args.tool_name
716 ), "## Tool Factory expects a tool name - eg --tool_name=DESeq"
717 assert (
718 args.interpreter_name or args.exe_package
719 ), "## Tool Factory wrapper expects an interpreter or an executable package"
720 assert args.exe_package or (
721 len(args.script_path) > 0 and os.path.isfile(args.script_path)
722 ), "## Tool Factory wrapper expects a script path - eg --script_path=foo.R if no executable"
723 args.input_files = [
724 x.replace('"', "").replace("'", "") for x in args.input_files
725 ]
726 # remove quotes we need to deal with spaces in CL params
727 for i, x in enumerate(args.additional_parameters):
728 args.additional_parameters[i] = args.additional_parameters[i].replace(
729 '"', ""
730 )
731 r = ScriptRunner(args)
732 if args.make_Tool:
733 retcode = r.makeTooltar()
734 else:
735 retcode = r.run()
736 if retcode:
737 sys.exit(retcode) # indicate failure to job runner
738
739
740 if __name__ == "__main__":
741 main()