Mercurial > repos > fubar > tool_factory_2

comparison toolfactory/sample_toolfactory_tools.ga @ 35:5d38cb3d9be8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
added patched galaxyxml code temporarily until PR accepted
author fubar
date Sat, 08 Aug 2020 19:55:55 -0400
parents
children
comparison
equal deleted inserted replaced
34:5052ac89c036 35:5d38cb3d9be8
1 {
2 "a_galaxy_workflow": "true",
3 "annotation": "",
4 "format-version": "0.1",
5 "name": "workflow to generate a bunch of sample toolfactory tools",
6 "steps": {
7 "0": {
8 "annotation": "",
9 "content_id": null,
10 "errors": null,
11 "id": 0,
12 "input_connections": {},
13 "inputs": [
14 {
15 "description": "",
16 "name": "rgToolFactory2.py"
17 }
18 ],
19 "label": "rgToolFactory2.py",
20 "name": "Input dataset",
21 "outputs": [],
22 "position": {
23 "bottom": 235.25,
24 "height": 81,
25 "left": 711.84375,
26 "right": 911.84375,
27 "top": 154.25,
28 "width": 200,
29 "x": 711.84375,
30 "y": 154.25
31 },
32 "tool_id": null,
33 "tool_state": "{\"optional\": false}",
34 "tool_version": null,
35 "type": "data_input",
36 "uuid": "b717b6ee-51d0-415d-876d-f19b42f67666",
37 "workflow_outputs": [
38 {
39 "label": null,
40 "output_name": "output",
41 "uuid": "09acd6fd-4e2b-44a8-8757-35eca8d0de89"
42 }
43 ]
44 },
45 "1": {
46 "annotation": "",
47 "content_id": null,
48 "errors": null,
49 "id": 1,
50 "input_connections": {},
51 "inputs": [
52 {
53 "description": "",
54 "name": "README.md"
55 }
56 ],
57 "label": "README.md",
58 "name": "Input dataset",
59 "outputs": [],
60 "position": {
61 "bottom": 760.25,
62 "height": 61,
63 "left": 711.84375,
64 "right": 911.84375,
65 "top": 699.25,
66 "width": 200,
67 "x": 711.84375,
68 "y": 699.25
69 },
70 "tool_id": null,
71 "tool_state": "{\"optional\": false}",
72 "tool_version": null,
73 "type": "data_input",
74 "uuid": "8aefae07-4fd1-44a6-bea2-5d377567ac27",
75 "workflow_outputs": [
76 {
77 "label": null,
78 "output_name": "output",
79 "uuid": "5f8453d0-abd1-41d9-a4a7-1f8b82f1f095"
80 }
81 ]
82 },
83 "2": {
84 "annotation": "",
85 "content_id": null,
86 "errors": null,
87 "id": 2,
88 "input_connections": {},
89 "inputs": [
90 {
91 "description": "",
92 "name": "testtext"
93 }
94 ],
95 "label": "testtext",
96 "name": "Input dataset",
97 "outputs": [],
98 "position": {
99 "bottom": 235.25,
100 "height": 61,
101 "left": 989.84375,
102 "right": 1189.84375,
103 "top": 174.25,
104 "width": 200,
105 "x": 989.84375,
106 "y": 174.25
107 },
108 "tool_id": null,
109 "tool_state": "{\"optional\": false}",
110 "tool_version": null,
111 "type": "data_input",
112 "uuid": "02a35533-a67b-44c0-bce8-96a8adddc5a9",
113 "workflow_outputs": [
114 {
115 "label": null,
116 "output_name": "output",
117 "uuid": "abe4a1b1-2c0b-44d1-95f8-4f9bb38e9daa"
118 }
119 ]
120 },
121 "3": {
122 "annotation": "",
123 "content_id": "rgTF2",
124 "errors": null,
125 "id": 3,
126 "input_connections": {
127 "ppass|history_inputs_0|input_files": {
128 "id": 1,
129 "output_name": "output"
130 }
131 },
132 "inputs": [],
133 "label": null,
134 "name": "toolfactory",
135 "outputs": [
136 {
137 "name": "ToolFactory_Outputs",
138 "type": "input"
139 },
140 {
141 "name": "new_tool",
142 "type": "tgz"
143 }
144 ],
145 "position": {
146 "bottom": 636.25,
147 "height": 222,
148 "left": 989.84375,
149 "right": 1189.84375,
150 "top": 414.25,
151 "width": 200,
152 "x": 989.84375,
153 "y": 414.25
154 },
155 "post_job_actions": {},
156 "tool_id": "rgTF2",
157 "tool_state": "{\"__input_ext\": \"txt\", \"chromInfo\": \"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"interexe\": {\"interpreter\": \"bash\", \"__current_case__\": 5, \"interpreter_version\": \"\", \"exe_package_version\": \"\", \"dynScript\": \"rev | tac\"}, \"makeMode\": {\"make_Tool\": \"yes\", \"__current_case__\": 0, \"tool_version\": \"0.01\", \"tool_desc\": \"tacrev\", \"help_text\": \"**What it Does**\", \"citations\": []}, \"ppass\": {\"parampass\": \"0\", \"__current_case__\": 2, \"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"txt\"], \"input_label\": \"input file\", \"input_help\": \"parameter_help\", \"input_CL\": \"1\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"outfile\", \"history_format\": \"txt\", \"history_CL\": \"2\"}]}, \"tool_name\": \"tacrev\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
158 "tool_version": "2.00",
159 "type": "tool",
160 "uuid": "8fab16a0-5303-4e5c-8bf6-d6ebc70aa9af",
161 "workflow_outputs": [
162 {
163 "label": null,
164 "output_name": "ToolFactory_Outputs",
165 "uuid": "68d1a0b8-d897-48e9-a304-25d289e139e9"
166 },
167 {
168 "label": null,
169 "output_name": "new_tool",
170 "uuid": "8669863e-a1a5-4ed6-a412-c7f341f66176"
171 }
172 ]
173 },
174 "4": {
175 "annotation": "",
176 "content_id": "rgTF2",
177 "errors": null,
178 "id": 4,
179 "input_connections": {
180 "ppass|history_inputs_0|input_files": {
181 "id": 1,
182 "output_name": "output"
183 }
184 },
185 "inputs": [],
186 "label": null,
187 "name": "toolfactory",
188 "outputs": [
189 {
190 "name": "ToolFactory_Outputs",
191 "type": "input"
192 },
193 {
194 "name": "new_tool",
195 "type": "tgz"
196 }
197 ],
198 "position": {
199 "bottom": 916.25,
200 "height": 242,
201 "left": 989.84375,
202 "right": 1189.84375,
203 "top": 674.25,
204 "width": 200,
205 "x": 989.84375,
206 "y": 674.25
207 },
208 "post_job_actions": {},
209 "tool_id": "rgTF2",
210 "tool_state": "{\"__input_ext\": \"txt\", \"chromInfo\": \"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"interexe\": {\"interpreter\": \"python\", \"__current_case__\": 2, \"interpreter_version\": \"\", \"exe_package_version\": \"\", \"dynScript\": \"# reverse order of text by row\\nimport sys\\ninp = sys.argv[1]\\noutp = sys.argv[2]\\ni = open(inp,'r').readlines()\\no = open(outp,'w')\\nfor row in i:\\n rs = row.rstrip()\\n rs = list(rs)\\n rs.reverse()\\n o.write(''.join(rs))\\n o.write('\\\\n')\\no.close()\"}, \"makeMode\": {\"make_Tool\": \"yes\", \"__current_case__\": 0, \"tool_version\": \"0.01\", \"tool_desc\": \"pyrevpos\", \"help_text\": \"**What it Does**\", \"citations\": []}, \"ppass\": {\"parampass\": \"positional\", \"__current_case__\": 1, \"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"txt\"], \"input_label\": \"inputfile\", \"input_help\": \"parameter_help\", \"input_CL\": \"1\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"output\", \"history_format\": \"txt\", \"history_CL\": \"2\"}], \"edit_params\": \"yes\", \"additional_parameters\": []}, \"tool_name\": \"pyrevpos\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
211 "tool_version": "2.00",
212 "type": "tool",
213 "uuid": "ea0f8bbe-6b0d-4aff-bf06-6192faf8fe22",
214 "workflow_outputs": [
215 {
216 "label": null,
217 "output_name": "ToolFactory_Outputs",
218 "uuid": "70755c1b-6f92-43a3-aacb-8cc508a89b74"
219 },
220 {
221 "label": null,
222 "output_name": "new_tool",
223 "uuid": "ea9482d9-7836-442d-b753-ce4a201fd8c9"
224 }
225 ]
226 },
227 "5": {
228 "annotation": "",
229 "content_id": "rgTF2",
230 "errors": null,
231 "id": 5,
232 "input_connections": {
233 "ppass|history_inputs_0|input_files": {
234 "id": 1,
235 "output_name": "output"
236 }
237 },
238 "inputs": [],
239 "label": null,
240 "name": "toolfactory",
241 "outputs": [
242 {
243 "name": "ToolFactory_Outputs",
244 "type": "input"
245 },
246 {
247 "name": "new_tool",
248 "type": "tgz"
249 }
250 ],
251 "position": {
252 "bottom": 1216.25,
253 "height": 262,
254 "left": 989.84375,
255 "right": 1189.84375,
256 "top": 954.25,
257 "width": 200,
258 "x": 989.84375,
259 "y": 954.25
260 },
261 "post_job_actions": {},
262 "tool_id": "rgTF2",
263 "tool_state": "{\"__input_ext\": \"txt\", \"chromInfo\": \"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"interexe\": {\"interpreter\": \"python\", \"__current_case__\": 2, \"interpreter_version\": \"\", \"exe_package_version\": \"\", \"dynScript\": \"# reverse order of text by row\\nimport sys\\nimport argparse\\nparser = argparse.ArgumentParser()\\na = parser.add_argument\\na('--infile',default='')\\na('--outfile',default=None)\\nargs = parser.parse_args()\\ninp = args.infile\\noutp = args.outfile\\ni = open(inp,'r').readlines()\\no = open(outp,'w')\\nfor row in i:\\n rs = row.rstrip()\\n rs = list(rs)\\n rs.reverse()\\n o.write(''.join(rs))\\n o.write('\\\\n')\\no.close()\"}, \"makeMode\": {\"make_Tool\": \"yes\", \"__current_case__\": 0, \"tool_version\": \"0.01\", \"tool_desc\": \"reverse argparse\", \"help_text\": \"**What it Does**\", \"citations\": []}, \"ppass\": {\"parampass\": \"argparse\", \"__current_case__\": 0, \"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"txt\"], \"input_label\": \"infile\", \"input_help\": \"parameter_help\", \"input_CL\": \"infile\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"outfile\", \"history_format\": \"txt\", \"history_CL\": \"outfile\"}], \"edit_params\": \"yes\", \"additional_parameters\": []}, \"tool_name\": \"pyrevargparse\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
264 "tool_version": "2.00",
265 "type": "tool",
266 "uuid": "065b274a-ae73-43b0-b015-8b60d90db78f",
267 "workflow_outputs": [
268 {
269 "label": null,
270 "output_name": "ToolFactory_Outputs",
271 "uuid": "bec62d2d-b462-49bb-9646-28fea9136778"
272 },
273 {
274 "label": null,
275 "output_name": "new_tool",
276 "uuid": "2e1ed464-bcff-4354-8bf3-ed01167b280f"
277 }
278 ]
279 },
280 "6": {
281 "annotation": "",
282 "content_id": "rgTF2",
283 "errors": null,
284 "id": 6,
285 "input_connections": {
286 "ppass|history_inputs_0|input_files": {
287 "id": 1,
288 "output_name": "output"
289 }
290 },
291 "inputs": [],
292 "label": null,
293 "name": "toolfactory",
294 "outputs": [
295 {
296 "name": "ToolFactory_Outputs",
297 "type": "input"
298 },
299 {
300 "name": "new_tool",
301 "type": "tgz"
302 }
303 ],
304 "position": {
305 "bottom": 1496.25,
306 "height": 242,
307 "left": 989.84375,
308 "right": 1189.84375,
309 "top": 1254.25,
310 "width": 200,
311 "x": 989.84375,
312 "y": 1254.25
313 },
314 "post_job_actions": {},
315 "tool_id": "rgTF2",
316 "tool_state": "{\"__input_ext\": \"txt\", \"chromInfo\": \"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"interexe\": {\"interpreter\": \"python\", \"__current_case__\": 2, \"interpreter_version\": \"\", \"exe_package_version\": \"\", \"dynScript\": \"# reverse order of text by row\\nimport sys\\ninp = sys.argv[1]\\noutp = sys.argv[2]\\nappendme = sys.argv[3]\\ni = open(inp,'r').readlines()\\no = open(outp,'w')\\nfor row in i:\\n rs = row.rstrip()\\n rs = list(rs)\\n rs.reverse()\\n o.write(''.join(rs))\\n o.write(appendme)\\n o.write('\\\\n')\\no.close()\"}, \"makeMode\": {\"make_Tool\": \"yes\", \"__current_case__\": 0, \"tool_version\": \"0.01\", \"tool_desc\": \"pyrevpos\", \"help_text\": \"**What it Does**\", \"citations\": []}, \"ppass\": {\"parampass\": \"positional\", \"__current_case__\": 1, \"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"txt\"], \"input_label\": \"inputfile\", \"input_help\": \"parameter_help\", \"input_CL\": \"1\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"output\", \"history_format\": \"txt\", \"history_CL\": \"2\"}], \"edit_params\": \"yes\", \"additional_parameters\": [{\"__index__\": 0, \"param_name\": \"appendme\", \"param_type\": \"text\", \"param_value\": \"added at the end\", \"param_label\": \"append string\", \"param_help\": \"parameter_help\", \"param_CL\": \"3\"}]}, \"tool_name\": \"pyrevaddpos\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
317 "tool_version": "2.00",
318 "type": "tool",
319 "uuid": "5954323f-4ca1-4957-8250-746703dfa7c5",
320 "workflow_outputs": [
321 {
322 "label": null,
323 "output_name": "ToolFactory_Outputs",
324 "uuid": "6466bf24-51b2-4fae-aac8-fc1d78faac89"
325 },
326 {
327 "label": null,
328 "output_name": "new_tool",
329 "uuid": "f37589e2-3582-4443-bce8-5759485a7220"
330 }
331 ]
332 },
333 "7": {
334 "annotation": "",
335 "content_id": "rgTF2",
336 "errors": null,
337 "id": 7,
338 "input_connections": {
339 "ppass|history_inputs_0|input_files": {
340 "id": 2,
341 "output_name": "output"
342 }
343 },
344 "inputs": [],
345 "label": null,
346 "name": "toolfactory",
347 "outputs": [
348 {
349 "name": "ToolFactory_Outputs",
350 "type": "input"
351 },
352 {
353 "name": "new_tool",
354 "type": "tgz"
355 }
356 ],
357 "position": {
358 "bottom": 376.25,
359 "height": 222,
360 "left": 1267.84375,
361 "right": 1467.84375,
362 "top": 154.25,
363 "width": 200,
364 "x": 1267.84375,
365 "y": 154.25
366 },
367 "post_job_actions": {},
368 "tool_id": "rgTF2",
369 "tool_state": "{\"__input_ext\": \"txt\", \"chromInfo\": \"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"interexe\": {\"interpreter\": \"system\", \"__current_case__\": 1, \"exe_package\": \"sed\", \"exe_package_version\": \"\"}, \"makeMode\": {\"make_Tool\": \"yes\", \"__current_case__\": 0, \"tool_version\": \"0.01\", \"tool_desc\": \"sed runner\", \"help_text\": \"sed '/old/new/g input.txt\", \"citations\": []}, \"ppass\": {\"parampass\": \"positional\", \"__current_case__\": 1, \"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"txt\"], \"input_label\": \"input text\", \"input_help\": \"parameter_help\", \"input_CL\": \"3\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"output\", \"history_format\": \"txt\", \"history_CL\": \"STDOUT\"}], \"edit_params\": \"yes\", \"additional_parameters\": [{\"__index__\": 0, \"param_name\": \"sedstring\", \"param_type\": \"text\", \"param_value\": \"s/Old/New/g\", \"param_label\": \"parameter_label\", \"param_help\": \"parameter_help\", \"param_CL\": \"1\"}]}, \"tool_name\": \"sedtest\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
370 "tool_version": "2.00",
371 "type": "tool",
372 "uuid": "e26df7b6-3899-42fb-8efc-5f13d53668f8",
373 "workflow_outputs": [
374 {
375 "label": null,
376 "output_name": "ToolFactory_Outputs",
377 "uuid": "0a819390-acd4-4be6-aac9-ec3322302b0f"
378 },
379 {
380 "label": null,
381 "output_name": "new_tool",
382 "uuid": "f7555059-144d-4f64-a303-b70d189e6e35"
383 }
384 ]
385 },
386 "8": {
387 "annotation": "",
388 "content_id": "rgTF2",
389 "errors": null,
390 "id": 8,
391 "input_connections": {
392 "ppass|history_inputs_0|input_files": {
393 "id": 5,
394 "output_name": "new_tool"
395 }
396 },
397 "inputs": [],
398 "label": null,
399 "name": "toolfactory",
400 "outputs": [
401 {
402 "name": "ToolFactory_Outputs",
403 "type": "input"
404 },
405 {
406 "name": "new_tool",
407 "type": "tgz"
408 }
409 ],
410 "position": {
411 "bottom": 1271.25,
412 "height": 242,
413 "left": 1267.84375,
414 "right": 1467.84375,
415 "top": 1029.25,
416 "width": 200,
417 "x": 1267.84375,
418 "y": 1029.25
419 },
420 "post_job_actions": {},
421 "tool_id": "rgTF2",
422 "tool_state": "{\"__input_ext\": \"tgz\", \"chromInfo\": \"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"interexe\": {\"interpreter\": \"python\", \"__current_case__\": 2, \"interpreter_version\": \"\", \"exe_package_version\": \"\", \"dynScript\": \"import argparse\\nimport tarfile\\nimport os\\nimport tempfile\\nimport subprocess\\n\\n\\\"\\\"\\\"\\nplanemo test --no_cleanup --no_dependency_resolution --skip_venv --galaxy_root ~/galaxy ~/galaxy/tools/tool_makers/pyrevargparse/ &> pyrevargparse\\n\\\"\\\"\\\"\\n\\nparser = argparse.ArgumentParser()\\na = parser.add_argument\\na('--tooltgz',default='')\\na('--report',default=None)\\na('--toolout',default=None)\\na('--galaxy_root',default=None)\\nargs = parser.parse_args()\\ntoolname = args.toolout.split(os.sep)[-1]\\ntoolpath = os.path.join(args.galaxy_root,args.toolout)\\ntf = tarfile.open(args.tooltgz,\\\"r:gz\\\")\\ntf.extractall(toolpath)\\ncl = \\\"planemo test --skip_venv --galaxy_root %s %s\\\" % (args.galaxy_root,toolpath)\\ncll = cl.split(' ')\\nsto = open(args.report, 'w')\\np = subprocess.run(cll, shell=False, stdout=sto)\\nretval = p.returncode\\nsto.close()\\n\"}, \"makeMode\": {\"make_Tool\": \"yes\", \"__current_case__\": 0, \"tool_version\": \"0.01\", \"tool_desc\": \"Tool to test toolshed tool archives generated by the tool factory.\", \"help_text\": \"**What it Does**\\n\\nGiven a toolshed tgz file generated by a tool factory run, this will unpack it and run planemo test, returning the planemo stdout as a report\\nIt was generated using the tool factory.\", \"citations\": []}, \"ppass\": {\"parampass\": \"argparse\", \"__current_case__\": 0, \"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"tgz\"], \"input_label\": \"tool toolshed tgz archive from history\", \"input_help\": \"Run planemo test on a tool shed tool archive tgz format file generated by the ToolFactory or Planemo\", \"input_CL\": \"tooltgz\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"report\", \"history_format\": \"txt\", \"history_CL\": \"report\"}], \"edit_params\": \"yes\", \"additional_parameters\": [{\"__index__\": 0, \"param_name\": \"toolout\", \"param_type\": \"text\", \"param_value\": \"tools/toolmakers/planemotest\", \"param_label\": \"output path under galaxy root\", \"param_help\": \"This is where the tgz file will be extracted and tested by planemo\", \"param_CL\": \"toolout\"}, {\"__index__\": 1, \"param_name\": \"galaxy_root\", \"param_type\": \"text\", \"param_value\": \"/home/ross/galaxy\", \"param_label\": \"your galaxy root to use for running planemo\", \"param_help\": \"This will form the galaxy_root parameter for running planemo using an existing Galaxy source tree, and the tgz will be extracted at a path relative to that root\", \"param_CL\": \"galaxy_root\"}]}, \"tool_name\": \"planemotest\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
423 "tool_version": "2.00",
424 "type": "tool",
425 "uuid": "c72a7aae-3801-431b-a331-be6938d34fbd",
426 "workflow_outputs": [
427 {
428 "label": null,
429 "output_name": "ToolFactory_Outputs",
430 "uuid": "75aa9815-5bd6-44a7-8210-889d3b7e5027"
431 },
432 {
433 "label": null,
434 "output_name": "new_tool",
435 "uuid": "744499de-5d7e-4415-b427-315057c81ebc"
436 }
437 ]
438 }
439 },
440 "tags": [],
441 "uuid": "490d9c7f-eea3-4616-a8b7-13510da0430b",
442 "version": 1
443 }