Mercurial > repos > fubar > tool_factory_2
comparison docker/TF_example_wf.ga @ 42:b938475235e3 draft
Uploaded
author | fubar |
---|---|
date | Sun, 16 Aug 2020 08:33:09 -0400 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
41:f8c1694190f0 | 42:b938475235e3 |
---|---|
1 { | |
2 "a_galaxy_workflow": "true", | |
3 "annotation": "", | |
4 "format-version": "0.1", | |
5 "name": "TF examples", | |
6 "steps": { | |
7 "0": { | |
8 "annotation": "a fasta file - gc ratio will be estimated", | |
9 "content_id": null, | |
10 "errors": null, | |
11 "id": 0, | |
12 "input_connections": {}, | |
13 "inputs": [ | |
14 { | |
15 "description": "a fasta file - gc ratio will be estimated", | |
16 "name": "phiX.fasta" | |
17 } | |
18 ], | |
19 "label": "phiX.fasta", | |
20 "name": "Input dataset", | |
21 "outputs": [], | |
22 "position": { | |
23 "bottom": 231, | |
24 "height": 61, | |
25 "left": 393, | |
26 "right": 593, | |
27 "top": 170, | |
28 "width": 200, | |
29 "x": 393, | |
30 "y": 170 | |
31 }, | |
32 "tool_id": null, | |
33 "tool_state": "{\"optional\": false}", | |
34 "tool_version": null, | |
35 "type": "data_input", | |
36 "uuid": "7e2e24c8-2327-4893-a5b3-6b696a6ecd33", | |
37 "workflow_outputs": [ | |
38 { | |
39 "label": null, | |
40 "output_name": "output", | |
41 "uuid": "f5ce2386-b80c-4691-a0a7-abeec8854461" | |
42 } | |
43 ] | |
44 }, | |
45 "1": { | |
46 "annotation": "Any text file to be reversed lots of times and bjorked once.", | |
47 "content_id": null, | |
48 "errors": null, | |
49 "id": 1, | |
50 "input_connections": {}, | |
51 "inputs": [ | |
52 { | |
53 "description": "Any text file to be reversed lots of times and bjorked once.", | |
54 "name": "rgToolFactory2.py" | |
55 } | |
56 ], | |
57 "label": "rgToolFactory2.py", | |
58 "name": "Input dataset", | |
59 "outputs": [], | |
60 "position": { | |
61 "bottom": 371, | |
62 "height": 81, | |
63 "left": 393, | |
64 "right": 593, | |
65 "top": 290, | |
66 "width": 200, | |
67 "x": 393, | |
68 "y": 290 | |
69 }, | |
70 "tool_id": null, | |
71 "tool_state": "{\"optional\": false}", | |
72 "tool_version": null, | |
73 "type": "data_input", | |
74 "uuid": "f530b390-2424-4aae-8bd9-dd9d30277561", | |
75 "workflow_outputs": [ | |
76 { | |
77 "label": null, | |
78 "output_name": "output", | |
79 "uuid": "3d2a1699-50af-46e1-8981-dc6c3de2cf6c" | |
80 } | |
81 ] | |
82 }, | |
83 "2": { | |
84 "annotation": "", | |
85 "content_id": "rgTF2", | |
86 "errors": null, | |
87 "id": 2, | |
88 "input_connections": { | |
89 "ppass|history_inputs_0|input_files": { | |
90 "id": 0, | |
91 "output_name": "output" | |
92 } | |
93 }, | |
94 "inputs": [], | |
95 "label": null, | |
96 "name": "toolfactory", | |
97 "outputs": [ | |
98 { | |
99 "name": "TF_run_report", | |
100 "type": "input" | |
101 }, | |
102 { | |
103 "name": "new_tool", | |
104 "type": "tgz" | |
105 } | |
106 ], | |
107 "position": { | |
108 "bottom": 372, | |
109 "height": 202, | |
110 "left": 613, | |
111 "right": 813, | |
112 "top": 170, | |
113 "width": 200, | |
114 "x": 613, | |
115 "y": 170 | |
116 }, | |
117 "post_job_actions": {}, | |
118 "tool_id": "rgTF2", | |
119 "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"interexe\": {\"interpreter\": \"perl\", \"__current_case__\": 4, \"interpreter_version\": \"\", \"exe_package_version\": \"\", \"dynScript\": \"\\n# usage : perl toolExample.pl <FASTA file> <output file>\\n\\nopen (IN, \\\"<$ARGV[0]\\\");\\nopen (OUT, \\\">$ARGV[1]\\\");\\nwhile (<IN>) {\\n chop;\\n if (m/^>/) {\\n s/^>//;\\n if ($. > 1) {\\n print OUT sprintf(\\\"%.3f\\\", $gc/$length) . \\\"\\\\n\\\";\\n }\\n $gc = 0;\\n $length = 0;\\n } else {\\n ++$gc while m/[gc]/ig;\\n $length += length $_;\\n }\\n}\\nprint OUT sprintf(\\\"%.3f\\\", $gc/$length) . \\\"\\\\n\\\";\\nclose( IN );\\nclose( OUT );\"}, \"makeMode\": {\"make_Tool\": \"yes\", \"__current_case__\": 0, \"tool_version\": \"0.01\", \"tool_desc\": \"perl version of gc counter from planemo example\", \"help_text\": \"**What it Does**\\ncounts gc using, ugh, perl...\\n\", \"citations\": []}, \"ppass\": {\"parampass\": \"positional\", \"__current_case__\": 1, \"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"fasta\"], \"input_label\": \"input fasta file\", \"input_help\": \"parameter_help\", \"input_CL\": \"1\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"output\", \"history_format\": \"tsv\", \"history_CL\": \"2\"}], \"edit_params\": \"no\", \"additional_parameters\": []}, \"tool_name\": \"perlgc\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", | |
120 "tool_version": "2.00", | |
121 "type": "tool", | |
122 "uuid": "3b6aab01-4759-4df6-801f-626678639e51", | |
123 "workflow_outputs": [ | |
124 { | |
125 "label": null, | |
126 "output_name": "TF_run_report", | |
127 "uuid": "7aea56bd-4f39-4d3b-8254-a6675161d059" | |
128 }, | |
129 { | |
130 "label": null, | |
131 "output_name": "new_tool", | |
132 "uuid": "f964e779-2f92-4c81-9819-3e1ebc156664" | |
133 } | |
134 ] | |
135 }, | |
136 "3": { | |
137 "annotation": "", | |
138 "content_id": "rgTF2", | |
139 "errors": null, | |
140 "id": 3, | |
141 "input_connections": { | |
142 "ppass|history_inputs_0|input_files": { | |
143 "id": 1, | |
144 "output_name": "output" | |
145 } | |
146 }, | |
147 "inputs": [], | |
148 "label": null, | |
149 "name": "toolfactory", | |
150 "outputs": [ | |
151 { | |
152 "name": "TF_run_report", | |
153 "type": "input" | |
154 }, | |
155 { | |
156 "name": "new_tool", | |
157 "type": "tgz" | |
158 } | |
159 ], | |
160 "position": { | |
161 "bottom": 492, | |
162 "height": 202, | |
163 "left": 613, | |
164 "right": 813, | |
165 "top": 290, | |
166 "width": 200, | |
167 "x": 613, | |
168 "y": 290 | |
169 }, | |
170 "post_job_actions": {}, | |
171 "tool_id": "rgTF2", | |
172 "tool_state": "{\"__input_ext\": \"input\", \"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/def/bjork!bjorkdef/g\", \"param_label\": \"parameter_label\", \"param_help\": \"parameter_help\", \"param_CL\": \"1\", \"param_CLprefixed\": \"\"}]}, \"tool_name\": \"sedtest\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", | |
173 "tool_version": "2.00", | |
174 "type": "tool", | |
175 "uuid": "2138c717-5128-4c4b-bc22-4809cd001c34", | |
176 "workflow_outputs": [ | |
177 { | |
178 "label": null, | |
179 "output_name": "TF_run_report", | |
180 "uuid": "b0be8c95-7380-42b8-a16d-8e08578d4dd7" | |
181 }, | |
182 { | |
183 "label": null, | |
184 "output_name": "new_tool", | |
185 "uuid": "56635519-a9a0-49eb-8305-59cc1fcef99f" | |
186 } | |
187 ] | |
188 }, | |
189 "4": { | |
190 "annotation": "", | |
191 "content_id": "rgTF2", | |
192 "errors": null, | |
193 "id": 4, | |
194 "input_connections": { | |
195 "ppass|history_inputs_0|input_files": { | |
196 "id": 1, | |
197 "output_name": "output" | |
198 } | |
199 }, | |
200 "inputs": [], | |
201 "label": null, | |
202 "name": "toolfactory", | |
203 "outputs": [ | |
204 { | |
205 "name": "TF_run_report", | |
206 "type": "input" | |
207 }, | |
208 { | |
209 "name": "new_tool", | |
210 "type": "tgz" | |
211 } | |
212 ], | |
213 "position": { | |
214 "bottom": 652, | |
215 "height": 242, | |
216 "left": 613, | |
217 "right": 813, | |
218 "top": 410, | |
219 "width": 200, | |
220 "x": 613, | |
221 "y": 410 | |
222 }, | |
223 "post_job_actions": {}, | |
224 "tool_id": "rgTF2", | |
225 "tool_state": "{\"__input_ext\": \"input\", \"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\", \"param_CLprefixed\": \"\"}]}, \"tool_name\": \"pyrevaddpos\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", | |
226 "tool_version": "2.00", | |
227 "type": "tool", | |
228 "uuid": "30dbe033-30c4-4228-b0cb-854df30f5594", | |
229 "workflow_outputs": [ | |
230 { | |
231 "label": null, | |
232 "output_name": "TF_run_report", | |
233 "uuid": "37fdd905-471d-4479-a98a-4dfbaa6314be" | |
234 }, | |
235 { | |
236 "label": null, | |
237 "output_name": "new_tool", | |
238 "uuid": "7c8a8dba-1e8c-49d5-b51d-a0ab09931932" | |
239 } | |
240 ] | |
241 }, | |
242 "5": { | |
243 "annotation": "", | |
244 "content_id": "rgTF2", | |
245 "errors": null, | |
246 "id": 5, | |
247 "input_connections": { | |
248 "ppass|history_inputs_0|input_files": { | |
249 "id": 1, | |
250 "output_name": "output" | |
251 } | |
252 }, | |
253 "inputs": [], | |
254 "label": null, | |
255 "name": "toolfactory", | |
256 "outputs": [ | |
257 { | |
258 "name": "TF_run_report", | |
259 "type": "input" | |
260 }, | |
261 { | |
262 "name": "new_tool", | |
263 "type": "tgz" | |
264 } | |
265 ], | |
266 "position": { | |
267 "bottom": 772, | |
268 "height": 242, | |
269 "left": 613, | |
270 "right": 813, | |
271 "top": 530, | |
272 "width": 200, | |
273 "x": 613, | |
274 "y": 530 | |
275 }, | |
276 "post_job_actions": {}, | |
277 "tool_id": "rgTF2", | |
278 "tool_state": "{\"__input_ext\": \"input\", \"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}", | |
279 "tool_version": "2.00", | |
280 "type": "tool", | |
281 "uuid": "91a0dccf-384c-491a-ae08-f426888d26cf", | |
282 "workflow_outputs": [ | |
283 { | |
284 "label": null, | |
285 "output_name": "TF_run_report", | |
286 "uuid": "61a5271d-3940-4855-9093-a0710dc3fe08" | |
287 }, | |
288 { | |
289 "label": null, | |
290 "output_name": "new_tool", | |
291 "uuid": "a6602e23-dc1c-44b7-8ed7-cd9971ff9d30" | |
292 } | |
293 ] | |
294 }, | |
295 "6": { | |
296 "annotation": "", | |
297 "content_id": "rgTF2", | |
298 "errors": null, | |
299 "id": 6, | |
300 "input_connections": { | |
301 "ppass|history_inputs_0|input_files": { | |
302 "id": 1, | |
303 "output_name": "output" | |
304 } | |
305 }, | |
306 "inputs": [], | |
307 "label": null, | |
308 "name": "toolfactory", | |
309 "outputs": [ | |
310 { | |
311 "name": "TF_run_report", | |
312 "type": "input" | |
313 }, | |
314 { | |
315 "name": "new_tool", | |
316 "type": "tgz" | |
317 } | |
318 ], | |
319 "position": { | |
320 "bottom": 852, | |
321 "height": 202, | |
322 "left": 613, | |
323 "right": 813, | |
324 "top": 650, | |
325 "width": 200, | |
326 "x": 613, | |
327 "y": 650 | |
328 }, | |
329 "post_job_actions": {}, | |
330 "tool_id": "rgTF2", | |
331 "tool_state": "{\"__input_ext\": \"input\", \"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}", | |
332 "tool_version": "2.00", | |
333 "type": "tool", | |
334 "uuid": "edb5d852-908b-45bf-8892-e0e8c337c31d", | |
335 "workflow_outputs": [ | |
336 { | |
337 "label": null, | |
338 "output_name": "TF_run_report", | |
339 "uuid": "c1394cf9-bb03-4ac3-8466-8ee0cc30c0a0" | |
340 }, | |
341 { | |
342 "label": null, | |
343 "output_name": "new_tool", | |
344 "uuid": "e45566f4-d40e-4ad0-ad27-72ce814b13da" | |
345 } | |
346 ] | |
347 }, | |
348 "7": { | |
349 "annotation": "", | |
350 "content_id": "rgTF2", | |
351 "errors": null, | |
352 "id": 7, | |
353 "input_connections": { | |
354 "ppass|history_inputs_0|input_files": { | |
355 "id": 1, | |
356 "output_name": "output" | |
357 } | |
358 }, | |
359 "inputs": [], | |
360 "label": null, | |
361 "name": "toolfactory", | |
362 "outputs": [ | |
363 { | |
364 "name": "TF_run_report", | |
365 "type": "input" | |
366 }, | |
367 { | |
368 "name": "new_tool", | |
369 "type": "tgz" | |
370 } | |
371 ], | |
372 "position": { | |
373 "bottom": 992, | |
374 "height": 222, | |
375 "left": 613, | |
376 "right": 813, | |
377 "top": 770, | |
378 "width": 200, | |
379 "x": 613, | |
380 "y": 770 | |
381 }, | |
382 "post_job_actions": {}, | |
383 "tool_id": "rgTF2", | |
384 "tool_state": "{\"__input_ext\": \"input\", \"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}", | |
385 "tool_version": "2.00", | |
386 "type": "tool", | |
387 "uuid": "08a48555-8700-4652-a76b-df1f54197049", | |
388 "workflow_outputs": [ | |
389 { | |
390 "label": null, | |
391 "output_name": "TF_run_report", | |
392 "uuid": "b5bd73bb-1ddc-4161-be2e-370bab9aebbe" | |
393 }, | |
394 { | |
395 "label": null, | |
396 "output_name": "new_tool", | |
397 "uuid": "e96ae086-a92a-4018-8f07-ebf4974807e6" | |
398 } | |
399 ] | |
400 }, | |
401 "8": { | |
402 "annotation": "", | |
403 "content_id": "rgTF2", | |
404 "errors": null, | |
405 "id": 8, | |
406 "input_connections": { | |
407 "ppass|history_inputs_0|input_files": { | |
408 "id": 7, | |
409 "output_name": "new_tool" | |
410 } | |
411 }, | |
412 "inputs": [], | |
413 "label": null, | |
414 "name": "toolfactory", | |
415 "outputs": [ | |
416 { | |
417 "name": "TF_run_report", | |
418 "type": "input" | |
419 }, | |
420 { | |
421 "name": "new_tool", | |
422 "type": "tgz" | |
423 } | |
424 ], | |
425 "position": { | |
426 "bottom": 412, | |
427 "height": 242, | |
428 "left": 833, | |
429 "right": 1033, | |
430 "top": 170, | |
431 "width": 200, | |
432 "x": 833, | |
433 "y": 170 | |
434 }, | |
435 "post_job_actions": {}, | |
436 "tool_id": "rgTF2", | |
437 "tool_state": "{\"__input_ext\": \"input\", \"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\", \"param_CLprefixed\": \"\"}, {\"__index__\": 1, \"param_name\": \"galaxy_root\", \"param_type\": \"text\", \"param_value\": \"/home/ross/galaxy\", \"param_label\": \"Galaxy source root directory to use for running planemo\", \"param_help\": \"This will form the galaxy_root parameter for rnning planemo using an existing Galaxy source tree, and the tgz will be extracted at a path relative to that rootu\", \"param_CL\": \"galaxy_root\", \"param_CLprefixed\": \"\"}]}, \"tool_name\": \"planemotest\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", | |
438 "tool_version": "2.00", | |
439 "type": "tool", | |
440 "uuid": "b9bfb1a4-4c0c-4d39-9e74-223da72f8abc", | |
441 "workflow_outputs": [ | |
442 { | |
443 "label": null, | |
444 "output_name": "TF_run_report", | |
445 "uuid": "09ba44ea-4da8-46f5-a411-ca054ccedd3b" | |
446 }, | |
447 { | |
448 "label": null, | |
449 "output_name": "new_tool", | |
450 "uuid": "50a8ff4a-702a-4983-8202-8a79c0a3c978" | |
451 } | |
452 ] | |
453 } | |
454 }, | |
455 "tags": [], | |
456 "uuid": "321a7f9f-c287-453c-807a-43afd948770e", | |
457 "version": 1 | |
458 } |