Mercurial > repos > fubar_too > toolfactory
comparison toolfactory/ToolFactoryDemosApril30.ga @ 2:cc1a8fbb0f48 draft
Uploaded
author | fubar_too |
---|---|
date | Fri, 21 May 2021 00:16:01 +0000 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
1:34ff94460cc3 | 2:cc1a8fbb0f48 |
---|---|
1 { | |
2 "a_galaxy_workflow": "true", | |
3 "annotation": "", | |
4 "format-version": "0.1", | |
5 "name": "ToolFactory - make, test and install demonstration tools", | |
6 "steps": { | |
7 "0": { | |
8 "annotation": "", | |
9 "content_id": "rgtf2", | |
10 "errors": null, | |
11 "id": 0, | |
12 "input_connections": {}, | |
13 "inputs": [], | |
14 "label": null, | |
15 "name": "toolfactory", | |
16 "outputs": [ | |
17 { | |
18 "name": "new_tool", | |
19 "type": "toolshed.gz" | |
20 } | |
21 ], | |
22 "position": { | |
23 "bottom": -152.39999389648438, | |
24 "height": 102.60000610351562, | |
25 "left": 252.5, | |
26 "right": 452.5, | |
27 "top": -255, | |
28 "width": 200, | |
29 "x": 252.5, | |
30 "y": -255 | |
31 }, | |
32 "post_job_actions": {}, | |
33 "tool_id": "rgtf2", | |
34 "tool_state": "{\"__input_ext\": \"input\", \"__workflow_invocation_uuid__\": \"dbb99db2a98811ebbc9e0242ac1b0004\", \"chromInfo\": \"/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"citations\": [], \"cl_prefix\": \"\", \"cl_suffix\": \"\", \"cover\": {\"commover\": \"no\", \"__current_case__\": 0, \"command_override\": \"\", \"test_override\": \"\"}, \"deps\": {\"packages\": \"\", \"usescript\": {\"choosescript\": \"yes\", \"__current_case__\": 1, \"scriptrunner\": \"bash\", \"dynScript\": \"echo \\\"Hello $1\\\"\"}}, \"help_text\": \"**What it Does**\", \"install\": \"false\", \"io_param\": {\"ppass\": {\"parampass\": \"positional\", \"__current_case__\": 1, \"io\": {\"history_inputs\": [], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"Hello_output\", \"history_format\": \"txt\", \"history_CL\": \"STDOUT\", \"history_test\": \"diff:0\"}], \"collection_outputs\": []}, \"addparam\": {\"edit_params\": \"yes\", \"additional_parameters\": [{\"__index__\": 0, \"param_name\": \"say_hello_to\", \"ap_type\": {\"param_type\": \"text\", \"__current_case__\": 0, \"param_value\": \"\"}, \"param_label\": \"Say hello to\", \"param_help\": \"\", \"param_CL\": \"1\", \"param_CLprefixed\": \"\", \"param_repeat\": \"false\"}]}}}, \"make\": {\"makeMode\": {\"__current_case__\": 1, \"citations\": [], \"galaxy_apikey\": \"fakekey\", \"galaxy_url\": \"http://localhost:8080\", \"help_text\": \"**What it Does**\\nToolFactory demonstration - hello world in Galaxy\", \"make_Tool\": \"gentest\", \"tool_desc\": \"Says hello\", \"tool_version\": \"0.01\", \"toolshed_apikey\": \"fakekey\", \"toolshed_url\": \"http://localhost:9009\"}}, \"run_test\": \"true\", \"tool_desc\": \"\", \"tool_name\": \"hello_toolshed\", \"tool_version\": \"0.01\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", | |
35 "tool_version": "2.00", | |
36 "type": "tool", | |
37 "uuid": "f07cf7c8-4a96-4c4f-bd7b-d43c30642369", | |
38 "workflow_outputs": [ | |
39 { | |
40 "label": null, | |
41 "output_name": "new_tool", | |
42 "uuid": "5e1e49e0-ed56-4c7a-95fe-2f66aa4d7165" | |
43 } | |
44 ] | |
45 }, | |
46 "1": { | |
47 "annotation": "", | |
48 "content_id": null, | |
49 "errors": null, | |
50 "id": 1, | |
51 "input_connections": {}, | |
52 "inputs": [ | |
53 { | |
54 "description": "", | |
55 "name": "bwa-mem-fastq1.fq" | |
56 } | |
57 ], | |
58 "label": "bwa-mem-fastq1.fq", | |
59 "name": "Input dataset", | |
60 "outputs": [], | |
61 "position": { | |
62 "bottom": 353.1999969482422, | |
63 "height": 82.19999694824219, | |
64 "left": 252.5, | |
65 "right": 452.5, | |
66 "top": 271, | |
67 "width": 200, | |
68 "x": 252.5, | |
69 "y": 271 | |
70 }, | |
71 "tool_id": null, | |
72 "tool_state": "{\"optional\": false}", | |
73 "tool_version": null, | |
74 "type": "data_input", | |
75 "uuid": "e1c43d57-ee0e-42ea-aed7-d86c595d06e7", | |
76 "workflow_outputs": [ | |
77 { | |
78 "label": null, | |
79 "output_name": "output", | |
80 "uuid": "ecd799ad-b7be-4b58-87ea-050884620d99" | |
81 } | |
82 ] | |
83 }, | |
84 "2": { | |
85 "annotation": "", | |
86 "content_id": null, | |
87 "errors": null, | |
88 "id": 2, | |
89 "input_connections": {}, | |
90 "inputs": [ | |
91 { | |
92 "description": "", | |
93 "name": "bwa-mem-mt-genome.fa" | |
94 } | |
95 ], | |
96 "label": "bwa-mem-mt-genome.fa", | |
97 "name": "Input dataset", | |
98 "outputs": [], | |
99 "position": { | |
100 "bottom": 473.1999969482422, | |
101 "height": 82.19999694824219, | |
102 "left": 252.5, | |
103 "right": 452.5, | |
104 "top": 391, | |
105 "width": 200, | |
106 "x": 252.5, | |
107 "y": 391 | |
108 }, | |
109 "tool_id": null, | |
110 "tool_state": "{\"optional\": false}", | |
111 "tool_version": null, | |
112 "type": "data_input", | |
113 "uuid": "98ae8bb5-cd5c-4330-b0cc-4d2252b0eee1", | |
114 "workflow_outputs": [ | |
115 { | |
116 "label": null, | |
117 "output_name": "output", | |
118 "uuid": "c0b94cf6-886f-4260-9e63-a2e57435a628" | |
119 } | |
120 ] | |
121 }, | |
122 "3": { | |
123 "annotation": "", | |
124 "content_id": null, | |
125 "errors": null, | |
126 "id": 3, | |
127 "input_connections": {}, | |
128 "inputs": [ | |
129 { | |
130 "description": "", | |
131 "name": "hello_toolshed_toolshed.gz" | |
132 } | |
133 ], | |
134 "label": "hello_toolshed_toolshed.gz", | |
135 "name": "Input dataset", | |
136 "outputs": [], | |
137 "position": { | |
138 "bottom": -333.8000030517578, | |
139 "height": 82.19999694824219, | |
140 "left": 252.5, | |
141 "right": 452.5, | |
142 "top": -416, | |
143 "width": 200, | |
144 "x": 252.5, | |
145 "y": -416 | |
146 }, | |
147 "tool_id": null, | |
148 "tool_state": "{\"optional\": false}", | |
149 "tool_version": null, | |
150 "type": "data_input", | |
151 "uuid": "f65affe8-b8b2-4e54-9e1a-57f038e31d04", | |
152 "workflow_outputs": [ | |
153 { | |
154 "label": null, | |
155 "output_name": "output", | |
156 "uuid": "68da073d-aa54-470c-aab5-a429846870eb" | |
157 } | |
158 ] | |
159 }, | |
160 "4": { | |
161 "annotation": "", | |
162 "content_id": "rgtf2", | |
163 "errors": null, | |
164 "id": 4, | |
165 "input_connections": {}, | |
166 "inputs": [], | |
167 "label": null, | |
168 "name": "toolfactory", | |
169 "outputs": [ | |
170 { | |
171 "name": "new_tool", | |
172 "type": "toolshed.gz" | |
173 } | |
174 ], | |
175 "position": { | |
176 "bottom": -313.3999938964844, | |
177 "height": 102.60000610351562, | |
178 "left": 530.5, | |
179 "right": 730.5, | |
180 "top": -416, | |
181 "width": 200, | |
182 "x": 530.5, | |
183 "y": -416 | |
184 }, | |
185 "post_job_actions": {}, | |
186 "tool_id": "rgtf2", | |
187 "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"citations\": [], \"cl_suffix\": \"\", \"cover\": {\"commover\": \"no\", \"__current_case__\": 0, \"command_override\": \"\", \"test_override\": \"\"}, \"deps\": {\"packages\": \"swi-prolog\", \"usescript\": {\"choosescript\": \"yes\", \"__current_case__\": 1, \"scriptrunner\": \"swipl -q -g main -s \", \"dynScript\": \"parent(pam,bob).\\nparent(tom,bob).\\nparent(tom,liz).\\nparent(bob,ann).\\nparent(bob,pat).\\nparent(pat,jim).\\n\\nmain :-\\n parent(X,jim),\\n format('~a is the parent of jim~n', [X]),\\n halt.\"}}, \"help_text\": \"**What it Does**\", \"install\": \"true\", \"io_param\": {\"ppass\": {\"parampass\": \"positional\", \"__current_case__\": 1, \"io\": {\"history_inputs\": [], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"prolog_out\", \"history_format\": \"txt\", \"history_CL\": \"STDOUT\", \"history_test\": \"diff:0\"}], \"collection_outputs\": []}, \"addparam\": {\"edit_params\": \"yes\", \"additional_parameters\": []}}}, \"run_test\": \"true\", \"tool_desc\": \"\", \"tool_name\": \"prolog_demo\", \"tool_version\": \"0.01\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", | |
188 "tool_version": "2.00", | |
189 "type": "tool", | |
190 "uuid": "b912fc6c-2ac9-4b29-8b29-abb960e75468", | |
191 "workflow_outputs": [ | |
192 { | |
193 "label": null, | |
194 "output_name": "new_tool", | |
195 "uuid": "4d4d0421-9ae5-4b3a-8c81-ccfbe02cbada" | |
196 } | |
197 ] | |
198 }, | |
199 "5": { | |
200 "annotation": "", | |
201 "content_id": null, | |
202 "errors": null, | |
203 "id": 5, | |
204 "input_connections": {}, | |
205 "inputs": [ | |
206 { | |
207 "description": "", | |
208 "name": "phiX.fasta" | |
209 } | |
210 ], | |
211 "label": "phiX.fasta", | |
212 "name": "Input dataset", | |
213 "outputs": [], | |
214 "position": { | |
215 "bottom": -176.1999969482422, | |
216 "height": 61.80000305175781, | |
217 "left": 808.5, | |
218 "right": 1008.5, | |
219 "top": -238, | |
220 "width": 200, | |
221 "x": 808.5, | |
222 "y": -238 | |
223 }, | |
224 "tool_id": null, | |
225 "tool_state": "{\"optional\": false}", | |
226 "tool_version": null, | |
227 "type": "data_input", | |
228 "uuid": "0e9d6723-9165-413d-95e0-cb7cad549c86", | |
229 "workflow_outputs": [ | |
230 { | |
231 "label": null, | |
232 "output_name": "output", | |
233 "uuid": "cd0767ab-f0f3-47c1-8eb0-ac40700c3a5e" | |
234 } | |
235 ] | |
236 }, | |
237 "6": { | |
238 "annotation": "", | |
239 "content_id": "rgtf2", | |
240 "errors": null, | |
241 "id": 6, | |
242 "input_connections": {}, | |
243 "inputs": [], | |
244 "label": null, | |
245 "name": "toolfactory", | |
246 "outputs": [ | |
247 { | |
248 "name": "new_tool", | |
249 "type": "toolshed.gz" | |
250 } | |
251 ], | |
252 "position": { | |
253 "bottom": -313.3999938964844, | |
254 "height": 102.60000610351562, | |
255 "left": 808.5, | |
256 "right": 1008.5, | |
257 "top": -416, | |
258 "width": 200, | |
259 "x": 808.5, | |
260 "y": -416 | |
261 }, | |
262 "post_job_actions": {}, | |
263 "tool_id": "rgtf2", | |
264 "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"citations\": [], \"cl_suffix\": \"\", \"cover\": {\"commover\": \"no\", \"__current_case__\": 0, \"command_override\": \"\", \"test_override\": \"\"}, \"deps\": {\"packages\": \"\", \"usescript\": {\"choosescript\": \"yes\", \"__current_case__\": 1, \"scriptrunner\": \"bash\", \"dynScript\": \"echo \\\"Hello $1\\\"\"}}, \"help_text\": \"**What it Does**\\nPrototype bash script with a text input and a new history output.\\nRemarkably useful as a starting point - add a new bash script and add the appropriate parameters to make a new tool.\", \"install\": \"true\", \"io_param\": {\"ppass\": {\"parampass\": \"positional\", \"__current_case__\": 1, \"io\": {\"history_inputs\": [], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"Hello_output\", \"history_format\": \"txt\", \"history_CL\": \"STDOUT\", \"history_test\": \"diff:0\"}], \"collection_outputs\": []}, \"addparam\": {\"edit_params\": \"yes\", \"additional_parameters\": [{\"__index__\": 0, \"param_name\": \"say_hello_to\", \"ap_type\": {\"param_type\": \"text\", \"__current_case__\": 0, \"param_value\": \"Hello from the ToolFactory!\"}, \"param_label\": \"Say hello to\", \"param_help\": \"\", \"param_CL\": \"1\", \"param_CLprefixed\": \"\", \"param_repeat\": \"false\"}]}}}, \"run_test\": \"true\", \"tool_desc\": \"ToolFactory demonstration using a bash script.\", \"tool_name\": \"hello_toolshed\", \"tool_version\": \"0.01\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", | |
265 "tool_version": "2.00", | |
266 "type": "tool", | |
267 "uuid": "877a5d8c-e46f-48b0-9c54-5bbf302c8719", | |
268 "workflow_outputs": [ | |
269 { | |
270 "label": null, | |
271 "output_name": "new_tool", | |
272 "uuid": "56928b22-2cb6-4b3a-ab79-987d3cdbbba2" | |
273 } | |
274 ] | |
275 }, | |
276 "7": { | |
277 "annotation": "", | |
278 "content_id": null, | |
279 "errors": null, | |
280 "id": 7, | |
281 "input_connections": {}, | |
282 "inputs": [ | |
283 { | |
284 "description": "", | |
285 "name": "rgToolFactory2.py" | |
286 } | |
287 ], | |
288 "label": "rgToolFactory2.py", | |
289 "name": "Input dataset", | |
290 "outputs": [], | |
291 "position": { | |
292 "bottom": 562.1999969482422, | |
293 "height": 82.19999694824219, | |
294 "left": 818.5, | |
295 "right": 1018.5, | |
296 "top": 480, | |
297 "width": 200, | |
298 "x": 818.5, | |
299 "y": 480 | |
300 }, | |
301 "tool_id": null, | |
302 "tool_state": "{\"optional\": false}", | |
303 "tool_version": null, | |
304 "type": "data_input", | |
305 "uuid": "60049d1f-78bd-4a84-bad4-23263ea7d023", | |
306 "workflow_outputs": [ | |
307 { | |
308 "label": null, | |
309 "output_name": "output", | |
310 "uuid": "3d75794b-a995-4f36-b622-71fd91edd084" | |
311 } | |
312 ] | |
313 }, | |
314 "8": { | |
315 "annotation": "", | |
316 "content_id": "rgtf2", | |
317 "errors": null, | |
318 "id": 8, | |
319 "input_connections": {}, | |
320 "inputs": [], | |
321 "label": null, | |
322 "name": "toolfactory", | |
323 "outputs": [ | |
324 { | |
325 "name": "new_tool", | |
326 "type": "toolshed.gz" | |
327 } | |
328 ], | |
329 "position": { | |
330 "bottom": -313.3999938964844, | |
331 "height": 102.60000610351562, | |
332 "left": 1086.5, | |
333 "right": 1286.5, | |
334 "top": -416, | |
335 "width": 200, | |
336 "x": 1086.5, | |
337 "y": -416 | |
338 }, | |
339 "post_job_actions": {}, | |
340 "tool_id": "rgtf2", | |
341 "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"citations\": [], \"cl_suffix\": \"\", \"cover\": {\"commover\": \"no\", \"__current_case__\": 0, \"command_override\": \"\", \"test_override\": \"\"}, \"deps\": {\"packages\": \"\", \"usescript\": {\"choosescript\": \"yes\", \"__current_case__\": 1, \"scriptrunner\": \"bash\", \"dynScript\": \"echo \\\"You chose $1\\\"\"}}, \"help_text\": \"**What it Does**\\nDemonstrates select parameters generated by ToolFactory forms\", \"install\": \"true\", \"io_param\": {\"ppass\": {\"parampass\": \"positional\", \"__current_case__\": 1, \"io\": {\"history_inputs\": [], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"select_out\", \"history_format\": \"txt\", \"history_CL\": \"STDOUT\", \"history_test\": \"diff:0\"}], \"collection_outputs\": []}, \"addparam\": {\"edit_params\": \"yes\", \"additional_parameters\": [{\"__index__\": 0, \"param_name\": \"choose\", \"ap_type\": {\"param_type\": \"selecttext\", \"__current_case__\": 4, \"selectTexts\": [{\"__index__\": 0, \"select_text\": \"one\", \"select_value\": \"won\"}, {\"__index__\": 1, \"select_text\": \"two\", \"select_value\": \"too\"}, {\"__index__\": 2, \"select_text\": \"three\", \"select_value\": \"free\"}]}, \"param_label\": \"Choose\", \"param_help\": \"\", \"param_CL\": \"1\", \"param_CLprefixed\": \"\", \"param_repeat\": \"false\"}]}}}, \"run_test\": \"true\", \"tool_desc\": \"ToolFactory select demonstration\", \"tool_name\": \"select_test\", \"tool_version\": \"0.01\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", | |
342 "tool_version": "2.00", | |
343 "type": "tool", | |
344 "uuid": "f9c9d681-b626-426c-b8fb-19503ea4571e", | |
345 "workflow_outputs": [ | |
346 { | |
347 "label": null, | |
348 "output_name": "new_tool", | |
349 "uuid": "3de506bf-9ad1-4d1f-be29-e42ae6f37a34" | |
350 } | |
351 ] | |
352 }, | |
353 "9": { | |
354 "annotation": "", | |
355 "content_id": null, | |
356 "errors": null, | |
357 "id": 9, | |
358 "input_connections": {}, | |
359 "inputs": [ | |
360 { | |
361 "description": "", | |
362 "name": "hello_lisp.txt" | |
363 } | |
364 ], | |
365 "label": "hello_lisp.txt", | |
366 "name": "Input dataset", | |
367 "outputs": [], | |
368 "position": { | |
369 "bottom": -4.1999969482421875, | |
370 "height": 61.80000305175781, | |
371 "left": 1364.5, | |
372 "right": 1564.5, | |
373 "top": -66, | |
374 "width": 200, | |
375 "x": 1364.5, | |
376 "y": -66 | |
377 }, | |
378 "tool_id": null, | |
379 "tool_state": "{\"optional\": false}", | |
380 "tool_version": null, | |
381 "type": "data_input", | |
382 "uuid": "4883c5d1-15ec-4595-8488-9c5ce453d632", | |
383 "workflow_outputs": [ | |
384 { | |
385 "label": null, | |
386 "output_name": "output", | |
387 "uuid": "9af42c99-a5bf-4835-8408-767d7273ceb0" | |
388 } | |
389 ] | |
390 }, | |
391 "10": { | |
392 "annotation": "", | |
393 "content_id": "rgtf2", | |
394 "errors": null, | |
395 "id": 10, | |
396 "input_connections": {}, | |
397 "inputs": [], | |
398 "label": null, | |
399 "name": "toolfactory", | |
400 "outputs": [ | |
401 { | |
402 "name": "new_tool", | |
403 "type": "toolshed.gz" | |
404 } | |
405 ], | |
406 "position": { | |
407 "bottom": -313.3999938964844, | |
408 "height": 102.60000610351562, | |
409 "left": 1364.5, | |
410 "right": 1564.5, | |
411 "top": -416, | |
412 "width": 200, | |
413 "x": 1364.5, | |
414 "y": -416 | |
415 }, | |
416 "post_job_actions": {}, | |
417 "tool_id": "rgtf2", | |
418 "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"citations\": [], \"cl_suffix\": \"\", \"cover\": {\"commover\": \"no\", \"__current_case__\": 0, \"command_override\": \"\", \"test_override\": \"\"}, \"deps\": {\"packages\": \"r-base\", \"usescript\": {\"choosescript\": \"yes\", \"__current_case__\": 1, \"scriptrunner\": \"Rscript\", \"dynScript\": \"# demo\\nargs = commandArgs(trailingOnly=TRUE)\\nif (length(args)==0) {\\n n_plots = 3 \\n} else {\\n n_plots = as.integer(args[1]) }\\ndir.create('plots')\\nfor (i in 1:n_plots) {\\n foo = runif(100)\\n bar = rnorm(100)\\n bar = foo + 0.05*bar\\n pdf(paste('plots/yet',i,\\\"anotherplot.pdf\\\",sep='_'))\\n plot(foo,bar,main=paste(\\\"Foo by Bar plot #\\\",i),col=\\\"maroon\\\", pch=3,cex=0.6)\\n dev.off()\\n foo = data.frame(a=runif(100),b=runif(100),c=runif(100),d=runif(100),e=runif(100),f=runif(100))\\n bar = as.matrix(foo)\\n pdf(paste('plots/yet',i,\\\"anotherheatmap.pdf\\\",sep='_'))\\n heatmap(bar,main='Random Heatmap')\\n dev.off()\\n}\\n\"}}, \"help_text\": \"**What it Does**\\nToolFactory demonstration of a collection to hide lots of outputs from a tool in a single history item to avoid clutter.\\nAs many random plots as you want.\\nViewable inside the resulting history collection\\nScript is responsible for writing all the appropriate outputs into a directory called the same name as the collection as shown here.\\nVery handy for things not useful downstream but useful for the user to review and study.\", \"install\": \"true\", \"io_param\": {\"ppass\": {\"parampass\": \"positional\", \"__current_case__\": 1, \"io\": {\"history_inputs\": [], \"history_outputs\": [], \"collection_outputs\": [{\"__index__\": 0, \"name\": \"plots\", \"kind\": \"list\", \"label\": \"Plots\", \"discover\": \"__name_and_ext__\"}]}, \"addparam\": {\"edit_params\": \"yes\", \"additional_parameters\": [{\"__index__\": 0, \"param_name\": \"nplot\", \"ap_type\": {\"param_type\": \"text\", \"__current_case__\": 0, \"param_value\": \"3\"}, \"param_label\": \"Number of random plots pairs to draw\", \"param_help\": \"\", \"param_CL\": \"1\", \"param_CLprefixed\": \"\", \"param_repeat\": \"false\"}]}}}, \"run_test\": \"true\", \"tool_desc\": \"Collection demonstration\", \"tool_name\": \"plotter\", \"tool_version\": \"0.01\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", | |
419 "tool_version": "2.00", | |
420 "type": "tool", | |
421 "uuid": "d00bd283-f69e-4537-9ccc-a5fa753e9f53", | |
422 "workflow_outputs": [ | |
423 { | |
424 "label": null, | |
425 "output_name": "new_tool", | |
426 "uuid": "4d769d8b-370c-444e-9245-2b2fa719ca99" | |
427 } | |
428 ] | |
429 }, | |
430 "11": { | |
431 "annotation": "", | |
432 "content_id": "rgtf2", | |
433 "errors": null, | |
434 "id": 11, | |
435 "input_connections": {}, | |
436 "inputs": [], | |
437 "label": null, | |
438 "name": "toolfactory", | |
439 "outputs": [ | |
440 { | |
441 "name": "new_tool", | |
442 "type": "toolshed.gz" | |
443 } | |
444 ], | |
445 "position": { | |
446 "bottom": -293, | |
447 "height": 123, | |
448 "left": 1642.5, | |
449 "right": 1842.5, | |
450 "top": -416, | |
451 "width": 200, | |
452 "x": 1642.5, | |
453 "y": -416 | |
454 }, | |
455 "post_job_actions": {}, | |
456 "tool_id": "rgtf2", | |
457 "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"citations\": [], \"cl_suffix\": \"\", \"cover\": {\"commover\": \"no\", \"__current_case__\": 0, \"command_override\": \"\", \"test_override\": \"\"}, \"deps\": {\"packages\": \"\", \"usescript\": {\"choosescript\": \"yes\", \"__current_case__\": 1, \"scriptrunner\": \"bash\", \"dynScript\": \"# pathetic attempt at a malicious script in Galaxy\\n# it fails because the job execution environment gives write access to few places\\necho \\\"ls -la\\\"\\nls -la\\ncd /\\necho \\\"ls -la after changing to /\\\"\\nls -la\\ntouch \\\"foo_was.here\\\"\\necho \\\"ls -la in root after touch foo_was.here - foo_was_not.here more like it\\\"\\nls -la\\n\"}}, \"help_text\": \"**What it Does**\\nShows what you can't do with a bash script\\nCheck the tool stderr - it isn't captured but should be. Send code.\\nResults vary - in a biocontainer, you are root so can do anything.\\nIn a normal Galaxy, not so much.\\nThis is a very interesting way to see what a tool can do on your machine.\", \"install\": \"true\", \"io_param\": {\"ppass\": {\"parampass\": \"positional\", \"__current_case__\": 1, \"io\": {\"history_inputs\": [], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"evil_script_output\", \"history_format\": \"txt\", \"history_CL\": \"STDOUT\", \"history_test\": \"sim_size:0.05\"}], \"collection_outputs\": []}, \"addparam\": {\"edit_params\": \"yes\", \"additional_parameters\": []}}}, \"run_test\": \"true\", \"tool_desc\": \"Tries some naughty things\", \"tool_name\": \"evil_script_that_fails\", \"tool_version\": \"0.01\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", | |
458 "tool_version": "2.00", | |
459 "type": "tool", | |
460 "uuid": "4c24a895-4cf6-43ec-8517-769974115809", | |
461 "workflow_outputs": [ | |
462 { | |
463 "label": null, | |
464 "output_name": "new_tool", | |
465 "uuid": "d19ecbb5-e61e-46f1-a37b-2b54e0eaba1b" | |
466 } | |
467 ] | |
468 }, | |
469 "12": { | |
470 "annotation": "", | |
471 "content_id": "rgtf2", | |
472 "errors": null, | |
473 "id": 12, | |
474 "input_connections": { | |
475 "io_param|ppass|io|history_inputs_0|input_files": { | |
476 "id": 0, | |
477 "output_name": "new_tool" | |
478 } | |
479 }, | |
480 "inputs": [], | |
481 "label": null, | |
482 "name": "toolfactory", | |
483 "outputs": [ | |
484 { | |
485 "name": "new_tool", | |
486 "type": "toolshed.gz" | |
487 } | |
488 ], | |
489 "position": { | |
490 "bottom": -96.60000610351562, | |
491 "height": 154.39999389648438, | |
492 "left": 530.5, | |
493 "right": 730.5, | |
494 "top": -251, | |
495 "width": 200, | |
496 "x": 530.5, | |
497 "y": -251 | |
498 }, | |
499 "post_job_actions": {}, | |
500 "tool_id": "rgtf2", | |
501 "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"citations\": [], \"cl_suffix\": \"\", \"cover\": {\"commover\": \"no\", \"__current_case__\": 0, \"command_override\": \"\", \"test_override\": \"\"}, \"deps\": {\"packages\": \"planemo=0.74.1\", \"usescript\": {\"choosescript\": \"yes\", \"__current_case__\": 1, \"scriptrunner\": \"bash\", \"dynScript\": \"cp $1 foo.tar \\ntar -xvf foo.tar\\nTOOLNAME=`find . -name \\\"*.xml\\\"`\\necho \\\"$$$$$TOOLNAME = $TOOLNAME\\\" > $2\\nplanemo lint $TOOLNAME >> $2\"}}, \"help_text\": \"**What it Does**\\nToolFactory demonstration script using bash to run planemo lint from a history tarball\", \"install\": \"true\", \"io_param\": {\"ppass\": {\"parampass\": \"positional\", \"__current_case__\": 1, \"io\": {\"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"tgz\", \"toolshed.gz\"], \"input_label\": \"Toolshed archive to be linted\", \"input_help\": \"\", \"input_CL\": \"1\", \"input_repeat\": \"false\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"lint_output\", \"history_format\": \"txt\", \"history_CL\": \"2\", \"history_test\": \"diff:5\"}], \"collection_outputs\": []}, \"addparam\": {\"edit_params\": \"yes\", \"additional_parameters\": []}}}, \"run_test\": \"true\", \"tool_desc\": \"Runs Planemo lint on any toolshed.gz file\", \"tool_name\": \"planemo_lint\", \"tool_version\": \"0.01\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", | |
502 "tool_version": "2.00", | |
503 "type": "tool", | |
504 "uuid": "170f36c8-8681-477e-ba9d-8e6c8965f735", | |
505 "workflow_outputs": [ | |
506 { | |
507 "label": null, | |
508 "output_name": "new_tool", | |
509 "uuid": "0e7fba79-fda8-44e7-912c-324f79d2caf2" | |
510 } | |
511 ] | |
512 }, | |
513 "13": { | |
514 "annotation": "", | |
515 "content_id": "rgtf2", | |
516 "errors": null, | |
517 "id": 13, | |
518 "input_connections": { | |
519 "io_param|ppass|io|history_inputs_0|input_files": { | |
520 "id": 2, | |
521 "output_name": "output" | |
522 }, | |
523 "io_param|ppass|io|history_inputs_1|input_files": { | |
524 "id": 1, | |
525 "output_name": "output" | |
526 } | |
527 }, | |
528 "inputs": [], | |
529 "label": null, | |
530 "name": "toolfactory", | |
531 "outputs": [ | |
532 { | |
533 "name": "new_tool", | |
534 "type": "toolshed.gz" | |
535 } | |
536 ], | |
537 "position": { | |
538 "bottom": 485.6000061035156, | |
539 "height": 225.60000610351562, | |
540 "left": 540.5, | |
541 "right": 740.5, | |
542 "top": 260, | |
543 "width": 200, | |
544 "x": 540.5, | |
545 "y": 260 | |
546 }, | |
547 "post_job_actions": {}, | |
548 "tool_id": "rgtf2", | |
549 "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"citations\": [], \"cl_suffix\": \"\", \"cover\": {\"commover\": \"yes\", \"__current_case__\": 1, \"command_override\": \"## Build reference\\n#set $reference_fasta_filename = \\\"localref.fa\\\"\\nln -s \\\"${ref_file}\\\" \\\"${reference_fasta_filename}\\\" ;\\nbwa index -a is \\\"${reference_fasta_filename}\\\" ;\\nbwa mem -t \\\"\\\\${GALAXY_SLOTS:-4}\\\" -v 1 \\\"${reference_fasta_filename}\\\" \\\"${fastq_input1}\\\" | samtools view -Sb - > temporary_bam_file.bam ;\\nsamtools sort -o \\\"${bwa_test_commover_bam_output}\\\" temporary_bam_file.bam\", \"test_override\": \"\"}, \"deps\": {\"packages\": \"bwa=0.7.15, samtools=1.3\", \"usescript\": {\"choosescript\": \"no\", \"__current_case__\": 0, \"dynScript\": \"\", \"scriptrunner\": \"\"}}, \"help_text\": \"**What it Does**\\nTrivial example from a Planemo documentation example\\nIt can be useful. It is sort of bash with substitutions from the tool form.\\nIf you need it, it's here.\", \"install\": \"true\", \"io_param\": {\"ppass\": {\"parampass\": \"argparse\", \"__current_case__\": 0, \"io\": {\"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"fasta\"], \"input_label\": \"Reference sequence to align reads\", \"input_help\": \"\", \"input_CL\": \"ref_file\", \"input_repeat\": \"false\"}, {\"__index__\": 1, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"fastqsanger\"], \"input_label\": \"Fastqsanger file containing reads to be mapped against reference\", \"input_help\": \"\", \"input_CL\": \"fastq_input1\", \"input_repeat\": \"false\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"bwa_test_commover_bam_output\", \"history_format\": \"bam\", \"history_CL\": \"\", \"history_test\": \"sim_size:0.1\"}], \"collection_outputs\": []}, \"addparam\": {\"edit_params\": \"yes\", \"additional_parameters\": []}}}, \"run_test\": \"true\", \"tool_desc\": \"Command over-ride demonstration\", \"tool_name\": \"bwa_test_command_override\", \"tool_version\": \"0.01\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", | |
550 "tool_version": "2.00", | |
551 "type": "tool", | |
552 "uuid": "43535a6f-1066-4b85-b347-f310858995a7", | |
553 "workflow_outputs": [ | |
554 { | |
555 "label": null, | |
556 "output_name": "new_tool", | |
557 "uuid": "a48f2e86-7017-47b8-8c2b-e81b25cf9590" | |
558 } | |
559 ] | |
560 }, | |
561 "14": { | |
562 "annotation": "", | |
563 "content_id": "rgtf2", | |
564 "errors": null, | |
565 "id": 14, | |
566 "input_connections": { | |
567 "io_param|ppass|io|history_inputs_0|input_files": { | |
568 "id": 2, | |
569 "output_name": "output" | |
570 }, | |
571 "io_param|ppass|io|history_inputs_1|input_files": { | |
572 "id": 1, | |
573 "output_name": "output" | |
574 } | |
575 }, | |
576 "inputs": [], | |
577 "label": null, | |
578 "name": "toolfactory", | |
579 "outputs": [ | |
580 { | |
581 "name": "new_tool", | |
582 "type": "toolshed.gz" | |
583 } | |
584 ], | |
585 "position": { | |
586 "bottom": 749.6000061035156, | |
587 "height": 225.60000610351562, | |
588 "left": 540.5, | |
589 "right": 740.5, | |
590 "top": 524, | |
591 "width": 200, | |
592 "x": 540.5, | |
593 "y": 524 | |
594 }, | |
595 "post_job_actions": {}, | |
596 "tool_id": "rgtf2", | |
597 "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"citations\": [], \"cl_suffix\": \"\", \"cover\": {\"commover\": \"no\", \"__current_case__\": 0, \"command_override\": \"\", \"test_override\": \"\"}, \"deps\": {\"packages\": \"bwa=0.7.15, samtools=1.3\", \"usescript\": {\"choosescript\": \"yes\", \"__current_case__\": 1, \"scriptrunner\": \"bash\", \"dynScript\": \"REFFILE=$1\\nFASTQ=$2\\nBAMOUT=$3\\nrm -f \\\"refalias\\\"\\nln -s \\\"$REFFILE\\\" \\\"refalias\\\"\\nbwa index -a is \\\"refalias\\\"\\nbwa mem -t \\\"2\\\" -v 1 \\\"refalias\\\" \\\"$FASTQ\\\" > tempsam\\nsamtools view -Sb tempsam > temporary_bam_file.bam\\nsamtools sort -o \\\"$BAMOUT\\\" temporary_bam_file.bam\\n\"}}, \"help_text\": \"**What it Does**\\nSame thing as the command over-ride version but using a bash script and passing parameters.\\nProbably more familiar to many non-Galaxy developers.\", \"install\": \"true\", \"io_param\": {\"ppass\": {\"parampass\": \"positional\", \"__current_case__\": 1, \"io\": {\"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"fasta\"], \"input_label\": \"Reference sequence to map reads against\", \"input_help\": \"\", \"input_CL\": \"1\", \"input_repeat\": \"false\"}, {\"__index__\": 1, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"fastq\"], \"input_label\": \"Reads to map\", \"input_help\": \"\", \"input_CL\": \"2\", \"input_repeat\": \"false\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"bwa_test_bash_output\", \"history_format\": \"bam\", \"history_CL\": \"3\", \"history_test\": \"sim_size:0.1\"}], \"collection_outputs\": []}, \"addparam\": {\"edit_params\": \"yes\", \"additional_parameters\": []}}}, \"run_test\": \"true\", \"tool_desc\": \"Bash script equivalent of the bwa command over-ride.\", \"tool_name\": \"bwa_test_toolfactory_positional_bash\", \"tool_version\": \"0.01\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", | |
598 "tool_version": "2.00", | |
599 "type": "tool", | |
600 "uuid": "dc44d183-23e3-45cc-978a-336280ec70a6", | |
601 "workflow_outputs": [ | |
602 { | |
603 "label": null, | |
604 "output_name": "new_tool", | |
605 "uuid": "c7943d13-c9c1-41ec-a055-a7cb1af39b6e" | |
606 } | |
607 ] | |
608 }, | |
609 "15": { | |
610 "annotation": "", | |
611 "content_id": "rgtf2", | |
612 "errors": null, | |
613 "id": 15, | |
614 "input_connections": { | |
615 "io_param|ppass|io|history_inputs_0|input_files": { | |
616 "id": 5, | |
617 "output_name": "output" | |
618 } | |
619 }, | |
620 "inputs": [], | |
621 "label": null, | |
622 "name": "toolfactory", | |
623 "outputs": [ | |
624 { | |
625 "name": "new_tool", | |
626 "type": "toolshed.gz" | |
627 } | |
628 ], | |
629 "position": { | |
630 "bottom": 91.39999389648438, | |
631 "height": 154.39999389648438, | |
632 "left": 1086.5, | |
633 "right": 1286.5, | |
634 "top": -63, | |
635 "width": 200, | |
636 "x": 1086.5, | |
637 "y": -63 | |
638 }, | |
639 "post_job_actions": {}, | |
640 "tool_id": "rgtf2", | |
641 "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"citations\": [], \"cl_suffix\": \"\", \"cover\": {\"commover\": \"no\", \"__current_case__\": 0, \"command_override\": \"\", \"test_override\": \"\"}, \"deps\": {\"packages\": \"perl\", \"usescript\": {\"choosescript\": \"yes\", \"__current_case__\": 1, \"scriptrunner\": \"perl\", \"dynScript\": \"#!/usr/bin/perl -w\\n\\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 );\"}}, \"help_text\": \"**What it Does**\\nPerl is also possible.\\nIt is also hard to maintain but we are a welcoming community so have it your way if you must.\", \"install\": \"true\", \"io_param\": {\"ppass\": {\"parampass\": \"positional\", \"__current_case__\": 1, \"io\": {\"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"fasta\"], \"input_label\": \"Input fasta for GC estimate\", \"input_help\": \"\", \"input_CL\": \"1\", \"input_repeat\": \"false\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"perl_gc_output\", \"history_format\": \"txt\", \"history_CL\": \"2\", \"history_test\": \"diff:0\"}], \"collection_outputs\": []}, \"addparam\": {\"edit_params\": \"yes\", \"additional_parameters\": []}}}, \"run_test\": \"true\", \"tool_desc\": \"Perl script demonstration\", \"tool_name\": \"perl_gc_counter\", \"tool_version\": \"0.01\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", | |
642 "tool_version": "2.00", | |
643 "type": "tool", | |
644 "uuid": "5b481ff7-6f1c-4184-8927-9cfdee297c26", | |
645 "workflow_outputs": [ | |
646 { | |
647 "label": null, | |
648 "output_name": "new_tool", | |
649 "uuid": "a3c89cac-ec48-4f1d-83f3-39d9a565b899" | |
650 } | |
651 ] | |
652 }, | |
653 "16": { | |
654 "annotation": "", | |
655 "content_id": "rgtf2", | |
656 "errors": null, | |
657 "id": 16, | |
658 "input_connections": { | |
659 "io_param|ppass|io|history_inputs_0|input_files": { | |
660 "id": 5, | |
661 "output_name": "output" | |
662 } | |
663 }, | |
664 "inputs": [], | |
665 "label": null, | |
666 "name": "toolfactory", | |
667 "outputs": [ | |
668 { | |
669 "name": "new_tool", | |
670 "type": "toolshed.gz" | |
671 } | |
672 ], | |
673 "position": { | |
674 "bottom": -100.60000610351562, | |
675 "height": 154.39999389648438, | |
676 "left": 1086.5, | |
677 "right": 1286.5, | |
678 "top": -255, | |
679 "width": 200, | |
680 "x": 1086.5, | |
681 "y": -255 | |
682 }, | |
683 "post_job_actions": {}, | |
684 "tool_id": "rgtf2", | |
685 "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"citations\": [], \"cl_suffix\": \"\", \"cover\": {\"commover\": \"no\", \"__current_case__\": 0, \"command_override\": \"\", \"test_override\": \"\"}, \"deps\": {\"packages\": \"sed\", \"usescript\": {\"choosescript\": \"no\", \"__current_case__\": 0, \"dynScript\": \"\", \"scriptrunner\": \"\"}}, \"help_text\": \"**What it Does**\", \"install\": \"true\", \"io_param\": {\"ppass\": {\"parampass\": \"positional\", \"__current_case__\": 1, \"io\": {\"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"txt\"], \"input_label\": \"Input text to be edited\", \"input_help\": \"\", \"input_CL\": \"2\", \"input_repeat\": \"false\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"sedtest_edited_output\", \"history_format\": \"txt\", \"history_CL\": \"STDOUT\", \"history_test\": \"diff:0\"}], \"collection_outputs\": []}, \"addparam\": {\"edit_params\": \"yes\", \"additional_parameters\": [{\"__index__\": 0, \"param_name\": \"sedstring\", \"ap_type\": {\"param_type\": \"text\", \"__current_case__\": 0, \"param_value\": \"s/A/Abjork!/g\"}, \"param_label\": \"sed edit string - subsitute some text for some other text globally\", \"param_help\": \"\", \"param_CL\": \"1\", \"param_CLprefixed\": \"\", \"param_repeat\": \"false\"}]}}}, \"run_test\": \"false\", \"tool_desc\": \"\", \"tool_name\": \"sedtest_toolshed\", \"tool_version\": \"0.01\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", | |
686 "tool_version": "2.00", | |
687 "type": "tool", | |
688 "uuid": "b468577d-7026-45bd-b36f-2e4e4e8110df", | |
689 "workflow_outputs": [ | |
690 { | |
691 "label": null, | |
692 "output_name": "new_tool", | |
693 "uuid": "7fd24cc1-bf68-4c55-b2b1-9f4383d0f211" | |
694 } | |
695 ] | |
696 }, | |
697 "17": { | |
698 "annotation": "", | |
699 "content_id": "rgtf2", | |
700 "errors": null, | |
701 "id": 17, | |
702 "input_connections": { | |
703 "io_param|ppass|io|history_inputs_0|input_files": { | |
704 "id": 7, | |
705 "output_name": "output" | |
706 } | |
707 }, | |
708 "inputs": [], | |
709 "label": null, | |
710 "name": "toolfactory", | |
711 "outputs": [ | |
712 { | |
713 "name": "new_tool", | |
714 "type": "toolshed.gz" | |
715 } | |
716 ], | |
717 "position": { | |
718 "bottom": 434.8000030517578, | |
719 "height": 174.8000030517578, | |
720 "left": 1096.5, | |
721 "right": 1296.5, | |
722 "top": 260, | |
723 "width": 200, | |
724 "x": 1096.5, | |
725 "y": 260 | |
726 }, | |
727 "post_job_actions": {}, | |
728 "tool_id": "rgtf2", | |
729 "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"citations\": [], \"cl_suffix\": \"\", \"cover\": {\"commover\": \"no\", \"__current_case__\": 0, \"command_override\": \"\", \"test_override\": \"\"}, \"deps\": {\"packages\": \"python\", \"usescript\": {\"choosescript\": \"yes\", \"__current_case__\": 1, \"scriptrunner\": \"python\", \"dynScript\": \"# reverse order of text by row\\nimport argparse\\nparser = argparse.ArgumentParser()\\na = parser.add_argument\\na('--infile',default='')\\na('--pyrevargparse_outfile',default=None)\\nargs = parser.parse_args()\\ninp = args.infile\\noutp = args.pyrevargparse_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()\"}}, \"help_text\": \"**What it Does**\\nDemonstrates argparse - script must correctly parse the names given on the form for this to work.\\nArgparse argument names your script should expect are constructed according to the parameter type - please read the tool form carefully.\", \"install\": \"true\", \"io_param\": {\"ppass\": {\"parampass\": \"argparse\", \"__current_case__\": 0, \"io\": {\"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"txt\"], \"input_label\": \"input file to be reversed\", \"input_help\": \"\", \"input_CL\": \"infile\", \"input_repeat\": \"false\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"pyrevargparse_outfile\", \"history_format\": \"txt\", \"history_CL\": \"pyrevargparse_outfile\", \"history_test\": \"diff:0\"}], \"collection_outputs\": []}, \"addparam\": {\"edit_params\": \"yes\", \"additional_parameters\": []}}}, \"run_test\": \"true\", \"tool_desc\": \"ToolFactory demonstration python script with argparse parameters\", \"tool_name\": \"pyrev_argparse_test\", \"tool_version\": \"0.01\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", | |
730 "tool_version": "2.00", | |
731 "type": "tool", | |
732 "uuid": "d86af8cb-0ed5-4581-9fce-87210c09230e", | |
733 "workflow_outputs": [ | |
734 { | |
735 "label": null, | |
736 "output_name": "new_tool", | |
737 "uuid": "10516bab-d1aa-4554-99c2-0ed6694dbdb6" | |
738 } | |
739 ] | |
740 }, | |
741 "18": { | |
742 "annotation": "", | |
743 "content_id": "rgtf2", | |
744 "errors": null, | |
745 "id": 18, | |
746 "input_connections": { | |
747 "io_param|ppass|io|history_inputs_0|input_files": { | |
748 "id": 7, | |
749 "output_name": "output" | |
750 } | |
751 }, | |
752 "inputs": [], | |
753 "label": null, | |
754 "name": "toolfactory", | |
755 "outputs": [ | |
756 { | |
757 "name": "new_tool", | |
758 "type": "toolshed.gz" | |
759 } | |
760 ], | |
761 "position": { | |
762 "bottom": 627.3999938964844, | |
763 "height": 154.39999389648438, | |
764 "left": 1096.5, | |
765 "right": 1296.5, | |
766 "top": 473, | |
767 "width": 200, | |
768 "x": 1096.5, | |
769 "y": 473 | |
770 }, | |
771 "post_job_actions": {}, | |
772 "tool_id": "rgtf2", | |
773 "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"citations\": [], \"cl_suffix\": \"\", \"cover\": {\"commover\": \"no\", \"__current_case__\": 0, \"command_override\": \"\", \"test_override\": \"\"}, \"deps\": {\"packages\": \"python\", \"usescript\": {\"choosescript\": \"yes\", \"__current_case__\": 1, \"scriptrunner\": \"python\", \"dynScript\": \"## reverse order of text by row\\n## ToolFactory demonstration\\n## positional parameters\\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()\"}}, \"help_text\": \"**What it Does**\", \"install\": \"true\", \"io_param\": {\"ppass\": {\"parampass\": \"positional\", \"__current_case__\": 1, \"io\": {\"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"txt\"], \"input_label\": \"Input text file to be reversed\", \"input_help\": \"\", \"input_CL\": \"1\", \"input_repeat\": \"false\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"pyrev_positionalparse_output\", \"history_format\": \"txt\", \"history_CL\": \"2\", \"history_test\": \"diff:0\"}], \"collection_outputs\": []}, \"addparam\": {\"edit_params\": \"yes\", \"additional_parameters\": []}}}, \"run_test\": \"true\", \"tool_desc\": \"\", \"tool_name\": \"pyrev_pos_test\", \"tool_version\": \"0.01\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", | |
774 "tool_version": "2.00", | |
775 "type": "tool", | |
776 "uuid": "5550dfd1-91ad-4c43-a852-0028da606c57", | |
777 "workflow_outputs": [ | |
778 { | |
779 "label": null, | |
780 "output_name": "new_tool", | |
781 "uuid": "2b413dbd-a019-4265-9d67-936519084f32" | |
782 } | |
783 ] | |
784 }, | |
785 "19": { | |
786 "annotation": "", | |
787 "content_id": "rgtf2", | |
788 "errors": null, | |
789 "id": 19, | |
790 "input_connections": { | |
791 "io_param|ppass|io|history_inputs_0|input_files": { | |
792 "id": 7, | |
793 "output_name": "output" | |
794 } | |
795 }, | |
796 "inputs": [], | |
797 "label": null, | |
798 "name": "toolfactory", | |
799 "outputs": [ | |
800 { | |
801 "name": "new_tool", | |
802 "type": "toolshed.gz" | |
803 } | |
804 ], | |
805 "position": { | |
806 "bottom": 819.3999938964844, | |
807 "height": 154.39999389648438, | |
808 "left": 1096.5, | |
809 "right": 1296.5, | |
810 "top": 665, | |
811 "width": 200, | |
812 "x": 1096.5, | |
813 "y": 665 | |
814 }, | |
815 "post_job_actions": {}, | |
816 "tool_id": "rgtf2", | |
817 "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"citations\": [], \"cl_suffix\": \"\", \"cover\": {\"commover\": \"no\", \"__current_case__\": 0, \"command_override\": \"\", \"test_override\": \"\"}, \"deps\": {\"packages\": \"\", \"usescript\": {\"choosescript\": \"yes\", \"__current_case__\": 1, \"scriptrunner\": \"bash\", \"dynScript\": \"tac | rev\"}}, \"help_text\": \"**What it Does**\", \"install\": \"true\", \"io_param\": {\"ppass\": {\"parampass\": \"0\", \"__current_case__\": 2, \"io\": {\"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"txt\"], \"input_label\": \"Input text file to be reversed\", \"input_help\": \"\", \"input_CL\": \"STDIN\", \"input_repeat\": \"false\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"tacrev_reversed_output\", \"history_format\": \"txt\", \"history_CL\": \"STDOUT\", \"history_test\": \"diff:0\"}], \"collection_outputs\": []}}}, \"run_test\": \"true\", \"tool_desc\": \"\", \"tool_name\": \"tacrev\", \"tool_version\": \"0.01\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", | |
818 "tool_version": "2.00", | |
819 "type": "tool", | |
820 "uuid": "e8b1cf36-b3d9-47a4-8c84-37e92f1722bf", | |
821 "workflow_outputs": [ | |
822 { | |
823 "label": null, | |
824 "output_name": "new_tool", | |
825 "uuid": "8edeb5fa-6c11-4508-9876-8e267ef78618" | |
826 } | |
827 ] | |
828 }, | |
829 "20": { | |
830 "annotation": "", | |
831 "content_id": "lisp_demo", | |
832 "errors": null, | |
833 "id": 20, | |
834 "input_connections": { | |
835 "SBCL_Lisp_script_to_execute": { | |
836 "id": 9, | |
837 "output_name": "output" | |
838 } | |
839 }, | |
840 "inputs": [], | |
841 "label": null, | |
842 "name": "lisp_demo", | |
843 "outputs": [ | |
844 { | |
845 "name": "lisp_out", | |
846 "type": "txt" | |
847 } | |
848 ], | |
849 "position": { | |
850 "bottom": 30.199996948242188, | |
851 "height": 93.19999694824219, | |
852 "left": 1642.5, | |
853 "right": 1842.5, | |
854 "top": -63, | |
855 "width": 200, | |
856 "x": 1642.5, | |
857 "y": -63 | |
858 }, | |
859 "post_job_actions": {}, | |
860 "tool_id": "lisp_demo", | |
861 "tool_state": "{\"SBCL_Lisp_script_to_execute\": {\"__class__\": \"ConnectedValue\"}, \"__input_ext\": \"txt\", \"chromInfo\": \"/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", | |
862 "tool_version": "0.01", | |
863 "type": "tool", | |
864 "uuid": "ced975df-0054-4642-b831-665f6f88d73d", | |
865 "workflow_outputs": [ | |
866 { | |
867 "label": null, | |
868 "output_name": "lisp_out", | |
869 "uuid": "c0bc1652-93ae-481f-8ad2-47d45b5b4326" | |
870 } | |
871 ] | |
872 }, | |
873 "21": { | |
874 "annotation": "", | |
875 "content_id": "rgtf2", | |
876 "errors": null, | |
877 "id": 21, | |
878 "input_connections": { | |
879 "io_param|ppass|io|history_inputs_0|input_files": { | |
880 "id": 9, | |
881 "output_name": "output" | |
882 } | |
883 }, | |
884 "inputs": [], | |
885 "label": null, | |
886 "name": "toolfactory", | |
887 "outputs": [ | |
888 { | |
889 "name": "new_tool", | |
890 "type": "toolshed.gz" | |
891 } | |
892 ], | |
893 "position": { | |
894 "bottom": 222.39999389648438, | |
895 "height": 154.39999389648438, | |
896 "left": 1642.5, | |
897 "right": 1842.5, | |
898 "top": 68, | |
899 "width": 200, | |
900 "x": 1642.5, | |
901 "y": 68 | |
902 }, | |
903 "post_job_actions": {}, | |
904 "tool_id": "rgtf2", | |
905 "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"citations\": [], \"cl_suffix\": \"\", \"cover\": {\"commover\": \"no\", \"__current_case__\": 0, \"command_override\": \"\", \"test_override\": \"\"}, \"deps\": {\"packages\": \"sbcl\", \"usescript\": {\"choosescript\": \"yes\", \"__current_case__\": 1, \"scriptrunner\": \"bash\", \"dynScript\": \"sbcl --script $1\"}}, \"help_text\": \"**What it Does**\\nSays hello world using a trivial lisp script.\\nIt will actually try to run any text file you like from your history but likely fail unless they happen to be valid lisp according to the interpreter dependency.\\nThese demonstrations show what is possible, not what is sensible.\\nPlease don't expose this anywhere.\", \"install\": \"true\", \"io_param\": {\"ppass\": {\"parampass\": \"positional\", \"__current_case__\": 1, \"io\": {\"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"txt\"], \"input_label\": \"SBCL Lisp script to execute\", \"input_help\": \"Provide a script in lisp to be interpreted by SBCL\", \"input_CL\": \"1\", \"input_repeat\": \"false\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"lisp_out\", \"history_format\": \"txt\", \"history_CL\": \"STDOUT\", \"history_test\": \"diff:0\"}], \"collection_outputs\": []}, \"addparam\": {\"edit_params\": \"yes\", \"additional_parameters\": []}}}, \"run_test\": \"true\", \"tool_desc\": \"ToolFactory demonstration using Lisp for the nostalgic.\", \"tool_name\": \"lisp_demo\", \"tool_version\": \"0.01\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", | |
906 "tool_version": "2.00", | |
907 "type": "tool", | |
908 "uuid": "0241fb8d-f8c7-43c2-953c-95a45d4af735", | |
909 "workflow_outputs": [ | |
910 { | |
911 "label": null, | |
912 "output_name": "new_tool", | |
913 "uuid": "789a7cc9-bea5-45d2-ae2e-7026265fc835" | |
914 } | |
915 ] | |
916 }, | |
917 "22": { | |
918 "annotation": "", | |
919 "content_id": "rgtf2", | |
920 "errors": null, | |
921 "id": 22, | |
922 "input_connections": { | |
923 "io_param|ppass|io|history_inputs_0|input_files": { | |
924 "id": 9, | |
925 "output_name": "output" | |
926 } | |
927 }, | |
928 "inputs": [], | |
929 "label": null, | |
930 "name": "toolfactory", | |
931 "outputs": [ | |
932 { | |
933 "name": "new_tool", | |
934 "type": "toolshed.gz" | |
935 } | |
936 ], | |
937 "position": { | |
938 "bottom": -100.60000610351562, | |
939 "height": 154.39999389648438, | |
940 "left": 1642.5, | |
941 "right": 1842.5, | |
942 "top": -255, | |
943 "width": 200, | |
944 "x": 1642.5, | |
945 "y": -255 | |
946 }, | |
947 "post_job_actions": {}, | |
948 "tool_id": "rgtf2", | |
949 "tool_state": "{\"__input_ext\": \"input\", \"__workflow_invocation_uuid__\": \"dbb99db2a98811ebbc9e0242ac1b0004\", \"chromInfo\": \"/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"citations\": [], \"cl_prefix\": \"\", \"cl_suffix\": \"\", \"cover\": {\"commover\": \"no\", \"__current_case__\": 0, \"command_override\": \"\", \"test_override\": \"\"}, \"deps\": {\"packages\": \"planemo\", \"usescript\": {\"choosescript\": \"yes\", \"__current_case__\": 1, \"scriptrunner\": \"bash\", \"dynScript\": \"cp $1 foo.tar.gz\\ntar -xvf foo.tar.gz\\nTOOLNAME=`find . -name \\\"*.xml\\\"`\\necho \\\"TOOLNAME = $TOOLNAME\\\"\\nplanemo test --test_output $2 $TOOLNAME\"}}, \"help_text\": \"**What it Does**\", \"install\": \"false\", \"io_param\": {\"ppass\": {\"parampass\": \"positional\", \"__current_case__\": 1, \"io\": {\"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"tgz\"], \"input_label\": \"ToolFactory toolshed archive from the history to test\", \"input_help\": \"\", \"input_CL\": \"1\", \"input_repeat\": \"false\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"planemo_test_output\", \"history_format\": \"txt\", \"history_CL\": \"2\", \"history_test\": \"sim_size:0.05\"}], \"collection_outputs\": []}, \"addparam\": {\"edit_params\": \"yes\", \"additional_parameters\": []}}}, \"make\": {\"makeMode\": {\"__current_case__\": 1, \"citations\": [], \"galaxy_apikey\": \"\", \"galaxy_url\": \"\", \"help_text\": \"**What it Does**\\n\\nRuns planemo test on a ToolFactory or other toolshed archive\", \"make_Tool\": \"gentest\", \"tool_desc\": \"Tests a ToolFactory tool\", \"tool_version\": \"0.01\", \"toolshed_apikey\": \"\", \"toolshed_url\": \"\"}}, \"run_test\": \"true\", \"tool_desc\": \"\", \"tool_name\": \"planemo_test\", \"tool_version\": \"0.01\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", | |
950 "tool_version": "2.00", | |
951 "type": "tool", | |
952 "uuid": "2d826252-a3fc-4e99-8791-2908926cda10", | |
953 "workflow_outputs": [ | |
954 { | |
955 "label": null, | |
956 "output_name": "new_tool", | |
957 "uuid": "659cabcf-e7db-4b61-8e3c-097a1d25c336" | |
958 } | |
959 ] | |
960 } | |
961 }, | |
962 "tags": [], | |
963 "uuid": "308d4b95-f04f-49b0-8674-f0ddf0587850", | |
964 "version": 1 | |
965 } |