Mercurial > repos > galaxyp > apostl
comparison Galaxy-Workflow-APOSTL_Workflow.ga @ 0:0b6e9cc279fc draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/apostl commit 79aa418c07e54b5f152681452767f7c8a40379b6
author | galaxyp |
---|---|
date | Thu, 11 May 2017 14:52:17 -0400 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:0b6e9cc279fc |
---|---|
1 { | |
2 "a_galaxy_workflow": "true", | |
3 "annotation": "", | |
4 "format-version": "0.1", | |
5 "name": "APOSTL Workflow", | |
6 "steps": { | |
7 "0": { | |
8 "annotation": "", | |
9 "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.2.1", | |
10 "id": 0, | |
11 "input_connections": {}, | |
12 "inputs": [], | |
13 "label": null, | |
14 "name": "Protein Database Downloader", | |
15 "outputs": [ | |
16 { | |
17 "name": "output_database", | |
18 "type": "fasta" | |
19 } | |
20 ], | |
21 "position": { | |
22 "left": 119, | |
23 "top": 428 | |
24 }, | |
25 "post_job_actions": { | |
26 "HideDatasetActionoutput_database": { | |
27 "action_arguments": {}, | |
28 "action_type": "HideDatasetAction", | |
29 "output_name": "output_database" | |
30 }, | |
31 "RenameDatasetActionoutput_database": { | |
32 "action_arguments": { | |
33 "newname": "Human SwissProt dB April 12, 2017" | |
34 }, | |
35 "action_type": "RenameDatasetAction", | |
36 "output_name": "output_database" | |
37 } | |
38 }, | |
39 "tool_errors": null, | |
40 "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.2.1", | |
41 "tool_shed_repository": { | |
42 "changeset_revision": "19ee2e85931a", | |
43 "name": "dbbuilder", | |
44 "owner": "galaxyp", | |
45 "tool_shed": "toolshed.g2.bx.psu.edu" | |
46 }, | |
47 "tool_state": "{\"source\": \"{\\\"url\\\": \\\"https://raw.githubusercontent.com/pravs3683/databases/master/uniprot_swissprot_12April2017.fasta\\\", \\\"from\\\": \\\"url\\\", \\\"__current_case__\\\": 2}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", | |
48 "tool_version": "0.2.1", | |
49 "type": "tool", | |
50 "uuid": "799e95bc-23e4-4c7b-b182-83c321892d42", | |
51 "workflow_outputs": [] | |
52 }, | |
53 "1": { | |
54 "annotation": "", | |
55 "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.2.1", | |
56 "id": 1, | |
57 "input_connections": {}, | |
58 "inputs": [], | |
59 "label": null, | |
60 "name": "Protein Database Downloader", | |
61 "outputs": [ | |
62 { | |
63 "name": "output_database", | |
64 "type": "fasta" | |
65 } | |
66 ], | |
67 "position": { | |
68 "left": 124, | |
69 "top": 532 | |
70 }, | |
71 "post_job_actions": { | |
72 "RenameDatasetActionoutput_database": { | |
73 "action_arguments": { | |
74 "newname": "cRAP dB (common Repository of Adventitious Proteins database)" | |
75 }, | |
76 "action_type": "RenameDatasetAction", | |
77 "output_name": "output_database" | |
78 } | |
79 }, | |
80 "tool_errors": null, | |
81 "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.2.1", | |
82 "tool_shed_repository": { | |
83 "changeset_revision": "19ee2e85931a", | |
84 "name": "dbbuilder", | |
85 "owner": "galaxyp", | |
86 "tool_shed": "toolshed.g2.bx.psu.edu" | |
87 }, | |
88 "tool_state": "{\"source\": \"{\\\"from\\\": \\\"cRAP\\\", \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", | |
89 "tool_version": "0.2.1", | |
90 "type": "tool", | |
91 "uuid": "2f17233d-f5aa-4f18-85ed-d6568fafb0e5", | |
92 "workflow_outputs": [] | |
93 }, | |
94 "2": { | |
95 "annotation": "", | |
96 "content_id": null, | |
97 "id": 2, | |
98 "input_connections": {}, | |
99 "inputs": [ | |
100 { | |
101 "description": "", | |
102 "name": "04112012_JL_HCC827_EGFR_TAP_1_run1.MGF" | |
103 } | |
104 ], | |
105 "label": null, | |
106 "name": "Input dataset", | |
107 "outputs": [], | |
108 "position": { | |
109 "left": 179, | |
110 "top": 653.5 | |
111 }, | |
112 "tool_errors": null, | |
113 "tool_id": null, | |
114 "tool_state": "{\"name\": \"04112012_JL_HCC827_EGFR_TAP_1_run1.MGF\"}", | |
115 "tool_version": null, | |
116 "type": "data_input", | |
117 "uuid": "a13b4ae7-cc8a-4d7a-9a97-3186076a7447", | |
118 "workflow_outputs": [ | |
119 { | |
120 "label": null, | |
121 "output_name": "output", | |
122 "uuid": "66b3639f-eba8-4c7a-9835-2819252a29dd" | |
123 } | |
124 ] | |
125 }, | |
126 "3": { | |
127 "annotation": "", | |
128 "content_id": null, | |
129 "id": 3, | |
130 "input_connections": {}, | |
131 "inputs": [ | |
132 { | |
133 "description": "", | |
134 "name": "04112012_JL_HCC827_EGFR_TAP_2_run1.MGF" | |
135 } | |
136 ], | |
137 "label": null, | |
138 "name": "Input dataset", | |
139 "outputs": [], | |
140 "position": { | |
141 "left": 187, | |
142 "top": 813.5 | |
143 }, | |
144 "tool_errors": null, | |
145 "tool_id": null, | |
146 "tool_state": "{\"name\": \"04112012_JL_HCC827_EGFR_TAP_2_run1.MGF\"}", | |
147 "tool_version": null, | |
148 "type": "data_input", | |
149 "uuid": "f47afc6b-3c68-46d2-a12b-5797abeb2301", | |
150 "workflow_outputs": [ | |
151 { | |
152 "label": null, | |
153 "output_name": "output", | |
154 "uuid": "31877ead-047e-4b8d-8075-4855d2c04aa3" | |
155 } | |
156 ] | |
157 }, | |
158 "4": { | |
159 "annotation": "", | |
160 "content_id": null, | |
161 "id": 4, | |
162 "input_connections": {}, | |
163 "inputs": [ | |
164 { | |
165 "description": "", | |
166 "name": "04112012_JL_HCC827_GFP_TAP_1_run1.MGF" | |
167 } | |
168 ], | |
169 "label": null, | |
170 "name": "Input dataset", | |
171 "outputs": [], | |
172 "position": { | |
173 "left": 192, | |
174 "top": 975.5 | |
175 }, | |
176 "tool_errors": null, | |
177 "tool_id": null, | |
178 "tool_state": "{\"name\": \"04112012_JL_HCC827_GFP_TAP_1_run1.MGF\"}", | |
179 "tool_version": null, | |
180 "type": "data_input", | |
181 "uuid": "7d1127e1-b214-4e82-9512-f64eecde737e", | |
182 "workflow_outputs": [ | |
183 { | |
184 "label": null, | |
185 "output_name": "output", | |
186 "uuid": "ebb996dc-618a-4171-93a7-01e1f1ea6733" | |
187 } | |
188 ] | |
189 }, | |
190 "5": { | |
191 "annotation": "", | |
192 "content_id": null, | |
193 "id": 5, | |
194 "input_connections": {}, | |
195 "inputs": [ | |
196 { | |
197 "description": "", | |
198 "name": "04112012_JL_HCC827_GFP_TAP_2_run1.MGF" | |
199 } | |
200 ], | |
201 "label": null, | |
202 "name": "Input dataset", | |
203 "outputs": [], | |
204 "position": { | |
205 "left": 201, | |
206 "top": 1158.5 | |
207 }, | |
208 "tool_errors": null, | |
209 "tool_id": null, | |
210 "tool_state": "{\"name\": \"04112012_JL_HCC827_GFP_TAP_2_run1.MGF\"}", | |
211 "tool_version": null, | |
212 "type": "data_input", | |
213 "uuid": "c20424e0-300b-49cf-952f-0d44ec3f7b0e", | |
214 "workflow_outputs": [ | |
215 { | |
216 "label": null, | |
217 "output_name": "output", | |
218 "uuid": "a287a9cf-dbb7-4958-b834-0f4ba4d455e1" | |
219 } | |
220 ] | |
221 }, | |
222 "6": { | |
223 "annotation": "", | |
224 "content_id": null, | |
225 "id": 6, | |
226 "input_connections": {}, | |
227 "inputs": [ | |
228 { | |
229 "description": "", | |
230 "name": "Bait File (bait.txt)" | |
231 } | |
232 ], | |
233 "label": null, | |
234 "name": "Input dataset", | |
235 "outputs": [], | |
236 "position": { | |
237 "left": 1357, | |
238 "top": 272.5 | |
239 }, | |
240 "tool_errors": null, | |
241 "tool_id": null, | |
242 "tool_state": "{\"name\": \"Bait File (bait.txt)\"}", | |
243 "tool_version": null, | |
244 "type": "data_input", | |
245 "uuid": "ef95a348-a99b-4a24-a760-8896f74d2430", | |
246 "workflow_outputs": [ | |
247 { | |
248 "label": null, | |
249 "output_name": "output", | |
250 "uuid": "bb47856c-4c16-410e-a666-3e8ca7845f96" | |
251 } | |
252 ] | |
253 }, | |
254 "7": { | |
255 "annotation": "", | |
256 "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.0", | |
257 "id": 7, | |
258 "input_connections": { | |
259 "inputs_0|input": { | |
260 "id": 0, | |
261 "output_name": "output_database" | |
262 }, | |
263 "inputs_1|input": { | |
264 "id": 1, | |
265 "output_name": "output_database" | |
266 } | |
267 }, | |
268 "inputs": [], | |
269 "label": null, | |
270 "name": "FASTA Merge Files and Filter Unique Sequences", | |
271 "outputs": [ | |
272 { | |
273 "name": "output", | |
274 "type": "fasta" | |
275 } | |
276 ], | |
277 "position": { | |
278 "left": 530, | |
279 "top": 434 | |
280 }, | |
281 "post_job_actions": { | |
282 "HideDatasetActionoutput": { | |
283 "action_arguments": {}, | |
284 "action_type": "HideDatasetAction", | |
285 "output_name": "output" | |
286 } | |
287 }, | |
288 "tool_errors": null, | |
289 "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.0", | |
290 "tool_shed_repository": { | |
291 "changeset_revision": "2904d46167da", | |
292 "name": "fasta_merge_files_and_filter_unique_sequences", | |
293 "owner": "galaxyp", | |
294 "tool_shed": "toolshed.g2.bx.psu.edu" | |
295 }, | |
296 "tool_state": "{\"inputs\": \"[{\\\"__index__\\\": 0, \\\"input\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}, {\\\"__index__\\\": 1, \\\"input\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}]\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", | |
297 "tool_version": "1.0", | |
298 "type": "tool", | |
299 "uuid": "51cd4b88-e1a1-4508-8379-45a60e22b407", | |
300 "workflow_outputs": [] | |
301 }, | |
302 "8": { | |
303 "annotation": "", | |
304 "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.2.11", | |
305 "id": 8, | |
306 "input_connections": { | |
307 "input_database": { | |
308 "id": 7, | |
309 "output_name": "output" | |
310 }, | |
311 "peak_lists": { | |
312 "id": 2, | |
313 "output_name": "output" | |
314 } | |
315 }, | |
316 "inputs": [ | |
317 { | |
318 "description": "runtime parameter for tool Search GUI", | |
319 "name": "peak_lists" | |
320 }, | |
321 { | |
322 "description": "runtime parameter for tool Search GUI", | |
323 "name": "input_database" | |
324 } | |
325 ], | |
326 "label": null, | |
327 "name": "Search GUI", | |
328 "outputs": [ | |
329 { | |
330 "name": "searchgui_results", | |
331 "type": "searchgui_archive" | |
332 } | |
333 ], | |
334 "position": { | |
335 "left": 560, | |
336 "top": 617 | |
337 }, | |
338 "post_job_actions": { | |
339 "RenameDatasetActionsearchgui_results": { | |
340 "action_arguments": { | |
341 "newname": "04112012_JL_HCC827_EGFR_TAP_1_run1 (SearchGUI)" | |
342 }, | |
343 "action_type": "RenameDatasetAction", | |
344 "output_name": "searchgui_results" | |
345 } | |
346 }, | |
347 "tool_errors": null, | |
348 "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.2.11", | |
349 "tool_shed_repository": { | |
350 "changeset_revision": "7f2aeb19650f", | |
351 "name": "peptideshaker", | |
352 "owner": "galaxyp", | |
353 "tool_shed": "toolshed.g2.bx.psu.edu" | |
354 }, | |
355 "tool_state": "{\"__page__\": 0, \"peak_lists\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"protein_database_options\": \"{\\\"update_gene_mapping\\\": \\\"false\\\", \\\"use_gene_mapping\\\": \\\"false\\\", \\\"create_decoy\\\": \\\"true\\\"}\", \"protein_digest_options\": \"{\\\"digestion\\\": {\\\"cleavage\\\": \\\"default\\\", \\\"missed_cleavages\\\": \\\"2\\\", \\\"__current_case__\\\": 0}}\", \"__rerun_remap_job_id__\": null, \"search_engines_options\": \"{\\\"engines\\\": [\\\"X!Tandem\\\", \\\"MSGF\\\", \\\"OMSSA\\\"]}\", \"precursor_options\": \"{\\\"forward_ion\\\": \\\"b\\\", \\\"max_charge\\\": \\\"6\\\", \\\"max_isotope\\\": \\\"1\\\", \\\"precursor_ion_tol_units\\\": \\\"1\\\", \\\"min_isotope\\\": \\\"0\\\", \\\"fragment_tol\\\": \\\"0.5\\\", \\\"min_charge\\\": \\\"2\\\", \\\"reverse_ion\\\": \\\"y\\\", \\\"precursor_ion_tol\\\": \\\"10.0\\\"}\", \"advanced_options\": \"{\\\"searchgui_advanced\\\": {\\\"searchgui_advanced_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}, \\\"xtandem\\\": {\\\"xtandem_quick_acetyl\\\": \\\"false\\\", \\\"xtandem_min_peaks\\\": \\\"15\\\", \\\"xtandem_quick_pyro\\\": \\\"false\\\", \\\"xtandem_stp_bias\\\": \\\"false\\\", \\\"xtandem_advanced\\\": \\\"yes\\\", \\\"xtandem_dynamic_range\\\": \\\"100\\\", \\\"xtandem_min_prec_mass\\\": \\\"200\\\", \\\"xtandem_output_sequences\\\": \\\"false\\\", \\\"__current_case__\\\": 1, \\\"xtandem_output_proteins\\\": \\\"false\\\", \\\"xtandem_output_spectra\\\": \\\"true\\\", \\\"xtandem_npeaks\\\": \\\"50\\\", \\\"xtandem_noise_suppr\\\": \\\"true\\\", \\\"xtandem_min_frag_mz\\\": \\\"200\\\", \\\"xtandem_evalue\\\": \\\"100.0\\\", \\\"xtandem_refine\\\": {\\\"xtandem_refine_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 0}}, \\\"msgf\\\": {\\\"msgf_advanced\\\": \\\"no\\\", \\\"__current_case__\\\": 0}, \\\"directtag\\\": {\\\"directtag_advanced\\\": \\\"no\\\", \\\"__current_case__\\\": 0}, \\\"comet\\\": {\\\"comet_advanced\\\": \\\"no\\\", \\\"__current_case__\\\": 0}, \\\"omssa\\\": {\\\"omssa_advanced\\\": \\\"no\\\", \\\"__current_case__\\\": 0}, \\\"novor\\\": {\\\"novor_advanced\\\": \\\"no\\\", \\\"__current_case__\\\": 0}}\", \"input_database\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"protein_modification_options\": \"{\\\"variable_modifications\\\": [\\\"Acetylation of protein N-term\\\", \\\"Oxidation of M\\\"], \\\"fixed_modifications\\\": [\\\"Carbamidomethylation of C\\\"]}\"}", | |
356 "tool_version": "3.2.11", | |
357 "type": "tool", | |
358 "uuid": "d8caa9eb-db82-4010-af2b-051332a0a685", | |
359 "workflow_outputs": [ | |
360 { | |
361 "label": null, | |
362 "output_name": "searchgui_results", | |
363 "uuid": "d60f276c-405e-4153-b582-4548d8362629" | |
364 } | |
365 ] | |
366 }, | |
367 "9": { | |
368 "annotation": "", | |
369 "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.2.11", | |
370 "id": 9, | |
371 "input_connections": { | |
372 "input_database": { | |
373 "id": 7, | |
374 "output_name": "output" | |
375 }, | |
376 "peak_lists": { | |
377 "id": 3, | |
378 "output_name": "output" | |
379 } | |
380 }, | |
381 "inputs": [ | |
382 { | |
383 "description": "runtime parameter for tool Search GUI", | |
384 "name": "peak_lists" | |
385 }, | |
386 { | |
387 "description": "runtime parameter for tool Search GUI", | |
388 "name": "input_database" | |
389 } | |
390 ], | |
391 "label": null, | |
392 "name": "Search GUI", | |
393 "outputs": [ | |
394 { | |
395 "name": "searchgui_results", | |
396 "type": "searchgui_archive" | |
397 } | |
398 ], | |
399 "position": { | |
400 "left": 570, | |
401 "top": 781 | |
402 }, | |
403 "post_job_actions": { | |
404 "RenameDatasetActionsearchgui_results": { | |
405 "action_arguments": { | |
406 "newname": "04112012_JL_HCC827_EGFR_TAP_2_run1 (SearchGUI Results)" | |
407 }, | |
408 "action_type": "RenameDatasetAction", | |
409 "output_name": "searchgui_results" | |
410 } | |
411 }, | |
412 "tool_errors": null, | |
413 "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.2.11", | |
414 "tool_shed_repository": { | |
415 "changeset_revision": "7f2aeb19650f", | |
416 "name": "peptideshaker", | |
417 "owner": "galaxyp", | |
418 "tool_shed": "toolshed.g2.bx.psu.edu" | |
419 }, | |
420 "tool_state": "{\"__page__\": 0, \"peak_lists\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"protein_database_options\": \"{\\\"update_gene_mapping\\\": \\\"false\\\", \\\"use_gene_mapping\\\": \\\"false\\\", \\\"create_decoy\\\": \\\"true\\\"}\", \"protein_digest_options\": \"{\\\"digestion\\\": {\\\"cleavage\\\": \\\"default\\\", \\\"missed_cleavages\\\": \\\"2\\\", \\\"__current_case__\\\": 0}}\", \"__rerun_remap_job_id__\": null, \"search_engines_options\": \"{\\\"engines\\\": [\\\"X!Tandem\\\", \\\"MSGF\\\", \\\"OMSSA\\\"]}\", \"precursor_options\": \"{\\\"forward_ion\\\": \\\"b\\\", \\\"max_charge\\\": \\\"6\\\", \\\"max_isotope\\\": \\\"1\\\", \\\"precursor_ion_tol_units\\\": \\\"1\\\", \\\"min_isotope\\\": \\\"0\\\", \\\"fragment_tol\\\": \\\"0.5\\\", \\\"min_charge\\\": \\\"2\\\", \\\"reverse_ion\\\": \\\"y\\\", \\\"precursor_ion_tol\\\": \\\"10.0\\\"}\", \"advanced_options\": \"{\\\"searchgui_advanced\\\": {\\\"searchgui_advanced_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}, \\\"xtandem\\\": {\\\"xtandem_quick_acetyl\\\": \\\"false\\\", \\\"xtandem_min_peaks\\\": \\\"15\\\", \\\"xtandem_quick_pyro\\\": \\\"false\\\", \\\"xtandem_stp_bias\\\": \\\"false\\\", \\\"xtandem_advanced\\\": \\\"yes\\\", \\\"xtandem_dynamic_range\\\": \\\"100\\\", \\\"xtandem_min_prec_mass\\\": \\\"200\\\", \\\"xtandem_output_sequences\\\": \\\"false\\\", \\\"__current_case__\\\": 1, \\\"xtandem_output_proteins\\\": \\\"false\\\", \\\"xtandem_output_spectra\\\": \\\"true\\\", \\\"xtandem_npeaks\\\": \\\"50\\\", \\\"xtandem_noise_suppr\\\": \\\"true\\\", \\\"xtandem_min_frag_mz\\\": \\\"200\\\", \\\"xtandem_evalue\\\": \\\"100.0\\\", \\\"xtandem_refine\\\": {\\\"xtandem_refine_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 0}}, \\\"msgf\\\": {\\\"msgf_advanced\\\": \\\"no\\\", \\\"__current_case__\\\": 0}, \\\"directtag\\\": {\\\"directtag_advanced\\\": \\\"no\\\", \\\"__current_case__\\\": 0}, \\\"comet\\\": {\\\"comet_advanced\\\": \\\"no\\\", \\\"__current_case__\\\": 0}, \\\"omssa\\\": {\\\"omssa_advanced\\\": \\\"no\\\", \\\"__current_case__\\\": 0}, \\\"novor\\\": {\\\"novor_advanced\\\": \\\"no\\\", \\\"__current_case__\\\": 0}}\", \"input_database\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"protein_modification_options\": \"{\\\"variable_modifications\\\": [\\\"Acetylation of protein N-term\\\", \\\"Oxidation of M\\\"], \\\"fixed_modifications\\\": [\\\"Carbamidomethylation of C\\\"]}\"}", | |
421 "tool_version": "3.2.11", | |
422 "type": "tool", | |
423 "uuid": "7c36f1c8-09db-46e5-beae-28fc17b82f4e", | |
424 "workflow_outputs": [ | |
425 { | |
426 "label": null, | |
427 "output_name": "searchgui_results", | |
428 "uuid": "59c10d40-c56e-48a8-a65f-2a57a52f3d2d" | |
429 } | |
430 ] | |
431 }, | |
432 "10": { | |
433 "annotation": "", | |
434 "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.2.11", | |
435 "id": 10, | |
436 "input_connections": { | |
437 "input_database": { | |
438 "id": 7, | |
439 "output_name": "output" | |
440 }, | |
441 "peak_lists": { | |
442 "id": 4, | |
443 "output_name": "output" | |
444 } | |
445 }, | |
446 "inputs": [ | |
447 { | |
448 "description": "runtime parameter for tool Search GUI", | |
449 "name": "peak_lists" | |
450 }, | |
451 { | |
452 "description": "runtime parameter for tool Search GUI", | |
453 "name": "input_database" | |
454 } | |
455 ], | |
456 "label": null, | |
457 "name": "Search GUI", | |
458 "outputs": [ | |
459 { | |
460 "name": "searchgui_results", | |
461 "type": "searchgui_archive" | |
462 } | |
463 ], | |
464 "position": { | |
465 "left": 577, | |
466 "top": 954 | |
467 }, | |
468 "post_job_actions": { | |
469 "RenameDatasetActionsearchgui_results": { | |
470 "action_arguments": { | |
471 "newname": "04112012_JL_HCC827_GFP_TAP_1_run1 (SearchGUI Results)" | |
472 }, | |
473 "action_type": "RenameDatasetAction", | |
474 "output_name": "searchgui_results" | |
475 } | |
476 }, | |
477 "tool_errors": null, | |
478 "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.2.11", | |
479 "tool_shed_repository": { | |
480 "changeset_revision": "7f2aeb19650f", | |
481 "name": "peptideshaker", | |
482 "owner": "galaxyp", | |
483 "tool_shed": "toolshed.g2.bx.psu.edu" | |
484 }, | |
485 "tool_state": "{\"__page__\": 0, \"peak_lists\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"protein_database_options\": \"{\\\"update_gene_mapping\\\": \\\"false\\\", \\\"use_gene_mapping\\\": \\\"false\\\", \\\"create_decoy\\\": \\\"true\\\"}\", \"protein_digest_options\": \"{\\\"digestion\\\": {\\\"cleavage\\\": \\\"default\\\", \\\"missed_cleavages\\\": \\\"2\\\", \\\"__current_case__\\\": 0}}\", \"__rerun_remap_job_id__\": null, \"search_engines_options\": \"{\\\"engines\\\": [\\\"X!Tandem\\\", \\\"MSGF\\\", \\\"OMSSA\\\"]}\", \"precursor_options\": \"{\\\"forward_ion\\\": \\\"b\\\", \\\"max_charge\\\": \\\"6\\\", \\\"max_isotope\\\": \\\"1\\\", \\\"precursor_ion_tol_units\\\": \\\"1\\\", \\\"min_isotope\\\": \\\"0\\\", \\\"fragment_tol\\\": \\\"0.5\\\", \\\"min_charge\\\": \\\"2\\\", \\\"reverse_ion\\\": \\\"y\\\", \\\"precursor_ion_tol\\\": \\\"10.0\\\"}\", \"advanced_options\": \"{\\\"searchgui_advanced\\\": {\\\"searchgui_advanced_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}, \\\"xtandem\\\": {\\\"xtandem_quick_acetyl\\\": \\\"false\\\", \\\"xtandem_min_peaks\\\": \\\"15\\\", \\\"xtandem_quick_pyro\\\": \\\"false\\\", \\\"xtandem_stp_bias\\\": \\\"false\\\", \\\"xtandem_advanced\\\": \\\"yes\\\", \\\"xtandem_dynamic_range\\\": \\\"100\\\", \\\"xtandem_min_prec_mass\\\": \\\"200\\\", \\\"xtandem_output_sequences\\\": \\\"false\\\", \\\"__current_case__\\\": 1, \\\"xtandem_output_proteins\\\": \\\"false\\\", \\\"xtandem_output_spectra\\\": \\\"true\\\", \\\"xtandem_npeaks\\\": \\\"50\\\", \\\"xtandem_noise_suppr\\\": \\\"true\\\", \\\"xtandem_min_frag_mz\\\": \\\"200\\\", \\\"xtandem_evalue\\\": \\\"100.0\\\", \\\"xtandem_refine\\\": {\\\"xtandem_refine_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 0}}, \\\"msgf\\\": {\\\"msgf_advanced\\\": \\\"no\\\", \\\"__current_case__\\\": 0}, \\\"directtag\\\": {\\\"directtag_advanced\\\": \\\"no\\\", \\\"__current_case__\\\": 0}, \\\"comet\\\": {\\\"comet_advanced\\\": \\\"no\\\", \\\"__current_case__\\\": 0}, \\\"omssa\\\": {\\\"omssa_advanced\\\": \\\"no\\\", \\\"__current_case__\\\": 0}, \\\"novor\\\": {\\\"novor_advanced\\\": \\\"no\\\", \\\"__current_case__\\\": 0}}\", \"input_database\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"protein_modification_options\": \"{\\\"variable_modifications\\\": [\\\"Acetylation of protein N-term\\\", \\\"Oxidation of M\\\"], \\\"fixed_modifications\\\": [\\\"Carbamidomethylation of C\\\"]}\"}", | |
486 "tool_version": "3.2.11", | |
487 "type": "tool", | |
488 "uuid": "cf449d43-a257-4f63-8a52-cccee9f7aa9c", | |
489 "workflow_outputs": [ | |
490 { | |
491 "label": null, | |
492 "output_name": "searchgui_results", | |
493 "uuid": "f0b50cb3-9c6a-42f2-a2ef-8d4c0b2d427b" | |
494 } | |
495 ] | |
496 }, | |
497 "11": { | |
498 "annotation": "", | |
499 "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.2.11", | |
500 "id": 11, | |
501 "input_connections": { | |
502 "input_database": { | |
503 "id": 7, | |
504 "output_name": "output" | |
505 }, | |
506 "peak_lists": { | |
507 "id": 5, | |
508 "output_name": "output" | |
509 } | |
510 }, | |
511 "inputs": [ | |
512 { | |
513 "description": "runtime parameter for tool Search GUI", | |
514 "name": "peak_lists" | |
515 }, | |
516 { | |
517 "description": "runtime parameter for tool Search GUI", | |
518 "name": "input_database" | |
519 } | |
520 ], | |
521 "label": null, | |
522 "name": "Search GUI", | |
523 "outputs": [ | |
524 { | |
525 "name": "searchgui_results", | |
526 "type": "searchgui_archive" | |
527 } | |
528 ], | |
529 "position": { | |
530 "left": 583, | |
531 "top": 1127 | |
532 }, | |
533 "post_job_actions": { | |
534 "RenameDatasetActionsearchgui_results": { | |
535 "action_arguments": { | |
536 "newname": "04112012_JL_HCC827_GFP_TAP_2_run1 (SearchGUI Results)" | |
537 }, | |
538 "action_type": "RenameDatasetAction", | |
539 "output_name": "searchgui_results" | |
540 } | |
541 }, | |
542 "tool_errors": null, | |
543 "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.2.11", | |
544 "tool_shed_repository": { | |
545 "changeset_revision": "7f2aeb19650f", | |
546 "name": "peptideshaker", | |
547 "owner": "galaxyp", | |
548 "tool_shed": "toolshed.g2.bx.psu.edu" | |
549 }, | |
550 "tool_state": "{\"__page__\": 0, \"peak_lists\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"protein_database_options\": \"{\\\"update_gene_mapping\\\": \\\"false\\\", \\\"use_gene_mapping\\\": \\\"false\\\", \\\"create_decoy\\\": \\\"true\\\"}\", \"protein_digest_options\": \"{\\\"digestion\\\": {\\\"cleavage\\\": \\\"default\\\", \\\"missed_cleavages\\\": \\\"2\\\", \\\"__current_case__\\\": 0}}\", \"__rerun_remap_job_id__\": null, \"search_engines_options\": \"{\\\"engines\\\": [\\\"X!Tandem\\\", \\\"MSGF\\\", \\\"OMSSA\\\"]}\", \"precursor_options\": \"{\\\"forward_ion\\\": \\\"b\\\", \\\"max_charge\\\": \\\"6\\\", \\\"max_isotope\\\": \\\"1\\\", \\\"precursor_ion_tol_units\\\": \\\"1\\\", \\\"min_isotope\\\": \\\"0\\\", \\\"fragment_tol\\\": \\\"0.5\\\", \\\"min_charge\\\": \\\"2\\\", \\\"reverse_ion\\\": \\\"y\\\", \\\"precursor_ion_tol\\\": \\\"10.0\\\"}\", \"advanced_options\": \"{\\\"searchgui_advanced\\\": {\\\"searchgui_advanced_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}, \\\"xtandem\\\": {\\\"xtandem_quick_acetyl\\\": \\\"false\\\", \\\"xtandem_min_peaks\\\": \\\"15\\\", \\\"xtandem_quick_pyro\\\": \\\"false\\\", \\\"xtandem_stp_bias\\\": \\\"false\\\", \\\"xtandem_advanced\\\": \\\"yes\\\", \\\"xtandem_dynamic_range\\\": \\\"100\\\", \\\"xtandem_min_prec_mass\\\": \\\"200\\\", \\\"xtandem_output_sequences\\\": \\\"false\\\", \\\"__current_case__\\\": 1, \\\"xtandem_output_proteins\\\": \\\"false\\\", \\\"xtandem_output_spectra\\\": \\\"true\\\", \\\"xtandem_npeaks\\\": \\\"50\\\", \\\"xtandem_noise_suppr\\\": \\\"true\\\", \\\"xtandem_min_frag_mz\\\": \\\"200\\\", \\\"xtandem_evalue\\\": \\\"100.0\\\", \\\"xtandem_refine\\\": {\\\"xtandem_refine_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 0}}, \\\"msgf\\\": {\\\"msgf_advanced\\\": \\\"no\\\", \\\"__current_case__\\\": 0}, \\\"directtag\\\": {\\\"directtag_advanced\\\": \\\"no\\\", \\\"__current_case__\\\": 0}, \\\"comet\\\": {\\\"comet_advanced\\\": \\\"no\\\", \\\"__current_case__\\\": 0}, \\\"omssa\\\": {\\\"omssa_advanced\\\": \\\"no\\\", \\\"__current_case__\\\": 0}, \\\"novor\\\": {\\\"novor_advanced\\\": \\\"no\\\", \\\"__current_case__\\\": 0}}\", \"input_database\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"protein_modification_options\": \"{\\\"variable_modifications\\\": [\\\"Acetylation of protein N-term\\\", \\\"Oxidation of M\\\"], \\\"fixed_modifications\\\": [\\\"Carbamidomethylation of C\\\"]}\"}", | |
551 "tool_version": "3.2.11", | |
552 "type": "tool", | |
553 "uuid": "016a97dc-03c8-409d-8168-d13bd2923672", | |
554 "workflow_outputs": [ | |
555 { | |
556 "label": null, | |
557 "output_name": "searchgui_results", | |
558 "uuid": "38d8b5ae-bc12-4297-a3e4-0ada3dc20422" | |
559 } | |
560 ] | |
561 }, | |
562 "12": { | |
563 "annotation": "", | |
564 "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.3", | |
565 "id": 12, | |
566 "input_connections": { | |
567 "searchgui_input": { | |
568 "id": 8, | |
569 "output_name": "searchgui_results" | |
570 } | |
571 }, | |
572 "inputs": [ | |
573 { | |
574 "description": "runtime parameter for tool Peptide Shaker", | |
575 "name": "searchgui_input" | |
576 } | |
577 ], | |
578 "label": null, | |
579 "name": "Peptide Shaker", | |
580 "outputs": [ | |
581 { | |
582 "name": "mzidentML", | |
583 "type": "mzid" | |
584 }, | |
585 { | |
586 "name": "output_cps", | |
587 "type": "peptideshaker_archive" | |
588 }, | |
589 { | |
590 "name": "output_zip", | |
591 "type": "zip" | |
592 }, | |
593 { | |
594 "name": "output_certificate", | |
595 "type": "txt" | |
596 }, | |
597 { | |
598 "name": "output_hierarchical", | |
599 "type": "tabular" | |
600 }, | |
601 { | |
602 "name": "output_psm_phosphorylation", | |
603 "type": "tabular" | |
604 }, | |
605 { | |
606 "name": "output_psm", | |
607 "type": "tabular" | |
608 }, | |
609 { | |
610 "name": "output_extended_psm", | |
611 "type": "tabular" | |
612 }, | |
613 { | |
614 "name": "output_peptides_phosphorylation", | |
615 "type": "tabular" | |
616 }, | |
617 { | |
618 "name": "output_peptides", | |
619 "type": "tabular" | |
620 }, | |
621 { | |
622 "name": "output_proteins_phosphorylation", | |
623 "type": "tabular" | |
624 }, | |
625 { | |
626 "name": "output_proteins", | |
627 "type": "tabular" | |
628 } | |
629 ], | |
630 "position": { | |
631 "left": 1015, | |
632 "top": 187 | |
633 }, | |
634 "post_job_actions": { | |
635 "HideDatasetActionmzidentML": { | |
636 "action_arguments": {}, | |
637 "action_type": "HideDatasetAction", | |
638 "output_name": "mzidentML" | |
639 }, | |
640 "HideDatasetActionoutput_cps": { | |
641 "action_arguments": {}, | |
642 "action_type": "HideDatasetAction", | |
643 "output_name": "output_cps" | |
644 }, | |
645 "HideDatasetActionoutput_extended_psm": { | |
646 "action_arguments": {}, | |
647 "action_type": "HideDatasetAction", | |
648 "output_name": "output_extended_psm" | |
649 }, | |
650 "HideDatasetActionoutput_hierarchical": { | |
651 "action_arguments": {}, | |
652 "action_type": "HideDatasetAction", | |
653 "output_name": "output_hierarchical" | |
654 }, | |
655 "HideDatasetActionoutput_peptides": { | |
656 "action_arguments": {}, | |
657 "action_type": "HideDatasetAction", | |
658 "output_name": "output_peptides" | |
659 }, | |
660 "HideDatasetActionoutput_peptides_phosphorylation": { | |
661 "action_arguments": {}, | |
662 "action_type": "HideDatasetAction", | |
663 "output_name": "output_peptides_phosphorylation" | |
664 }, | |
665 "HideDatasetActionoutput_proteins_phosphorylation": { | |
666 "action_arguments": {}, | |
667 "action_type": "HideDatasetAction", | |
668 "output_name": "output_proteins_phosphorylation" | |
669 }, | |
670 "HideDatasetActionoutput_psm_phosphorylation": { | |
671 "action_arguments": {}, | |
672 "action_type": "HideDatasetAction", | |
673 "output_name": "output_psm_phosphorylation" | |
674 }, | |
675 "HideDatasetActionoutput_zip": { | |
676 "action_arguments": {}, | |
677 "action_type": "HideDatasetAction", | |
678 "output_name": "output_zip" | |
679 }, | |
680 "RenameDatasetActionoutput_certificate": { | |
681 "action_arguments": { | |
682 "newname": "PeptideShaker Summary Report: 04112012_JL_HCC827_EGFR_TAP_1_run1" | |
683 }, | |
684 "action_type": "RenameDatasetAction", | |
685 "output_name": "output_certificate" | |
686 }, | |
687 "RenameDatasetActionoutput_proteins": { | |
688 "action_arguments": { | |
689 "newname": "PeptideShaker Protein Report: 04112012_JL_HCC827_EGFR_TAP_1_run1" | |
690 }, | |
691 "action_type": "RenameDatasetAction", | |
692 "output_name": "output_proteins" | |
693 }, | |
694 "RenameDatasetActionoutput_psm": { | |
695 "action_arguments": { | |
696 "newname": "PeptideShaker PSM Report: 04112012_JL_HCC827_EGFR_TAP_1_run1" | |
697 }, | |
698 "action_type": "RenameDatasetAction", | |
699 "output_name": "output_psm" | |
700 } | |
701 }, | |
702 "tool_errors": null, | |
703 "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.3", | |
704 "tool_shed_repository": { | |
705 "changeset_revision": "7f2aeb19650f", | |
706 "name": "peptideshaker", | |
707 "owner": "galaxyp", | |
708 "tool_shed": "toolshed.g2.bx.psu.edu" | |
709 }, | |
710 "tool_state": "{\"__page__\": 0, \"processing_options\": \"{\\\"peptide_fdr\\\": \\\"5.0\\\", \\\"protein_fdr\\\": \\\"5.0\\\", \\\"protein_fraction_mw_confidence\\\": \\\"95.0\\\", \\\"ptm_score\\\": {\\\"ptm_score_selector\\\": \\\"0\\\", \\\"__current_case__\\\": 0}, \\\"ptm_alignment\\\": \\\"true\\\", \\\"__current_case__\\\": 1, \\\"processing_options_selector\\\": \\\"yes\\\", \\\"psm_fdr\\\": \\\"5.0\\\"}\", \"__rerun_remap_job_id__\": null, \"filtering_options\": \"{\\\"max_precursor_error_type\\\": \\\"1\\\", \\\"filtering_options_selector\\\": \\\"yes\\\", \\\"__current_case__\\\": 1, \\\"max_precursor_error\\\": \\\"10.0\\\", \\\"exclude_unknown_ptms\\\": \\\"true\\\", \\\"max_peptide_length\\\": \\\"75\\\", \\\"min_peptide_length\\\": \\\"6\\\"}\", \"searchgui_input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"contact_options\": \"{\\\"contact_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"outputs\": \"[\\\"3\\\", \\\"7\\\", \\\"0\\\"]\", \"include_sequences\": \"\\\"false\\\"\"}", | |
711 "tool_version": "1.16.3", | |
712 "type": "tool", | |
713 "uuid": "6b56c797-782d-4f2f-b145-d752755cef44", | |
714 "workflow_outputs": [ | |
715 { | |
716 "label": null, | |
717 "output_name": "output_proteins", | |
718 "uuid": "0978c289-4a5b-41fc-80b5-e23e9745e9a3" | |
719 }, | |
720 { | |
721 "label": null, | |
722 "output_name": "output_psm", | |
723 "uuid": "450b67c3-e6c6-4fd7-bc4b-272ef4b3e3a5" | |
724 }, | |
725 { | |
726 "label": null, | |
727 "output_name": "output_certificate", | |
728 "uuid": "98aa4a9c-3a06-4ddd-8fa4-3978102875ac" | |
729 } | |
730 ] | |
731 }, | |
732 "13": { | |
733 "annotation": "", | |
734 "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.3", | |
735 "id": 13, | |
736 "input_connections": { | |
737 "searchgui_input": { | |
738 "id": 9, | |
739 "output_name": "searchgui_results" | |
740 } | |
741 }, | |
742 "inputs": [ | |
743 { | |
744 "description": "runtime parameter for tool Peptide Shaker", | |
745 "name": "searchgui_input" | |
746 } | |
747 ], | |
748 "label": null, | |
749 "name": "Peptide Shaker", | |
750 "outputs": [ | |
751 { | |
752 "name": "mzidentML", | |
753 "type": "mzid" | |
754 }, | |
755 { | |
756 "name": "output_cps", | |
757 "type": "peptideshaker_archive" | |
758 }, | |
759 { | |
760 "name": "output_zip", | |
761 "type": "zip" | |
762 }, | |
763 { | |
764 "name": "output_certificate", | |
765 "type": "txt" | |
766 }, | |
767 { | |
768 "name": "output_hierarchical", | |
769 "type": "tabular" | |
770 }, | |
771 { | |
772 "name": "output_psm_phosphorylation", | |
773 "type": "tabular" | |
774 }, | |
775 { | |
776 "name": "output_psm", | |
777 "type": "tabular" | |
778 }, | |
779 { | |
780 "name": "output_extended_psm", | |
781 "type": "tabular" | |
782 }, | |
783 { | |
784 "name": "output_peptides_phosphorylation", | |
785 "type": "tabular" | |
786 }, | |
787 { | |
788 "name": "output_peptides", | |
789 "type": "tabular" | |
790 }, | |
791 { | |
792 "name": "output_proteins_phosphorylation", | |
793 "type": "tabular" | |
794 }, | |
795 { | |
796 "name": "output_proteins", | |
797 "type": "tabular" | |
798 } | |
799 ], | |
800 "position": { | |
801 "left": 959, | |
802 "top": 313 | |
803 }, | |
804 "post_job_actions": { | |
805 "HideDatasetActionmzidentML": { | |
806 "action_arguments": {}, | |
807 "action_type": "HideDatasetAction", | |
808 "output_name": "mzidentML" | |
809 }, | |
810 "HideDatasetActionoutput_cps": { | |
811 "action_arguments": {}, | |
812 "action_type": "HideDatasetAction", | |
813 "output_name": "output_cps" | |
814 }, | |
815 "HideDatasetActionoutput_extended_psm": { | |
816 "action_arguments": {}, | |
817 "action_type": "HideDatasetAction", | |
818 "output_name": "output_extended_psm" | |
819 }, | |
820 "HideDatasetActionoutput_hierarchical": { | |
821 "action_arguments": {}, | |
822 "action_type": "HideDatasetAction", | |
823 "output_name": "output_hierarchical" | |
824 }, | |
825 "HideDatasetActionoutput_peptides": { | |
826 "action_arguments": {}, | |
827 "action_type": "HideDatasetAction", | |
828 "output_name": "output_peptides" | |
829 }, | |
830 "HideDatasetActionoutput_peptides_phosphorylation": { | |
831 "action_arguments": {}, | |
832 "action_type": "HideDatasetAction", | |
833 "output_name": "output_peptides_phosphorylation" | |
834 }, | |
835 "HideDatasetActionoutput_proteins_phosphorylation": { | |
836 "action_arguments": {}, | |
837 "action_type": "HideDatasetAction", | |
838 "output_name": "output_proteins_phosphorylation" | |
839 }, | |
840 "HideDatasetActionoutput_psm_phosphorylation": { | |
841 "action_arguments": {}, | |
842 "action_type": "HideDatasetAction", | |
843 "output_name": "output_psm_phosphorylation" | |
844 }, | |
845 "HideDatasetActionoutput_zip": { | |
846 "action_arguments": {}, | |
847 "action_type": "HideDatasetAction", | |
848 "output_name": "output_zip" | |
849 }, | |
850 "RenameDatasetActionoutput_certificate": { | |
851 "action_arguments": { | |
852 "newname": "PeptideShaker Summary Report: 04112012_JL_HCC827_EGFR_TAP_2_run1" | |
853 }, | |
854 "action_type": "RenameDatasetAction", | |
855 "output_name": "output_certificate" | |
856 }, | |
857 "RenameDatasetActionoutput_proteins": { | |
858 "action_arguments": { | |
859 "newname": "PeptideShaker Protein Report: 04112012_JL_HCC827_EGFR_TAP_2_run1" | |
860 }, | |
861 "action_type": "RenameDatasetAction", | |
862 "output_name": "output_proteins" | |
863 }, | |
864 "RenameDatasetActionoutput_psm": { | |
865 "action_arguments": { | |
866 "newname": "PeptideShaker PSM Report: 04112012_JL_HCC827_EGFR_TAP_2_run1" | |
867 }, | |
868 "action_type": "RenameDatasetAction", | |
869 "output_name": "output_psm" | |
870 } | |
871 }, | |
872 "tool_errors": null, | |
873 "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.3", | |
874 "tool_shed_repository": { | |
875 "changeset_revision": "7f2aeb19650f", | |
876 "name": "peptideshaker", | |
877 "owner": "galaxyp", | |
878 "tool_shed": "toolshed.g2.bx.psu.edu" | |
879 }, | |
880 "tool_state": "{\"__page__\": 0, \"processing_options\": \"{\\\"peptide_fdr\\\": \\\"5.0\\\", \\\"protein_fdr\\\": \\\"5.0\\\", \\\"protein_fraction_mw_confidence\\\": \\\"95.0\\\", \\\"ptm_score\\\": {\\\"ptm_score_selector\\\": \\\"0\\\", \\\"__current_case__\\\": 0}, \\\"ptm_alignment\\\": \\\"true\\\", \\\"__current_case__\\\": 1, \\\"processing_options_selector\\\": \\\"yes\\\", \\\"psm_fdr\\\": \\\"5.0\\\"}\", \"__rerun_remap_job_id__\": null, \"filtering_options\": \"{\\\"max_precursor_error_type\\\": \\\"1\\\", \\\"filtering_options_selector\\\": \\\"yes\\\", \\\"__current_case__\\\": 1, \\\"max_precursor_error\\\": \\\"10.0\\\", \\\"exclude_unknown_ptms\\\": \\\"true\\\", \\\"max_peptide_length\\\": \\\"75\\\", \\\"min_peptide_length\\\": \\\"6\\\"}\", \"searchgui_input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"contact_options\": \"{\\\"contact_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"outputs\": \"[\\\"3\\\", \\\"7\\\", \\\"0\\\"]\", \"include_sequences\": \"\\\"false\\\"\"}", | |
881 "tool_version": "1.16.3", | |
882 "type": "tool", | |
883 "uuid": "ba7821bf-c567-4fb4-803e-84608b3e3caa", | |
884 "workflow_outputs": [ | |
885 { | |
886 "label": null, | |
887 "output_name": "output_proteins", | |
888 "uuid": "34edffd6-1c64-450c-8e73-76470502022c" | |
889 }, | |
890 { | |
891 "label": null, | |
892 "output_name": "output_psm", | |
893 "uuid": "11989f3d-2a42-491d-88e5-0bb0792a8fb1" | |
894 }, | |
895 { | |
896 "label": null, | |
897 "output_name": "output_certificate", | |
898 "uuid": "79441850-bf30-441a-82e5-ecaebf4f0659" | |
899 } | |
900 ] | |
901 }, | |
902 "14": { | |
903 "annotation": "", | |
904 "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.3", | |
905 "id": 14, | |
906 "input_connections": { | |
907 "searchgui_input": { | |
908 "id": 10, | |
909 "output_name": "searchgui_results" | |
910 } | |
911 }, | |
912 "inputs": [ | |
913 { | |
914 "description": "runtime parameter for tool Peptide Shaker", | |
915 "name": "searchgui_input" | |
916 } | |
917 ], | |
918 "label": null, | |
919 "name": "Peptide Shaker", | |
920 "outputs": [ | |
921 { | |
922 "name": "mzidentML", | |
923 "type": "mzid" | |
924 }, | |
925 { | |
926 "name": "output_cps", | |
927 "type": "peptideshaker_archive" | |
928 }, | |
929 { | |
930 "name": "output_zip", | |
931 "type": "zip" | |
932 }, | |
933 { | |
934 "name": "output_certificate", | |
935 "type": "txt" | |
936 }, | |
937 { | |
938 "name": "output_hierarchical", | |
939 "type": "tabular" | |
940 }, | |
941 { | |
942 "name": "output_psm_phosphorylation", | |
943 "type": "tabular" | |
944 }, | |
945 { | |
946 "name": "output_psm", | |
947 "type": "tabular" | |
948 }, | |
949 { | |
950 "name": "output_extended_psm", | |
951 "type": "tabular" | |
952 }, | |
953 { | |
954 "name": "output_peptides_phosphorylation", | |
955 "type": "tabular" | |
956 }, | |
957 { | |
958 "name": "output_peptides", | |
959 "type": "tabular" | |
960 }, | |
961 { | |
962 "name": "output_proteins_phosphorylation", | |
963 "type": "tabular" | |
964 }, | |
965 { | |
966 "name": "output_proteins", | |
967 "type": "tabular" | |
968 } | |
969 ], | |
970 "position": { | |
971 "left": 905, | |
972 "top": 545 | |
973 }, | |
974 "post_job_actions": { | |
975 "HideDatasetActionmzidentML": { | |
976 "action_arguments": {}, | |
977 "action_type": "HideDatasetAction", | |
978 "output_name": "mzidentML" | |
979 }, | |
980 "HideDatasetActionoutput_cps": { | |
981 "action_arguments": {}, | |
982 "action_type": "HideDatasetAction", | |
983 "output_name": "output_cps" | |
984 }, | |
985 "HideDatasetActionoutput_extended_psm": { | |
986 "action_arguments": {}, | |
987 "action_type": "HideDatasetAction", | |
988 "output_name": "output_extended_psm" | |
989 }, | |
990 "HideDatasetActionoutput_hierarchical": { | |
991 "action_arguments": {}, | |
992 "action_type": "HideDatasetAction", | |
993 "output_name": "output_hierarchical" | |
994 }, | |
995 "HideDatasetActionoutput_peptides": { | |
996 "action_arguments": {}, | |
997 "action_type": "HideDatasetAction", | |
998 "output_name": "output_peptides" | |
999 }, | |
1000 "HideDatasetActionoutput_peptides_phosphorylation": { | |
1001 "action_arguments": {}, | |
1002 "action_type": "HideDatasetAction", | |
1003 "output_name": "output_peptides_phosphorylation" | |
1004 }, | |
1005 "HideDatasetActionoutput_proteins_phosphorylation": { | |
1006 "action_arguments": {}, | |
1007 "action_type": "HideDatasetAction", | |
1008 "output_name": "output_proteins_phosphorylation" | |
1009 }, | |
1010 "HideDatasetActionoutput_psm_phosphorylation": { | |
1011 "action_arguments": {}, | |
1012 "action_type": "HideDatasetAction", | |
1013 "output_name": "output_psm_phosphorylation" | |
1014 }, | |
1015 "HideDatasetActionoutput_zip": { | |
1016 "action_arguments": {}, | |
1017 "action_type": "HideDatasetAction", | |
1018 "output_name": "output_zip" | |
1019 }, | |
1020 "RenameDatasetActionoutput_certificate": { | |
1021 "action_arguments": { | |
1022 "newname": "PeptideShaker Summary Report: 04112012_JL_HCC827_GFP_TAP_1_run1" | |
1023 }, | |
1024 "action_type": "RenameDatasetAction", | |
1025 "output_name": "output_certificate" | |
1026 }, | |
1027 "RenameDatasetActionoutput_proteins": { | |
1028 "action_arguments": { | |
1029 "newname": "PeptideShaker Protein Report: 04112012_JL_HCC827_GFP_TAP_1_run1" | |
1030 }, | |
1031 "action_type": "RenameDatasetAction", | |
1032 "output_name": "output_proteins" | |
1033 }, | |
1034 "RenameDatasetActionoutput_psm": { | |
1035 "action_arguments": { | |
1036 "newname": "PeptideShaker PSM Report: 04112012_JL_HCC827_GFP_TAP_1_run1" | |
1037 }, | |
1038 "action_type": "RenameDatasetAction", | |
1039 "output_name": "output_psm" | |
1040 } | |
1041 }, | |
1042 "tool_errors": null, | |
1043 "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.3", | |
1044 "tool_shed_repository": { | |
1045 "changeset_revision": "7f2aeb19650f", | |
1046 "name": "peptideshaker", | |
1047 "owner": "galaxyp", | |
1048 "tool_shed": "toolshed.g2.bx.psu.edu" | |
1049 }, | |
1050 "tool_state": "{\"__page__\": 0, \"processing_options\": \"{\\\"peptide_fdr\\\": \\\"5.0\\\", \\\"protein_fdr\\\": \\\"5.0\\\", \\\"protein_fraction_mw_confidence\\\": \\\"95.0\\\", \\\"ptm_score\\\": {\\\"ptm_score_selector\\\": \\\"0\\\", \\\"__current_case__\\\": 0}, \\\"ptm_alignment\\\": \\\"true\\\", \\\"__current_case__\\\": 1, \\\"processing_options_selector\\\": \\\"yes\\\", \\\"psm_fdr\\\": \\\"5.0\\\"}\", \"__rerun_remap_job_id__\": null, \"filtering_options\": \"{\\\"max_precursor_error_type\\\": \\\"1\\\", \\\"filtering_options_selector\\\": \\\"yes\\\", \\\"__current_case__\\\": 1, \\\"max_precursor_error\\\": \\\"10.0\\\", \\\"exclude_unknown_ptms\\\": \\\"true\\\", \\\"max_peptide_length\\\": \\\"75\\\", \\\"min_peptide_length\\\": \\\"6\\\"}\", \"searchgui_input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"contact_options\": \"{\\\"contact_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"outputs\": \"[\\\"3\\\", \\\"7\\\", \\\"0\\\"]\", \"include_sequences\": \"\\\"false\\\"\"}", | |
1051 "tool_version": "1.16.3", | |
1052 "type": "tool", | |
1053 "uuid": "bb1a7289-73ec-4c0e-bb89-0f7547483867", | |
1054 "workflow_outputs": [ | |
1055 { | |
1056 "label": null, | |
1057 "output_name": "output_certificate", | |
1058 "uuid": "e878162e-ddc9-4751-a8a0-d80394e675e4" | |
1059 }, | |
1060 { | |
1061 "label": null, | |
1062 "output_name": "output_psm", | |
1063 "uuid": "c4d742d4-41f8-4855-82b3-a417af83c170" | |
1064 }, | |
1065 { | |
1066 "label": null, | |
1067 "output_name": "output_proteins", | |
1068 "uuid": "1c004ba8-4ae5-49c0-90d5-adc9262f16e9" | |
1069 } | |
1070 ] | |
1071 }, | |
1072 "15": { | |
1073 "annotation": "", | |
1074 "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.3", | |
1075 "id": 15, | |
1076 "input_connections": { | |
1077 "searchgui_input": { | |
1078 "id": 11, | |
1079 "output_name": "searchgui_results" | |
1080 } | |
1081 }, | |
1082 "inputs": [ | |
1083 { | |
1084 "description": "runtime parameter for tool Peptide Shaker", | |
1085 "name": "searchgui_input" | |
1086 } | |
1087 ], | |
1088 "label": null, | |
1089 "name": "Peptide Shaker", | |
1090 "outputs": [ | |
1091 { | |
1092 "name": "mzidentML", | |
1093 "type": "mzid" | |
1094 }, | |
1095 { | |
1096 "name": "output_cps", | |
1097 "type": "peptideshaker_archive" | |
1098 }, | |
1099 { | |
1100 "name": "output_zip", | |
1101 "type": "zip" | |
1102 }, | |
1103 { | |
1104 "name": "output_certificate", | |
1105 "type": "txt" | |
1106 }, | |
1107 { | |
1108 "name": "output_hierarchical", | |
1109 "type": "tabular" | |
1110 }, | |
1111 { | |
1112 "name": "output_psm_phosphorylation", | |
1113 "type": "tabular" | |
1114 }, | |
1115 { | |
1116 "name": "output_psm", | |
1117 "type": "tabular" | |
1118 }, | |
1119 { | |
1120 "name": "output_extended_psm", | |
1121 "type": "tabular" | |
1122 }, | |
1123 { | |
1124 "name": "output_peptides_phosphorylation", | |
1125 "type": "tabular" | |
1126 }, | |
1127 { | |
1128 "name": "output_peptides", | |
1129 "type": "tabular" | |
1130 }, | |
1131 { | |
1132 "name": "output_proteins_phosphorylation", | |
1133 "type": "tabular" | |
1134 }, | |
1135 { | |
1136 "name": "output_proteins", | |
1137 "type": "tabular" | |
1138 } | |
1139 ], | |
1140 "position": { | |
1141 "left": 873, | |
1142 "top": 829 | |
1143 }, | |
1144 "post_job_actions": { | |
1145 "HideDatasetActionmzidentML": { | |
1146 "action_arguments": {}, | |
1147 "action_type": "HideDatasetAction", | |
1148 "output_name": "mzidentML" | |
1149 }, | |
1150 "HideDatasetActionoutput_cps": { | |
1151 "action_arguments": {}, | |
1152 "action_type": "HideDatasetAction", | |
1153 "output_name": "output_cps" | |
1154 }, | |
1155 "HideDatasetActionoutput_extended_psm": { | |
1156 "action_arguments": {}, | |
1157 "action_type": "HideDatasetAction", | |
1158 "output_name": "output_extended_psm" | |
1159 }, | |
1160 "HideDatasetActionoutput_hierarchical": { | |
1161 "action_arguments": {}, | |
1162 "action_type": "HideDatasetAction", | |
1163 "output_name": "output_hierarchical" | |
1164 }, | |
1165 "HideDatasetActionoutput_peptides": { | |
1166 "action_arguments": {}, | |
1167 "action_type": "HideDatasetAction", | |
1168 "output_name": "output_peptides" | |
1169 }, | |
1170 "HideDatasetActionoutput_peptides_phosphorylation": { | |
1171 "action_arguments": {}, | |
1172 "action_type": "HideDatasetAction", | |
1173 "output_name": "output_peptides_phosphorylation" | |
1174 }, | |
1175 "HideDatasetActionoutput_proteins_phosphorylation": { | |
1176 "action_arguments": {}, | |
1177 "action_type": "HideDatasetAction", | |
1178 "output_name": "output_proteins_phosphorylation" | |
1179 }, | |
1180 "HideDatasetActionoutput_psm_phosphorylation": { | |
1181 "action_arguments": {}, | |
1182 "action_type": "HideDatasetAction", | |
1183 "output_name": "output_psm_phosphorylation" | |
1184 }, | |
1185 "HideDatasetActionoutput_zip": { | |
1186 "action_arguments": {}, | |
1187 "action_type": "HideDatasetAction", | |
1188 "output_name": "output_zip" | |
1189 }, | |
1190 "RenameDatasetActionoutput_certificate": { | |
1191 "action_arguments": { | |
1192 "newname": "PeptideShaker Summary Report: 04112012_JL_HCC827_GFP_TAP_2_run1" | |
1193 }, | |
1194 "action_type": "RenameDatasetAction", | |
1195 "output_name": "output_certificate" | |
1196 }, | |
1197 "RenameDatasetActionoutput_proteins": { | |
1198 "action_arguments": { | |
1199 "newname": "PeptideShaker Protein Report: 04112012_JL_HCC827_GFP_TAP_2_run1" | |
1200 }, | |
1201 "action_type": "RenameDatasetAction", | |
1202 "output_name": "output_proteins" | |
1203 }, | |
1204 "RenameDatasetActionoutput_psm": { | |
1205 "action_arguments": { | |
1206 "newname": "PeptideShaker PSM Report: 04112012_JL_HCC827_GFP_TAP_2_run1" | |
1207 }, | |
1208 "action_type": "RenameDatasetAction", | |
1209 "output_name": "output_psm" | |
1210 } | |
1211 }, | |
1212 "tool_errors": null, | |
1213 "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.3", | |
1214 "tool_shed_repository": { | |
1215 "changeset_revision": "7f2aeb19650f", | |
1216 "name": "peptideshaker", | |
1217 "owner": "galaxyp", | |
1218 "tool_shed": "toolshed.g2.bx.psu.edu" | |
1219 }, | |
1220 "tool_state": "{\"__page__\": 0, \"processing_options\": \"{\\\"peptide_fdr\\\": \\\"5.0\\\", \\\"protein_fdr\\\": \\\"5.0\\\", \\\"protein_fraction_mw_confidence\\\": \\\"95.0\\\", \\\"ptm_score\\\": {\\\"ptm_score_selector\\\": \\\"0\\\", \\\"__current_case__\\\": 0}, \\\"ptm_alignment\\\": \\\"true\\\", \\\"__current_case__\\\": 1, \\\"processing_options_selector\\\": \\\"yes\\\", \\\"psm_fdr\\\": \\\"5.0\\\"}\", \"__rerun_remap_job_id__\": null, \"filtering_options\": \"{\\\"max_precursor_error_type\\\": \\\"1\\\", \\\"filtering_options_selector\\\": \\\"yes\\\", \\\"__current_case__\\\": 1, \\\"max_precursor_error\\\": \\\"10.0\\\", \\\"exclude_unknown_ptms\\\": \\\"true\\\", \\\"max_peptide_length\\\": \\\"75\\\", \\\"min_peptide_length\\\": \\\"6\\\"}\", \"searchgui_input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"contact_options\": \"{\\\"contact_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"outputs\": \"[\\\"3\\\", \\\"7\\\", \\\"0\\\"]\", \"include_sequences\": \"\\\"false\\\"\"}", | |
1221 "tool_version": "1.16.3", | |
1222 "type": "tool", | |
1223 "uuid": "54bba191-2325-4beb-b13b-fbfc54248145", | |
1224 "workflow_outputs": [ | |
1225 { | |
1226 "label": null, | |
1227 "output_name": "output_certificate", | |
1228 "uuid": "fd4adacf-fc64-49b3-97fc-283eb89b6fd6" | |
1229 }, | |
1230 { | |
1231 "label": null, | |
1232 "output_name": "output_psm", | |
1233 "uuid": "20ffbbba-4caa-4ccd-8805-6e3183296ed9" | |
1234 }, | |
1235 { | |
1236 "label": null, | |
1237 "output_name": "output_proteins", | |
1238 "uuid": "7afcb5c6-2bcf-4d3e-a158-7eb9ac76cf1c" | |
1239 } | |
1240 ] | |
1241 }, | |
1242 "16": { | |
1243 "annotation": "", | |
1244 "content_id": "toolshed.g2.bx.psu.edu/repos/bornea/saint_preprocessing/SAINT_preprocessing_v6/1.0.0", | |
1245 "id": 16, | |
1246 "input_connections": { | |
1247 "type_select|bait_file_in": { | |
1248 "id": 6, | |
1249 "output_name": "output" | |
1250 }, | |
1251 "type_select|fasta_db": { | |
1252 "id": 7, | |
1253 "output_name": "output" | |
1254 }, | |
1255 "type_select|protein_inputs_0|protein_file": { | |
1256 "id": 15, | |
1257 "output_name": "output_proteins" | |
1258 }, | |
1259 "type_select|protein_inputs_1|protein_file": { | |
1260 "id": 14, | |
1261 "output_name": "output_proteins" | |
1262 }, | |
1263 "type_select|protein_inputs_2|protein_file": { | |
1264 "id": 13, | |
1265 "output_name": "output_proteins" | |
1266 }, | |
1267 "type_select|protein_inputs_3|protein_file": { | |
1268 "id": 12, | |
1269 "output_name": "output_proteins" | |
1270 } | |
1271 }, | |
1272 "inputs": [ | |
1273 { | |
1274 "description": "runtime parameter for tool SAINT pre-processing", | |
1275 "name": "type_select" | |
1276 }, | |
1277 { | |
1278 "description": "runtime parameter for tool SAINT pre-processing", | |
1279 "name": "type_select" | |
1280 } | |
1281 ], | |
1282 "label": null, | |
1283 "name": "SAINT pre-processing", | |
1284 "outputs": [ | |
1285 { | |
1286 "name": "Inter_file", | |
1287 "type": "txt" | |
1288 }, | |
1289 { | |
1290 "name": "Prey_file", | |
1291 "type": "txt" | |
1292 }, | |
1293 { | |
1294 "name": "Bait_file", | |
1295 "type": "txt" | |
1296 } | |
1297 ], | |
1298 "position": { | |
1299 "left": 1412.5, | |
1300 "top": 394 | |
1301 }, | |
1302 "post_job_actions": { | |
1303 "HideDatasetActionBait_file": { | |
1304 "action_arguments": {}, | |
1305 "action_type": "HideDatasetAction", | |
1306 "output_name": "Bait_file" | |
1307 }, | |
1308 "HideDatasetActionInter_file": { | |
1309 "action_arguments": {}, | |
1310 "action_type": "HideDatasetAction", | |
1311 "output_name": "Inter_file" | |
1312 }, | |
1313 "HideDatasetActionPrey_file": { | |
1314 "action_arguments": {}, | |
1315 "action_type": "HideDatasetAction", | |
1316 "output_name": "Prey_file" | |
1317 } | |
1318 }, | |
1319 "tool_errors": null, | |
1320 "tool_id": "toolshed.g2.bx.psu.edu/repos/bornea/saint_preprocessing/SAINT_preprocessing_v6/1.0.0", | |
1321 "tool_shed_repository": { | |
1322 "changeset_revision": "6ad498eac0e2", | |
1323 "name": "saint_preprocessing", | |
1324 "owner": "bornea", | |
1325 "tool_shed": "toolshed.g2.bx.psu.edu" | |
1326 }, | |
1327 "tool_state": "{\"bait\": \"[]\", \"__rerun_remap_job_id__\": null, \"type_select\": \"{\\\"protein_inputs\\\": [{\\\"__index__\\\": 0, \\\"protein_file\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}, {\\\"__index__\\\": 1, \\\"protein_file\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}, {\\\"__index__\\\": 2, \\\"protein_file\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}, {\\\"__index__\\\": 3, \\\"protein_file\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}], \\\"preybool\\\": \\\"true\\\", \\\"fasta_db\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"bait_file_in\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"bait_bool\\\": \\\"true\\\", \\\"__current_case__\\\": 3, \\\"use_metric\\\": \\\"Validated_Peptides\\\", \\\"type\\\": \\\"Peptideshaker_ordered_input\\\"}\", \"__page__\": 0}", | |
1328 "tool_version": "1.0.0", | |
1329 "type": "tool", | |
1330 "uuid": "7504f5ce-684d-46f6-bc00-d4b8eaf87b3a", | |
1331 "workflow_outputs": [] | |
1332 }, | |
1333 "17": { | |
1334 "annotation": "", | |
1335 "content_id": "toolshed.g2.bx.psu.edu/repos/bornea/query_crapome/CRAPomeQuery/1.0.0", | |
1336 "id": 17, | |
1337 "input_connections": { | |
1338 "fasta_db": { | |
1339 "id": 7, | |
1340 "output_name": "output" | |
1341 }, | |
1342 "input": { | |
1343 "id": 16, | |
1344 "output_name": "Prey_file" | |
1345 } | |
1346 }, | |
1347 "inputs": [ | |
1348 { | |
1349 "description": "runtime parameter for tool Query CRAPome", | |
1350 "name": "input" | |
1351 }, | |
1352 { | |
1353 "description": "runtime parameter for tool Query CRAPome", | |
1354 "name": "fasta_db" | |
1355 } | |
1356 ], | |
1357 "label": null, | |
1358 "name": "Query CRAPome", | |
1359 "outputs": [ | |
1360 { | |
1361 "name": "CrapomeFile", | |
1362 "type": "txt" | |
1363 } | |
1364 ], | |
1365 "position": { | |
1366 "left": 1267, | |
1367 "top": 723 | |
1368 }, | |
1369 "post_job_actions": { | |
1370 "RenameDatasetActionCrapomeFile": { | |
1371 "action_arguments": { | |
1372 "newname": "CRAPome File Output" | |
1373 }, | |
1374 "action_type": "RenameDatasetAction", | |
1375 "output_name": "CrapomeFile" | |
1376 } | |
1377 }, | |
1378 "tool_errors": null, | |
1379 "tool_id": "toolshed.g2.bx.psu.edu/repos/bornea/query_crapome/CRAPomeQuery/1.0.0", | |
1380 "tool_shed_repository": { | |
1381 "changeset_revision": "f1459638e1bc", | |
1382 "name": "query_crapome", | |
1383 "owner": "bornea", | |
1384 "tool_shed": "toolshed.g2.bx.psu.edu" | |
1385 }, | |
1386 "tool_state": "{\"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"fasta_db\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"species\": \"\\\"HUMAN\\\"\", \"__page__\": 0}", | |
1387 "tool_version": "1.0.0", | |
1388 "type": "tool", | |
1389 "uuid": "16096e29-d534-4a6d-9627-e7e287798c71", | |
1390 "workflow_outputs": [ | |
1391 { | |
1392 "label": null, | |
1393 "output_name": "CrapomeFile", | |
1394 "uuid": "1f90a8ba-22ee-45c4-9018-98a153162583" | |
1395 } | |
1396 ] | |
1397 }, | |
1398 "18": { | |
1399 "annotation": "", | |
1400 "content_id": "toolshed.g2.bx.psu.edu/repos/bornea/saintexpress/saint_wrapper/1.0.0", | |
1401 "id": 18, | |
1402 "input_connections": { | |
1403 "bait_input": { | |
1404 "id": 16, | |
1405 "output_name": "Bait_file" | |
1406 }, | |
1407 "inter_input": { | |
1408 "id": 16, | |
1409 "output_name": "Inter_file" | |
1410 }, | |
1411 "prey_input": { | |
1412 "id": 16, | |
1413 "output_name": "Prey_file" | |
1414 } | |
1415 }, | |
1416 "inputs": [ | |
1417 { | |
1418 "description": "runtime parameter for tool SAINTexpress", | |
1419 "name": "go_file" | |
1420 }, | |
1421 { | |
1422 "description": "runtime parameter for tool SAINTexpress", | |
1423 "name": "bait_input" | |
1424 }, | |
1425 { | |
1426 "description": "runtime parameter for tool SAINTexpress", | |
1427 "name": "inter_input" | |
1428 }, | |
1429 { | |
1430 "description": "runtime parameter for tool SAINTexpress", | |
1431 "name": "prey_input" | |
1432 } | |
1433 ], | |
1434 "label": null, | |
1435 "name": "SAINTexpress", | |
1436 "outputs": [ | |
1437 { | |
1438 "name": "SAINT_output", | |
1439 "type": "txt" | |
1440 } | |
1441 ], | |
1442 "position": { | |
1443 "left": 1763.5, | |
1444 "top": 524 | |
1445 }, | |
1446 "post_job_actions": { | |
1447 "RenameDatasetActionSAINT_output": { | |
1448 "action_arguments": { | |
1449 "newname": "SAINT Output File" | |
1450 }, | |
1451 "action_type": "RenameDatasetAction", | |
1452 "output_name": "SAINT_output" | |
1453 } | |
1454 }, | |
1455 "tool_errors": null, | |
1456 "tool_id": "toolshed.g2.bx.psu.edu/repos/bornea/saintexpress/saint_wrapper/1.0.0", | |
1457 "tool_shed_repository": { | |
1458 "changeset_revision": "67631a640534", | |
1459 "name": "saintexpress", | |
1460 "owner": "bornea", | |
1461 "tool_shed": "toolshed.g2.bx.psu.edu" | |
1462 }, | |
1463 "tool_state": "{\"rep_num\": \"\\\"100\\\"\", \"__page__\": 0, \"go_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"bait_input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"vc_bool\": \"\\\"false\\\"\", \"inter_input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"go_bool\": \"\\\"false\\\"\", \"prey_input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"vc_num\": \"\\\"1\\\"\"}", | |
1464 "tool_version": "1.0.0", | |
1465 "type": "tool", | |
1466 "uuid": "86e2c9ce-be72-496b-84c2-7e3027d0187e", | |
1467 "workflow_outputs": [ | |
1468 { | |
1469 "label": null, | |
1470 "output_name": "SAINT_output", | |
1471 "uuid": "f4c612f6-d132-444f-9474-f95f7b968382" | |
1472 } | |
1473 ] | |
1474 } | |
1475 }, | |
1476 "uuid": "4f118197-8eee-42d5-ba46-3abfcb3f127b" | |
1477 } |