Mercurial > repos > earlhaminst > geneseqtofamily

comparison GeneSeqToFamily.ga @ 6:266800d51605 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
author earlhaminst
date Thu, 10 Jun 2021 16:18:59 +0000
parents cc5419f7dff7
children e732a731f778
comparison
equal deleted inserted replaced
5:06470b2e491f 6:266800d51605
18 ], 18 ],
19 "label": "CDS", 19 "label": "CDS",
20 "name": "Input dataset", 20 "name": "Input dataset",
21 "outputs": [], 21 "outputs": [],
22 "position": { 22 "position": {
23 "left": 200, 23 "left": 225.984375,
24 "top": 266 24 "top": 532.5
25 }, 25 },
26 "tool_id": null, 26 "tool_id": null,
27 "tool_state": "{\"name\": \"CDS\"}", 27 "tool_state": "{\"name\": \"CDS\"}",
28 "tool_version": null, 28 "tool_version": null,
29 "type": "data_input", 29 "type": "data_input",
43 "id": 1, 43 "id": 1,
44 "input_connections": {}, 44 "input_connections": {},
45 "inputs": [ 45 "inputs": [
46 { 46 {
47 "description": "", 47 "description": "",
48 "name": "Species tree"
49 }
50 ],
51 "label": "Species tree",
52 "name": "Input dataset",
53 "outputs": [],
54 "position": {
55 "left": 244.875,
56 "top": 947.578125
57 },
58 "tool_id": null,
59 "tool_state": "{\"name\": \"Species tree\"}",
60 "tool_version": null,
61 "type": "data_input",
62 "uuid": "1f2ca308-faad-44fa-ba48-fff5aeecbbd3",
63 "workflow_outputs": [
64 {
65 "label": null,
66 "output_name": "output",
67 "uuid": "50734600-41fa-437a-9b2b-6572fd8763a2"
68 }
69 ]
70 },
71 "2": {
72 "annotation": "",
73 "content_id": null,
74 "errors": null,
75 "id": 2,
76 "input_connections": {},
77 "inputs": [
78 {
79 "description": "",
48 "name": "Gene feature information" 80 "name": "Gene feature information"
49 } 81 }
50 ], 82 ],
51 "label": "Gene feature information", 83 "label": "Gene feature information",
52 "name": "Input dataset", 84 "name": "Input dataset",
53 "outputs": [], 85 "outputs": [],
54 "position": { 86 "position": {
55 "left": 202.8125, 87 "left": 247.796875,
56 "top": 469.0625 88 "top": 1200.5625
57 }, 89 },
58 "tool_id": null, 90 "tool_id": null,
59 "tool_state": "{\"name\": \"Gene feature information\"}", 91 "tool_state": "{\"name\": \"Gene feature information\"}",
60 "tool_version": null, 92 "tool_version": null,
61 "type": "data_input", 93 "type": "data_input",
66 "output_name": "output", 98 "output_name": "output",
67 "uuid": "39787c6d-ecd8-4147-b718-83d739202b3b" 99 "uuid": "39787c6d-ecd8-4147-b718-83d739202b3b"
68 } 100 }
69 ] 101 ]
70 }, 102 },
71 "2": {
72 "annotation": "",
73 "content_id": null,
74 "errors": null,
75 "id": 2,
76 "input_connections": {},
77 "inputs": [
78 {
79 "description": "",
80 "name": "Species tree"
81 }
82 ],
83 "label": "Species tree",
84 "name": "Input dataset",
85 "outputs": [],
86 "position": {
87 "left": 201.921875,
88 "top": 903.09375
89 },
90 "tool_id": null,
91 "tool_state": "{\"name\": \"Species tree\"}",
92 "tool_version": null,
93 "type": "data_input",
94 "uuid": "1f2ca308-faad-44fa-ba48-fff5aeecbbd3",
95 "workflow_outputs": [
96 {
97 "label": null,
98 "output_name": "output",
99 "uuid": "50734600-41fa-437a-9b2b-6572fd8763a2"
100 }
101 ]
102 },
103 "3": { 103 "3": {
104 "annotation": "", 104 "annotation": "",
105 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: transeq101/5.0.0", 105 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: transeq101/5.0.0",
106 "errors": null, 106 "errors": null,
107 "id": 3, 107 "id": 3,
109 "input1": { 109 "input1": {
110 "id": 0, 110 "id": 0,
111 "output_name": "output" 111 "output_name": "output"
112 } 112 }
113 }, 113 },
114 "inputs": [ 114 "inputs": [],
115 {
116 "description": "runtime parameter for tool transeq",
117 "name": "input1"
118 }
119 ],
120 "label": null, 115 "label": null,
121 "name": "transeq", 116 "name": "transeq",
122 "outputs": [ 117 "outputs": [
123 { 118 {
124 "name": "out_file1", 119 "name": "out_file1",
125 "type": "fasta" 120 "type": "fasta"
126 } 121 }
127 ], 122 ],
128 "position": { 123 "position": {
129 "left": 460.0625, 124 "left": 550.046875,
130 "top": 200 125 "top": 260.484375
131 }, 126 },
132 "post_job_actions": { 127 "post_job_actions": {
133 "HideDatasetActionout_file1": { 128 "HideDatasetActionout_file1": {
134 "action_arguments": {}, 129 "action_arguments": {},
135 "action_type": "HideDatasetAction", 130 "action_type": "HideDatasetAction",
136 "output_name": "out_file1" 131 "output_name": "out_file1"
137 } 132 }
138 }, 133 },
139 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: transeq101/5.0.0", 134 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: transeq101/5.0.0",
140 "tool_shed_repository": { 135 "tool_shed_repository": {
141 "changeset_revision": "1b6538ec8b56", 136 "changeset_revision": "dc492eb6a4fc",
142 "name": "emboss_5", 137 "name": "emboss_5",
143 "owner": "devteam", 138 "owner": "devteam",
144 "tool_shed": "toolshed.g2.bx.psu.edu" 139 "tool_shed": "toolshed.g2.bx.psu.edu"
145 }, 140 },
146 "tool_state": "{\"trim\": \"\\\"no\\\"\", \"__page__\": null, \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"out_format1\": \"\\\"fasta\\\"\", \"frame\": \"\\\"1\\\"\", \"regions\": \"\\\"\\\"\", \"clean\": \"\\\"no\\\"\", \"table\": \"\\\"0\\\"\", \"alternative\": \"\\\"no\\\"\", \"__rerun_remap_job_id__\": null}", 141 "tool_state": "{\"trim\": \"\\\"yes\\\"\", \"__page__\": null, \"input1\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"out_format1\": \"\\\"fasta\\\"\", \"frame\": \"\\\"1\\\"\", \"regions\": \"\\\"\\\"\", \"clean\": \"\\\"no\\\"\", \"table\": \"\\\"0\\\"\", \"alternative\": \"\\\"no\\\"\", \"__rerun_remap_job_id__\": null}",
147 "tool_version": "5.0.0", 142 "tool_version": "5.0.0",
148 "type": "tool", 143 "type": "tool",
149 "uuid": "12722a4e-291d-4ba2-b7f8-77209049b0ac", 144 "uuid": "12722a4e-291d-4ba2-b7f8-77209049b0ac",
150 "workflow_outputs": [] 145 "workflow_outputs": []
151 }, 146 },
152 "4": { 147 "4": {
153 "annotation": "", 148 "annotation": "",
154 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.1.08", 149 "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.2",
155 "errors": null, 150 "errors": null,
156 "id": 4, 151 "id": 4,
157 "input_connections": { 152 "input_connections": {
158 "input_file": { 153 "input": {
159 "id": 3, 154 "id": 3,
160 "output_name": "out_file1" 155 "output_name": "out_file1"
161 } 156 }
162 }, 157 },
158 "inputs": [],
159 "label": null,
160 "name": "Filter FASTA",
161 "outputs": [
162 {
163 "name": "output",
164 "type": "fasta"
165 },
166 {
167 "name": "discarded",
168 "type": "fasta"
169 }
170 ],
171 "position": {
172 "left": 552.484375,
173 "top": 427.984375
174 },
175 "post_job_actions": {
176 "HideDatasetActiondiscarded": {
177 "action_arguments": {},
178 "action_type": "HideDatasetAction",
179 "output_name": "discarded"
180 },
181 "HideDatasetActionoutput": {
182 "action_arguments": {},
183 "action_type": "HideDatasetAction",
184 "output_name": "output"
185 }
186 },
187 "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.2",
188 "tool_shed_repository": {
189 "changeset_revision": "cd22452edec2",
190 "name": "filter_by_fasta_ids",
191 "owner": "galaxyp",
192 "tool_shed": "toolshed.g2.bx.psu.edu"
193 },
194 "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"dedup\": \"\\\"true\\\"\", \"input\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"header_criteria\": \"{\\\"__current_case__\\\": 0, \\\"header_criteria_select\\\": \\\"\\\"}\", \"output_discarded\": \"\\\"true\\\"\", \"sequence_criteria\": \"{\\\"__current_case__\\\": 2, \\\"regexp\\\": \\\"^[^*]+$\\\", \\\"sequence_criteria_select\\\": \\\"regexp\\\"}\"}",
195 "tool_version": "2.2",
196 "type": "tool",
197 "uuid": "8dd011eb-b442-42cf-b528-331739f3d252",
198 "workflow_outputs": []
199 },
200 "5": {
201 "annotation": "",
202 "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ucsc_fasplit/fasplit/332",
203 "errors": null,
204 "id": 5,
205 "input_connections": {
206 "input": {
207 "id": 4,
208 "output_name": "output"
209 }
210 },
211 "inputs": [
212 {
213 "description": "runtime parameter for tool faSplit",
214 "name": "O"
215 }
216 ],
217 "label": null,
218 "name": "faSplit",
219 "outputs": [
220 {
221 "name": "output_list",
222 "type": "input"
223 }
224 ],
225 "position": {
226 "left": 845.96875,
227 "top": 315
228 },
229 "post_job_actions": {
230 "HideDatasetActionoutput_list": {
231 "action_arguments": {},
232 "action_type": "HideDatasetAction",
233 "output_name": "output_list"
234 }
235 },
236 "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ucsc_fasplit/fasplit/332",
237 "tool_shed_repository": {
238 "changeset_revision": "dc36d50254d8",
239 "name": "ucsc_fasplit",
240 "owner": "iuc",
241 "tool_shed": "toolshed.g2.bx.psu.edu"
242 },
243 "tool_state": "{\"input\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"__rerun_remap_job_id__\": null, \"O\": \"{\\\"__current_case__\\\": 0, \\\"count\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"split_type\\\": \\\"sequence\\\"}\", \"__page__\": null}",
244 "tool_version": "332",
245 "type": "tool",
246 "uuid": "3f991f5d-a175-4df4-9870-0ff701437991",
247 "workflow_outputs": []
248 },
249 "6": {
250 "annotation": "",
251 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.3.0",
252 "errors": null,
253 "id": 6,
254 "input_connections": {
255 "input_file": {
256 "id": 4,
257 "output_name": "output"
258 }
259 },
163 "inputs": [ 260 "inputs": [
164 { 261 {
165 "description": "runtime parameter for tool NCBI BLAST+ makeblastdb", 262 "description": "runtime parameter for tool NCBI BLAST+ makeblastdb",
166 "name": "mask_data_file" 263 "name": "mask_data_file"
167 },
168 {
169 "description": "runtime parameter for tool NCBI BLAST+ makeblastdb",
170 "name": "input_file"
171 } 264 }
172 ], 265 ],
173 "label": null, 266 "label": null,
174 "name": "NCBI BLAST+ makeblastdb", 267 "name": "NCBI BLAST+ makeblastdb",
175 "outputs": [ 268 "outputs": [
177 "name": "outfile", 270 "name": "outfile",
178 "type": "data" 271 "type": "data"
179 } 272 }
180 ], 273 ],
181 "position": { 274 "position": {
182 "left": 644.171875, 275 "left": 832.140625,
183 "top": 294.890625 276 "top": 518.359375
184 }, 277 },
185 "post_job_actions": { 278 "post_job_actions": {
186 "HideDatasetActionoutfile": { 279 "HideDatasetActionoutfile": {
187 "action_arguments": {}, 280 "action_arguments": {},
188 "action_type": "HideDatasetAction", 281 "action_type": "HideDatasetAction",
189 "output_name": "outfile" 282 "output_name": "outfile"
190 } 283 }
191 }, 284 },
192 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.1.08", 285 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.3.0",
193 "tool_shed_repository": { 286 "tool_shed_repository": {
194 "changeset_revision": "6f386c5dc4fb", 287 "changeset_revision": "c877294f8025",
195 "name": "ncbi_blast_plus", 288 "name": "ncbi_blast_plus",
196 "owner": "devteam", 289 "owner": "devteam",
197 "tool_shed": "toolshed.g2.bx.psu.edu" 290 "tool_shed": "toolshed.g2.bx.psu.edu"
198 }, 291 },
199 "tool_state": "{\"__page__\": null, \"mask_data_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"dbtype\": \"\\\"prot\\\"\", \"__rerun_remap_job_id__\": null, \"hash_index\": \"\\\"true\\\"\", \"tax\": \"{\\\"__current_case__\\\": 0, \\\"taxselect\\\": \\\"\\\"}\", \"title\": \"\\\"\\\"\", \"parse_seqids\": \"\\\"false\\\"\"}", 292 "tool_state": "{\"__page__\": null, \"mask_data_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"input_file\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"dbtype\": \"\\\"prot\\\"\", \"__rerun_remap_job_id__\": null, \"hash_index\": \"\\\"true\\\"\", \"tax\": \"{\\\"__current_case__\\\": 0, \\\"taxselect\\\": \\\"\\\"}\", \"title\": \"\\\"\\\"\", \"parse_seqids\": \"\\\"false\\\"\"}",
200 "tool_version": "0.2.01", 293 "tool_version": "0.3.0",
201 "type": "tool", 294 "type": "tool",
202 "uuid": "c72477fb-cc1d-45ec-a0cd-8215be8fe8ee", 295 "uuid": "c72477fb-cc1d-45ec-a0cd-8215be8fe8ee",
203 "workflow_outputs": [] 296 "workflow_outputs": []
204 }, 297 },
205 "5": { 298 "7": {
206 "annotation": "", 299 "annotation": "",
207 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.1.08", 300 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.3.0",
208 "errors": null, 301 "errors": null,
209 "id": 5, 302 "id": 7,
210 "input_connections": { 303 "input_connections": {
211 "db_opts|histdb": { 304 "db_opts|histdb": {
212 "id": 4, 305 "id": 6,
213 "output_name": "outfile" 306 "output_name": "outfile"
214 }, 307 },
215 "query": { 308 "query": {
216 "id": 3, 309 "id": 5,
217 "output_name": "out_file1" 310 "output_name": "output_list"
218 } 311 }
219 }, 312 },
220 "inputs": [ 313 "inputs": [],
221 {
222 "description": "runtime parameter for tool NCBI BLAST+ blastp",
223 "name": "db_opts"
224 },
225 {
226 "description": "runtime parameter for tool NCBI BLAST+ blastp",
227 "name": "query"
228 }
229 ],
230 "label": null, 314 "label": null,
231 "name": "NCBI BLAST+ blastp", 315 "name": "NCBI BLAST+ blastp",
232 "outputs": [ 316 "outputs": [
233 { 317 {
234 "name": "output1", 318 "name": "output1",
235 "type": "tabular" 319 "type": "tabular"
236 } 320 }
237 ], 321 ],
238 "position": { 322 "position": {
239 "left": 929.421875, 323 "left": 1176.484375,
240 "top": 205.0625 324 "top": 228
241 }, 325 },
242 "post_job_actions": { 326 "post_job_actions": {
243 "HideDatasetActionoutput1": { 327 "HideDatasetActionoutput1": {
244 "action_arguments": {}, 328 "action_arguments": {},
245 "action_type": "HideDatasetAction", 329 "action_type": "HideDatasetAction",
246 "output_name": "output1" 330 "output_name": "output1"
247 } 331 }
248 }, 332 },
249 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.1.08", 333 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.3.0",
250 "tool_shed_repository": { 334 "tool_shed_repository": {
251 "changeset_revision": "6f386c5dc4fb", 335 "changeset_revision": "c877294f8025",
252 "name": "ncbi_blast_plus", 336 "name": "ncbi_blast_plus",
253 "owner": "devteam", 337 "owner": "devteam",
254 "tool_shed": "toolshed.g2.bx.psu.edu" 338 "tool_shed": "toolshed.g2.bx.psu.edu"
255 }, 339 },
256 "tool_state": "{\"evalue_cutoff\": \"\\\"1e-10\\\"\", \"__page__\": null, \"adv_opts\": \"{\\\"adv_optional_id_files_opts\\\": {\\\"__current_case__\\\": 0, \\\"adv_optional_id_files_opts_selector\\\": \\\"none\\\"}, \\\"use_sw_tback\\\": \\\"false\\\", \\\"matrix\\\": \\\"BLOSUM62\\\", \\\"max_hsps\\\": \\\"1\\\", \\\"adv_opts_selector\\\": \\\"advanced\\\", \\\"filter_query\\\": \\\"false\\\", \\\"word_size\\\": \\\"0\\\", \\\"__current_case__\\\": 1, \\\"parse_deflines\\\": \\\"false\\\", \\\"qcov_hsp_perc\\\": \\\"0.0\\\", \\\"max_hits\\\": \\\"0\\\"}\", \"__rerun_remap_job_id__\": null, \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"histdb\\\", \\\"subject\\\": \\\"\\\", \\\"histdb\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\"}\", \"query\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"blast_type\": \"\\\"blastp\\\"\", \"output\": \"{\\\"out_format\\\": \\\"ext\\\", \\\"__current_case__\\\": 1}\"}", 340 "tool_state": "{\"evalue_cutoff\": \"\\\"1e-10\\\"\", \"output\": \"{\\\"__current_case__\\\": 1, \\\"out_format\\\": \\\"ext\\\"}\", \"adv_opts\": \"{\\\"__current_case__\\\": 1, \\\"adv_optional_id_files_opts\\\": {\\\"__current_case__\\\": 0, \\\"adv_optional_id_files_opts_selector\\\": \\\"none\\\"}, \\\"adv_opts_selector\\\": \\\"advanced\\\", \\\"comp_based_stats\\\": \\\"\\\", \\\"filter_query\\\": \\\"false\\\", \\\"matrix_gapcosts\\\": {\\\"__current_case__\\\": 0, \\\"matrix\\\": \\\"\\\"}, \\\"max_hits\\\": \\\"0\\\", \\\"max_hsps\\\": \\\"1\\\", \\\"parse_deflines\\\": \\\"false\\\", \\\"qcov_hsp_perc\\\": \\\"50.0\\\", \\\"threshold\\\": \\\"\\\", \\\"use_sw_tback\\\": \\\"false\\\", \\\"window_size\\\": \\\"\\\", \\\"word_size\\\": \\\"\\\"}\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"db_opts\": \"{\\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\", \\\"db_opts_selector\\\": \\\"histdb\\\", \\\"histdb\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"subject\\\": \\\"\\\"}\", \"blast_type\": \"\\\"blastp\\\"\", \"query\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}",
257 "tool_version": "0.2.01", 341 "tool_version": "0.3.0",
258 "type": "tool", 342 "type": "tool",
259 "uuid": "7ee928f5-88bf-4d8d-9b0a-072560a9e410", 343 "uuid": "b67576ce-b912-4b00-8277-0e422399f70c",
260 "workflow_outputs": [] 344 "workflow_outputs": []
261 }, 345 },
262 "6": { 346 "8": {
263 "annotation": "", 347 "annotation": "",
264 "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/blast_parser/blast_parser/0.1.1", 348 "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0",
265 "errors": null, 349 "errors": null,
266 "id": 6, 350 "id": 8,
351 "input_connections": {
352 "inputs": {
353 "id": 7,
354 "output_name": "output1"
355 }
356 },
357 "inputs": [],
358 "label": null,
359 "name": "Concatenate datasets",
360 "outputs": [
361 {
362 "name": "out_file1",
363 "type": "input"
364 }
365 ],
366 "position": {
367 "left": 1214.484375,
368 "top": 439.984375
369 },
370 "post_job_actions": {
371 "HideDatasetActionout_file1": {
372 "action_arguments": {},
373 "action_type": "HideDatasetAction",
374 "output_name": "out_file1"
375 }
376 },
377 "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0",
378 "tool_shed_repository": {
379 "changeset_revision": "0a8c6b61f0f4",
380 "name": "text_processing",
381 "owner": "bgruening",
382 "tool_shed": "toolshed.g2.bx.psu.edu"
383 },
384 "tool_state": "{\"__page__\": null, \"inputs\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"__rerun_remap_job_id__\": null, \"queries\": \"[]\"}",
385 "tool_version": "0.1.0",
386 "type": "tool",
387 "uuid": "8c9b7c9a-b37d-46c2-8004-e5cbd302c048",
388 "workflow_outputs": []
389 },
390 "9": {
391 "annotation": "",
392 "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/blast_parser/blast_parser/0.1.2",
393 "errors": null,
394 "id": 9,
267 "input_connections": { 395 "input_connections": {
268 "input": { 396 "input": {
269 "id": 5, 397 "id": 8,
270 "output_name": "output1" 398 "output_name": "out_file1"
271 } 399 }
272 }, 400 },
273 "inputs": [ 401 "inputs": [],
274 {
275 "description": "runtime parameter for tool BLAST parser",
276 "name": "input"
277 }
278 ],
279 "label": null, 402 "label": null,
280 "name": "BLAST parser", 403 "name": "BLAST parser",
281 "outputs": [ 404 "outputs": [
282 { 405 {
283 "name": "output", 406 "name": "output",
284 "type": "tabular" 407 "type": "tabular"
285 } 408 }
286 ], 409 ],
287 "position": { 410 "position": {
288 "left": 1134.421875, 411 "left": 1266.390625,
289 "top": 380.921875 412 "top": 587.390625
290 }, 413 },
291 "post_job_actions": {}, 414 "post_job_actions": {},
292 "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/blast_parser/blast_parser/0.1.1", 415 "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/blast_parser/blast_parser/0.1.2",
293 "tool_shed_repository": { 416 "tool_shed_repository": {
294 "changeset_revision": "363f3480622d", 417 "changeset_revision": "363f3480622d",
295 "name": "blast_parser", 418 "name": "blast_parser",
296 "owner": "earlhaminst", 419 "owner": "earlhaminst",
297 "tool_shed": "toolshed.g2.bx.psu.edu" 420 "tool_shed": "toolshed.g2.bx.psu.edu"
298 }, 421 },
299 "tool_state": "{\"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"reciprocal\": \"\\\"true\\\"\", \"__page__\": null}", 422 "tool_state": "{\"input\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"__rerun_remap_job_id__\": null, \"reciprocal\": \"\\\"true\\\"\", \"__page__\": null}",
300 "tool_version": "0.1.2", 423 "tool_version": "0.1.2",
301 "type": "tool", 424 "type": "tool",
302 "uuid": "3eb98d54-a52d-4605-b068-28a700290d92", 425 "uuid": "3eb98d54-a52d-4605-b068-28a700290d92",
303 "workflow_outputs": [ 426 "workflow_outputs": [
304 { 427 {
305 "label": null, 428 "label": null,
306 "output_name": "output", 429 "output_name": "output",
307 "uuid": "6473f6a6-9036-43f2-ba10-961cecfb351f" 430 "uuid": "ecb78ea1-f143-4b34-96e3-ec4e885c17f2"
308 } 431 }
309 ] 432 ]
310 }, 433 },
311 "7": { 434 "10": {
312 "annotation": "", 435 "annotation": "",
313 "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/hcluster_sg/hcluster_sg/0.5.1", 436 "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/hcluster_sg/hcluster_sg/0.5.1.1",
314 "errors": null, 437 "errors": null,
315 "id": 7, 438 "id": 10,
316 "input_connections": { 439 "input_connections": {
317 "inputFile": { 440 "inputFile": {
318 "id": 6, 441 "id": 9,
319 "output_name": "output" 442 "output_name": "output"
320 } 443 }
321 }, 444 },
322 "inputs": [ 445 "inputs": [
323 { 446 {
324 "description": "runtime parameter for tool hcluster_sg", 447 "description": "runtime parameter for tool hcluster_sg",
325 "name": "c_conditional" 448 "name": "c_conditional"
326 },
327 {
328 "description": "runtime parameter for tool hcluster_sg",
329 "name": "inputFile"
330 } 449 }
331 ], 450 ],
332 "label": null, 451 "label": null,
333 "name": "hcluster_sg", 452 "name": "hcluster_sg",
334 "outputs": [ 453 "outputs": [
336 "name": "outputFile", 455 "name": "outputFile",
337 "type": "tabular" 456 "type": "tabular"
338 } 457 }
339 ], 458 ],
340 "position": { 459 "position": {
341 "left": 1317.921875, 460 "left": 1544.875,
342 "top": 207 461 "top": 392.484375
343 }, 462 },
344 "post_job_actions": { 463 "post_job_actions": {},
345 "HideDatasetActionoutputFile": { 464 "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/hcluster_sg/hcluster_sg/0.5.1.1",
346 "action_arguments": {},
347 "action_type": "HideDatasetAction",
348 "output_name": "outputFile"
349 }
350 },
351 "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/hcluster_sg/hcluster_sg/0.5.1",
352 "tool_shed_repository": { 465 "tool_shed_repository": {
353 "changeset_revision": "1d2de27d7a9c", 466 "changeset_revision": "1d2de27d7a9c",
354 "name": "hcluster_sg", 467 "name": "hcluster_sg",
355 "owner": "earlhaminst", 468 "owner": "earlhaminst",
356 "tool_shed": "toolshed.g2.bx.psu.edu" 469 "tool_shed": "toolshed.g2.bx.psu.edu"
357 }, 470 },
358 "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"c_conditional\": \"{\\\"c\\\": \\\"\\\", \\\"b\\\": \\\"0.1\\\", \\\"m\\\": \\\"500\\\", \\\"C\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"O\\\": {\\\"O_selector\\\": \\\"\\\", \\\"__current_case__\\\": 1}, \\\"L\\\": \\\"2\\\", \\\"s\\\": \\\"0.34\\\", \\\"__current_case__\\\": 1}\", \"w\": \"\\\"0\\\"\", \"inputFile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", 471 "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"c_conditional\": \"{\\\"C\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"L\\\": \\\"2\\\", \\\"O\\\": {\\\"O_selector\\\": \\\"\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 1, \\\"b\\\": \\\"0.1\\\", \\\"c\\\": \\\"\\\", \\\"m\\\": \\\"500\\\", \\\"s\\\": \\\"0.34\\\"}\", \"w\": \"\\\"0\\\"\", \"inputFile\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}",
359 "tool_version": "0.5.1.1", 472 "tool_version": "0.5.1.1",
360 "type": "tool", 473 "type": "tool",
361 "uuid": "d2b2ba89-b47d-4241-8adf-0d780f834412", 474 "uuid": "d2b2ba89-b47d-4241-8adf-0d780f834412",
362 "workflow_outputs": [] 475 "workflow_outputs": [
363 }, 476 {
364 "8": { 477 "label": null,
478 "output_name": "outputFile",
479 "uuid": "82fefa51-b192-49b2-bf41-e9914f179984"
480 }
481 ]
482 },
483 "11": {
365 "annotation": "", 484 "annotation": "",
366 "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/hcluster_sg_parser/hcluster_sg_parser/0.2.0", 485 "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/hcluster_sg_parser/hcluster_sg_parser/0.2.0",
367 "errors": null, 486 "errors": null,
368 "id": 8, 487 "id": 11,
369 "input_connections": { 488 "input_connections": {
370 "inputFile": { 489 "inputFile": {
371 "id": 7, 490 "id": 10,
372 "output_name": "outputFile" 491 "output_name": "outputFile"
373 } 492 }
374 }, 493 },
375 "inputs": [ 494 "inputs": [],
376 {
377 "description": "runtime parameter for tool hcluster_sg parser",
378 "name": "inputFile"
379 }
380 ],
381 "label": null, 495 "label": null,
382 "name": "hcluster_sg parser", 496 "name": "hcluster_sg parser",
383 "outputs": [ 497 "outputs": [
384 { 498 {
385 "name": "ids_lists", 499 "name": "ids_lists",
389 "name": "discarded", 503 "name": "discarded",
390 "type": "txt" 504 "type": "txt"
391 } 505 }
392 ], 506 ],
393 "position": { 507 "position": {
394 "left": 1298, 508 "left": 1548.984375,
395 "top": 505.09375 509 "top": 597.578125
396 }, 510 },
397 "post_job_actions": { 511 "post_job_actions": {
398 "HideDatasetActionids_lists": { 512 "HideDatasetActionids_lists": {
399 "action_arguments": {}, 513 "action_arguments": {},
400 "action_type": "HideDatasetAction", 514 "action_type": "HideDatasetAction",
406 "changeset_revision": "f9e418125021", 520 "changeset_revision": "f9e418125021",
407 "name": "hcluster_sg_parser", 521 "name": "hcluster_sg_parser",
408 "owner": "earlhaminst", 522 "owner": "earlhaminst",
409 "tool_shed": "toolshed.g2.bx.psu.edu" 523 "tool_shed": "toolshed.g2.bx.psu.edu"
410 }, 524 },
411 "tool_state": "{\"__page__\": null, \"max_elems\": \"\\\"200\\\"\", \"min_elems\": \"\\\"3\\\"\", \"__rerun_remap_job_id__\": null, \"inputFile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", 525 "tool_state": "{\"__page__\": null, \"max_elems\": \"\\\"200\\\"\", \"min_elems\": \"\\\"3\\\"\", \"__rerun_remap_job_id__\": null, \"inputFile\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}",
412 "tool_version": "0.2.0", 526 "tool_version": "0.2.0",
413 "type": "tool", 527 "type": "tool",
414 "uuid": "df3ae47f-f5a3-4f44-9b25-9bc36b049d60", 528 "uuid": "df3ae47f-f5a3-4f44-9b25-9bc36b049d60",
415 "workflow_outputs": [ 529 "workflow_outputs": [
416 { 530 {
417 "label": null, 531 "label": null,
418 "output_name": "discarded", 532 "output_name": "discarded",
419 "uuid": "465afc7e-afad-4228-bb28-2f7b1304a771" 533 "uuid": "cb6ee2ad-6310-4f91-9653-f7795c279e83"
420 } 534 }
421 ] 535 ]
422 }, 536 },
423 "9": { 537 "12": {
424 "annotation": "", 538 "annotation": "",
425 "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/t_coffee/11.0.8_1", 539 "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/t_coffee/11.0.8_1",
426 "errors": null, 540 "errors": null,
427 "id": 9, 541 "id": 12,
428 "input_connections": { 542 "input_connections": {
429 "input_type|fasta_input": { 543 "input_type|fasta_input": {
430 "id": 3, 544 "id": 4,
431 "output_name": "out_file1" 545 "output_name": "output"
432 }, 546 },
433 "input_type|identifiers": { 547 "input_type|identifiers": {
434 "id": 8, 548 "id": 11,
435 "output_name": "ids_lists" 549 "output_name": "ids_lists"
436 } 550 }
437 }, 551 },
438 "inputs": [ 552 "inputs": [],
439 {
440 "description": "runtime parameter for tool T-Coffee",
441 "name": "input_type"
442 },
443 {
444 "description": "runtime parameter for tool T-Coffee",
445 "name": "input_type"
446 }
447 ],
448 "label": null, 553 "label": null,
449 "name": "T-Coffee", 554 "name": "T-Coffee",
450 "outputs": [ 555 "outputs": [
451 {
452 "name": "clustalw_aln",
453 "type": "clustalw"
454 },
455 {
456 "name": "dnd",
457 "type": "nhx"
458 },
459 { 556 {
460 "name": "fasta_aln", 557 "name": "fasta_aln",
461 "type": "fasta" 558 "type": "fasta"
462 }, 559 }
463 { 560 ],
464 "name": "fasta_seq", 561 "position": {
465 "type": "fasta" 562 "left": 703.890625,
466 }, 563 "top": 739.046875
467 { 564 },
468 "name": "msf_aln", 565 "post_job_actions": {
469 "type": "msf"
470 },
471 {
472 "name": "phylip",
473 "type": "phyloxml"
474 },
475 {
476 "name": "pir_aln",
477 "type": "pir"
478 },
479 {
480 "name": "pir_seq",
481 "type": "pir"
482 },
483 {
484 "name": "score_ascii",
485 "type": "ascii"
486 },
487 {
488 "name": "score_html",
489 "type": "html"
490 }
491 ],
492 "position": {
493 "left": 713.921875,
494 "top": 521.5625
495 },
496 "post_job_actions": {
497 "HideDatasetActionclustalw_aln": {
498 "action_arguments": {},
499 "action_type": "HideDatasetAction",
500 "output_name": "clustalw_aln"
501 },
502 "HideDatasetActiondnd": {
503 "action_arguments": {},
504 "action_type": "HideDatasetAction",
505 "output_name": "dnd"
506 },
507 "HideDatasetActionfasta_aln": { 566 "HideDatasetActionfasta_aln": {
508 "action_arguments": {}, 567 "action_arguments": {},
509 "action_type": "HideDatasetAction", 568 "action_type": "HideDatasetAction",
510 "output_name": "fasta_aln" 569 "output_name": "fasta_aln"
511 },
512 "HideDatasetActionfasta_seq": {
513 "action_arguments": {},
514 "action_type": "HideDatasetAction",
515 "output_name": "fasta_seq"
516 },
517 "HideDatasetActionmsf_aln": {
518 "action_arguments": {},
519 "action_type": "HideDatasetAction",
520 "output_name": "msf_aln"
521 },
522 "HideDatasetActionphylip": {
523 "action_arguments": {},
524 "action_type": "HideDatasetAction",
525 "output_name": "phylip"
526 },
527 "HideDatasetActionpir_aln": {
528 "action_arguments": {},
529 "action_type": "HideDatasetAction",
530 "output_name": "pir_aln"
531 },
532 "HideDatasetActionpir_seq": {
533 "action_arguments": {},
534 "action_type": "HideDatasetAction",
535 "output_name": "pir_seq"
536 },
537 "HideDatasetActionscore_ascii": {
538 "action_arguments": {},
539 "action_type": "HideDatasetAction",
540 "output_name": "score_ascii"
541 },
542 "HideDatasetActionscore_html": {
543 "action_arguments": {},
544 "action_type": "HideDatasetAction",
545 "output_name": "score_html"
546 } 570 }
547 }, 571 },
548 "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/t_coffee/11.0.8_1", 572 "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/t_coffee/11.0.8_1",
549 "tool_shed_repository": { 573 "tool_shed_repository": {
550 "changeset_revision": "a91be6005274", 574 "changeset_revision": "c67bd5acbae2",
551 "name": "t_coffee", 575 "name": "t_coffee",
552 "owner": "earlhaminst", 576 "owner": "earlhaminst",
553 "tool_shed": "toolshed.g2.bx.psu.edu" 577 "tool_shed": "toolshed.g2.bx.psu.edu"
554 }, 578 },
555 "tool_state": "{\"__page__\": null, \"input_type\": \"{\\\"identifiers\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"filter_fasta\\\": \\\"yes\\\", \\\"fasta_input\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"outputs\": \"[\\\"fasta_aln\\\"]\", \"method03\": \"null\", \"method02\": \"[\\\"clustalw_msa\\\"]\", \"method01\": \"null\"}", 579 "tool_state": "{\"__page__\": null, \"outputs\": \"[\\\"fasta_aln\\\"]\", \"__rerun_remap_job_id__\": null, \"input_type\": \"{\\\"__current_case__\\\": 0, \\\"fasta_input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"filter_fasta\\\": \\\"yes\\\", \\\"identifiers\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}}\", \"method03\": \"null\", \"method02\": \"[\\\"clustalw_msa\\\"]\", \"method01\": \"null\"}",
556 "tool_version": "11.0.8_1", 580 "tool_version": "11.0.8_1",
557 "type": "tool", 581 "type": "tool",
558 "uuid": "827ba178-5028-4ae4-b5e1-f234bcfce9f8", 582 "uuid": "827ba178-5028-4ae4-b5e1-f234bcfce9f8",
559 "workflow_outputs": [] 583 "workflow_outputs": []
560 }, 584 },
561 "10": { 585 "13": {
562 "annotation": "", 586 "annotation": "",
563 "content_id": "trimmer", 587 "content_id": "trimmer",
564 "errors": null, 588 "errors": null,
565 "id": 10, 589 "id": 13,
566 "input_connections": { 590 "input_connections": {
567 "input1": { 591 "input1": {
568 "id": 8, 592 "id": 11,
569 "output_name": "ids_lists" 593 "output_name": "ids_lists"
570 } 594 }
571 }, 595 },
572 "inputs": [ 596 "inputs": [],
573 {
574 "description": "runtime parameter for tool Trim",
575 "name": "input1"
576 }
577 ],
578 "label": null, 597 "label": null,
579 "name": "Trim", 598 "name": "Trim",
580 "outputs": [ 599 "outputs": [
581 { 600 {
582 "name": "out_file1", 601 "name": "out_file1",
583 "type": "input" 602 "type": "input"
584 } 603 }
585 ], 604 ],
586 "position": { 605 "position": {
587 "left": 449.671875, 606 "left": 1537.640625,
588 "top": 777.09375 607 "top": 802.59375
589 }, 608 },
590 "post_job_actions": { 609 "post_job_actions": {
591 "HideDatasetActionout_file1": { 610 "HideDatasetActionout_file1": {
592 "action_arguments": {}, 611 "action_arguments": {},
593 "action_type": "HideDatasetAction", 612 "action_type": "HideDatasetAction",
594 "output_name": "out_file1" 613 "output_name": "out_file1"
595 } 614 }
596 }, 615 },
597 "tool_id": "trimmer", 616 "tool_id": "trimmer",
598 "tool_state": "{\"__page__\": null, \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"end\": \"\\\"-2\\\"\", \"fastq\": \"\\\"\\\"\", \"ignore\": \"null\", \"start\": \"\\\"1\\\"\", \"__rerun_remap_job_id__\": null, \"col\": \"\\\"0\\\"\"}", 617 "tool_state": "{\"__page__\": null, \"input1\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"end\": \"\\\"-2\\\"\", \"fastq\": \"\\\"\\\"\", \"ignore\": \"null\", \"start\": \"\\\"1\\\"\", \"__rerun_remap_job_id__\": null, \"col\": \"\\\"0\\\"\"}",
599 "tool_version": "0.0.1", 618 "tool_version": "0.0.1",
600 "type": "tool", 619 "type": "tool",
601 "uuid": "72a2109e-e01f-466e-a962-5c7ff5d0c2e3", 620 "uuid": "72a2109e-e01f-466e-a962-5c7ff5d0c2e3",
602 "workflow_outputs": [] 621 "workflow_outputs": []
603 }, 622 },
604 "11": { 623 "14": {
605 "annotation": "", 624 "annotation": "",
606 "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/1.0", 625 "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.2",
607 "errors": null, 626 "errors": null,
608 "id": 11, 627 "id": 14,
609 "input_connections": { 628 "input_connections": {
610 "identifiers": { 629 "header_criteria|identifiers": {
611 "id": 10, 630 "id": 13,
612 "output_name": "out_file1" 631 "output_name": "out_file1"
613 }, 632 },
614 "input": { 633 "input": {
615 "id": 0, 634 "id": 0,
616 "output_name": "output" 635 "output_name": "output"
617 } 636 }
618 }, 637 },
619 "inputs": [ 638 "inputs": [],
620 { 639 "label": null,
621 "description": "runtime parameter for tool Filter by FASTA IDs", 640 "name": "Filter FASTA",
622 "name": "input"
623 },
624 {
625 "description": "runtime parameter for tool Filter by FASTA IDs",
626 "name": "identifiers"
627 }
628 ],
629 "label": null,
630 "name": "Filter by FASTA IDs",
631 "outputs": [ 641 "outputs": [
632 { 642 {
633 "name": "output", 643 "name": "output",
634 "type": "fasta" 644 "type": "fasta"
635 } 645 }
636 ], 646 ],
637 "position": { 647 "position": {
638 "left": 575.8125, 648 "left": 1529.78125,
639 "top": 980 649 "top": 952.5
640 }, 650 },
641 "post_job_actions": { 651 "post_job_actions": {
642 "HideDatasetActionoutput": { 652 "HideDatasetActionoutput": {
643 "action_arguments": {}, 653 "action_arguments": {},
644 "action_type": "HideDatasetAction", 654 "action_type": "HideDatasetAction",
645 "output_name": "output" 655 "output_name": "output"
646 } 656 }
647 }, 657 },
648 "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/1.0", 658 "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.2",
649 "tool_shed_repository": { 659 "tool_shed_repository": {
650 "changeset_revision": "8d15aebf55fd", 660 "changeset_revision": "cd22452edec2",
651 "name": "filter_by_fasta_ids", 661 "name": "filter_by_fasta_ids",
652 "owner": "galaxyp", 662 "owner": "galaxyp",
653 "tool_shed": "toolshed.g2.bx.psu.edu" 663 "tool_shed": "toolshed.g2.bx.psu.edu"
654 }, 664 },
655 "tool_state": "{\"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"identifiers\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"dedup\": \"\\\"true\\\"\", \"__page__\": null}", 665 "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"dedup\": \"\\\"false\\\"\", \"input\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"header_criteria\": \"{\\\"__current_case__\\\": 1, \\\"header_criteria_select\\\": \\\"id_list\\\", \\\"id_regex\\\": {\\\"__current_case__\\\": 0, \\\"find\\\": \\\"beginning\\\"}, \\\"identifiers\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}}\", \"output_discarded\": \"\\\"false\\\"\", \"sequence_criteria\": \"{\\\"__current_case__\\\": 0, \\\"sequence_criteria_select\\\": \\\"\\\"}\"}",
656 "tool_version": "1.0", 666 "tool_version": "2.2",
657 "type": "tool", 667 "type": "tool",
658 "uuid": "b22832ea-47b0-46a1-87da-e362672133b1", 668 "uuid": "b22832ea-47b0-46a1-87da-e362672133b1",
659 "workflow_outputs": [] 669 "workflow_outputs": []
660 }, 670 },
661 "12": { 671 "15": {
662 "annotation": "", 672 "annotation": "",
663 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: tranalign100/5.0.0", 673 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: tranalign100/5.0.0",
664 "errors": null, 674 "errors": null,
665 "id": 12, 675 "id": 15,
666 "input_connections": { 676 "input_connections": {
667 "input1": { 677 "input1": {
668 "id": 11, 678 "id": 14,
669 "output_name": "output" 679 "output_name": "output"
670 }, 680 },
671 "input2": { 681 "input2": {
672 "id": 9, 682 "id": 12,
673 "output_name": "fasta_aln" 683 "output_name": "fasta_aln"
674 } 684 }
675 }, 685 },
676 "inputs": [ 686 "inputs": [],
677 {
678 "description": "runtime parameter for tool tranalign",
679 "name": "input2"
680 },
681 {
682 "description": "runtime parameter for tool tranalign",
683 "name": "input1"
684 }
685 ],
686 "label": null, 687 "label": null,
687 "name": "tranalign", 688 "name": "tranalign",
688 "outputs": [ 689 "outputs": [
689 { 690 {
690 "name": "out_file1", 691 "name": "out_file1",
691 "type": "fasta" 692 "type": "fasta"
692 } 693 }
693 ], 694 ],
694 "position": { 695 "position": {
695 "left": 952.84375, 696 "left": 994.828125,
696 "top": 879 697 "top": 1161.484375
697 }, 698 },
698 "post_job_actions": { 699 "post_job_actions": {
699 "HideDatasetActionout_file1": { 700 "HideDatasetActionout_file1": {
700 "action_arguments": {}, 701 "action_arguments": {},
701 "action_type": "HideDatasetAction", 702 "action_type": "HideDatasetAction",
702 "output_name": "out_file1" 703 "output_name": "out_file1"
703 } 704 }
704 }, 705 },
705 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: tranalign100/5.0.0", 706 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: tranalign100/5.0.0",
706 "tool_shed_repository": { 707 "tool_shed_repository": {
707 "changeset_revision": "1b6538ec8b56", 708 "changeset_revision": "dc492eb6a4fc",
708 "name": "emboss_5", 709 "name": "emboss_5",
709 "owner": "devteam", 710 "owner": "devteam",
710 "tool_shed": "toolshed.g2.bx.psu.edu" 711 "tool_shed": "toolshed.g2.bx.psu.edu"
711 }, 712 },
712 "tool_state": "{\"input2\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": null, \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"out_format1\": \"\\\"fasta\\\"\", \"__rerun_remap_job_id__\": null, \"table\": \"\\\"0\\\"\"}", 713 "tool_state": "{\"input2\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"__page__\": null, \"input1\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"out_format1\": \"\\\"fasta\\\"\", \"__rerun_remap_job_id__\": null, \"table\": \"\\\"0\\\"\"}",
713 "tool_version": "5.0.0", 714 "tool_version": "5.0.0",
714 "type": "tool", 715 "type": "tool",
715 "uuid": "e33d053e-1edf-44b7-a08a-abe8e5bcfbc6", 716 "uuid": "e33d053e-1edf-44b7-a08a-abe8e5bcfbc6",
716 "workflow_outputs": [] 717 "workflow_outputs": []
717 }, 718 },
718 "13": { 719 "16": {
719 "annotation": "", 720 "annotation": "",
720 "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/treebest_best/treebest_best/1.9.2", 721 "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/treebest_best/treebest_best/1.9.2.post0",
721 "errors": null, 722 "errors": null,
722 "id": 13, 723 "id": 16,
723 "input_connections": { 724 "input_connections": {
724 "aln": { 725 "aln": {
725 "id": 12, 726 "id": 15,
726 "output_name": "out_file1" 727 "output_name": "out_file1"
727 }, 728 },
728 "species_tree": { 729 "species_tree": {
729 "id": 2, 730 "id": 1,
730 "output_name": "output" 731 "output_name": "output"
731 } 732 }
732 }, 733 },
733 "inputs": [ 734 "inputs": [
734 {
735 "description": "runtime parameter for tool TreeBeST best",
736 "name": "aln"
737 },
738 { 735 {
739 "description": "runtime parameter for tool TreeBeST best", 736 "description": "runtime parameter for tool TreeBeST best",
740 "name": "C" 737 "name": "C"
741 },
742 {
743 "description": "runtime parameter for tool TreeBeST best",
744 "name": "species_tree"
745 } 738 }
746 ], 739 ],
747 "label": null, 740 "label": null,
748 "name": "TreeBeST best", 741 "name": "TreeBeST best",
749 "outputs": [ 742 "outputs": [
751 "name": "output", 744 "name": "output",
752 "type": "nhx" 745 "type": "nhx"
753 } 746 }
754 ], 747 ],
755 "position": { 748 "position": {
756 "left": 1173.921875, 749 "left": 1412.875,
757 "top": 967.5 750 "top": 1147.96875
758 }, 751 },
759 "post_job_actions": { 752 "post_job_actions": {
760 "HideDatasetActionoutput": { 753 "HideDatasetActionoutput": {
761 "action_arguments": {}, 754 "action_arguments": {},
762 "action_type": "HideDatasetAction", 755 "action_type": "HideDatasetAction",
763 "output_name": "output" 756 "output_name": "output"
764 } 757 }
765 }, 758 },
766 "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/treebest_best/treebest_best/1.9.2", 759 "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/treebest_best/treebest_best/1.9.2.post0",
767 "tool_shed_repository": { 760 "tool_shed_repository": {
768 "changeset_revision": "66170848da6c", 761 "changeset_revision": "b78b529f66db",
769 "name": "treebest_best", 762 "name": "treebest_best",
770 "owner": "earlhaminst", 763 "owner": "earlhaminst",
771 "tool_shed": "toolshed.g2.bx.psu.edu" 764 "tool_shed": "toolshed.g2.bx.psu.edu"
772 }, 765 },
773 "tool_state": "{\"A\": \"\\\"false\\\"\", \"aln\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"C\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"b\": \"\\\"0.01\\\"\", \"d\": \"\\\"0.15\\\"\", \"g\": \"\\\"false\\\"\", \"F\": \"\\\"11\\\"\", \"S\": \"\\\"false\\\"\", \"__page__\": null, \"k\": \"{\\\"__current_case__\\\": 0, \\\"k_selector\\\": \\\"yes\\\"}\", \"c\": \"\\\"2\\\"\", \"L\": \"\\\"0.2\\\"\", \"P\": \"\\\"false\\\"\", \"s\": \"\\\"false\\\"\", \"r\": \"\\\"false\\\"\", \"a\": \"{\\\"a_selector\\\": \\\"yes\\\", \\\"__current_case__\\\": 0}\", \"species_tree\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"N\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null, \"l\": \"\\\"0.1\\\"\"}", 766 "tool_state": "{\"A\": \"\\\"false\\\"\", \"aln\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"C\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"b\": \"\\\"0.01\\\"\", \"d\": \"\\\"0.15\\\"\", \"g\": \"\\\"false\\\"\", \"F\": \"\\\"11\\\"\", \"__page__\": null, \"s\": \"\\\"false\\\"\", \"k\": \"{\\\"__current_case__\\\": 0, \\\"k_selector\\\": \\\"yes\\\"}\", \"c\": \"\\\"2\\\"\", \"L\": \"\\\"0.2\\\"\", \"P\": \"\\\"false\\\"\", \"S\": \"\\\"false\\\"\", \"r\": \"\\\"false\\\"\", \"a\": \"{\\\"__current_case__\\\": 0, \\\"a_selector\\\": \\\"yes\\\"}\", \"species_tree\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"N\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null, \"l\": \"\\\"0.1\\\"\"}",
774 "tool_version": "1.9.2", 767 "tool_version": "1.9.2.post0",
775 "type": "tool", 768 "type": "tool",
776 "uuid": "3e42f4c3-7258-465b-bb24-7ea9e2d3ec40", 769 "uuid": "3e42f4c3-7258-465b-bb24-7ea9e2d3ec40",
777 "workflow_outputs": [] 770 "workflow_outputs": []
778 }, 771 },
779 "14": { 772 "17": {
773 "annotation": "",
774 "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/ete/ete_genetree_splitter/3.1.1",
775 "errors": null,
776 "id": 17,
777 "input_connections": {
778 "genetreeFile": {
779 "id": 16,
780 "output_name": "output"
781 }
782 },
783 "inputs": [],
784 "label": null,
785 "name": "ETE GeneTree splitter",
786 "outputs": [
787 {
788 "name": "genetrees_lists",
789 "type": "input"
790 }
791 ],
792 "position": {
793 "left": 1908.984375,
794 "top": 1125.984375
795 },
796 "post_job_actions": {
797 "HideDatasetActiongenetrees_lists": {
798 "action_arguments": {},
799 "action_type": "HideDatasetAction",
800 "output_name": "genetrees_lists"
801 }
802 },
803 "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/ete/ete_genetree_splitter/3.1.1",
804 "tool_shed_repository": {
805 "changeset_revision": "6a5282f71f82",
806 "name": "ete",
807 "owner": "earlhaminst",
808 "tool_shed": "toolshed.g2.bx.psu.edu"
809 },
810 "tool_state": "{\"__page__\": null, \"genetreeFile\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"output_format\": \"\\\"9\\\"\", \"gene_node\": \"\\\"0\\\"\", \"gainlose_conditional\": \"{\\\"__current_case__\\\": 0, \\\"gainlose\\\": \\\"False\\\"}\", \"__rerun_remap_job_id__\": null}",
811 "tool_version": "3.1.1",
812 "type": "tool",
813 "uuid": "ca969e72-b56e-44eb-a63e-72125b23f7c9",
814 "workflow_outputs": []
815 },
816 "18": {
780 "annotation": "", 817 "annotation": "",
781 "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/gafa/gafa/0.3.0", 818 "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/gafa/gafa/0.3.0",
782 "errors": null, 819 "errors": null,
783 "id": 14, 820 "id": 18,
784 "input_connections": { 821 "input_connections": {
785 "alignmentFile": { 822 "alignmentFile": {
786 "id": 9, 823 "id": 12,
787 "output_name": "fasta_aln" 824 "output_name": "fasta_aln"
788 }, 825 },
789 "genesFile": { 826 "genesFile": {
790 "id": 1, 827 "id": 2,
791 "output_name": "output" 828 "output_name": "output"
792 }, 829 },
793 "treeFile": { 830 "treeFile": {
794 "id": 13, 831 "id": 16,
795 "output_name": "output" 832 "output_name": "output"
796 } 833 }
797 }, 834 },
798 "inputs": [ 835 "inputs": [],
799 {
800 "description": "runtime parameter for tool Gene Align and Family Aggregator",
801 "name": "treeFile"
802 },
803 {
804 "description": "runtime parameter for tool Gene Align and Family Aggregator",
805 "name": "alignmentFile"
806 },
807 {
808 "description": "runtime parameter for tool Gene Align and Family Aggregator",
809 "name": "genesFile"
810 }
811 ],
812 "label": null, 836 "label": null,
813 "name": "Gene Align and Family Aggregator", 837 "name": "Gene Align and Family Aggregator",
814 "outputs": [ 838 "outputs": [
815 { 839 {
816 "name": "outputFile", 840 "name": "outputFile",
817 "type": "gafa.sqlite" 841 "type": "gafa.sqlite"
818 } 842 }
819 ], 843 ],
820 "position": { 844 "position": {
821 "left": 1299.921875, 845 "left": 2184.890625,
822 "top": 747.5 846 "top": 629.96875
823 }, 847 },
824 "post_job_actions": {}, 848 "post_job_actions": {},
825 "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/gafa/gafa/0.3.0", 849 "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/gafa/gafa/0.3.0",
826 "tool_shed_repository": { 850 "tool_shed_repository": {
827 "changeset_revision": "c388666f58e0", 851 "changeset_revision": "b9f1bcf5ee59",
828 "name": "gafa", 852 "name": "gafa",
829 "owner": "earlhaminst", 853 "owner": "earlhaminst",
830 "tool_shed": "toolshed.g2.bx.psu.edu" 854 "tool_shed": "toolshed.g2.bx.psu.edu"
831 }, 855 },
832 "tool_state": "{\"__page__\": null, \"treeFile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"alignmentFile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"genesFile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", 856 "tool_state": "{\"__page__\": null, \"treeFile\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"__rerun_remap_job_id__\": null, \"alignmentFile\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"genesFile\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}",
833 "tool_version": "0.3.0", 857 "tool_version": "0.3.0",
834 "type": "tool", 858 "type": "tool",
835 "uuid": "049fb5e1-4f3b-4cf5-80a6-2fa609674fc5", 859 "uuid": "049fb5e1-4f3b-4cf5-80a6-2fa609674fc5",
836 "workflow_outputs": [ 860 "workflow_outputs": [
837 { 861 {
838 "label": null, 862 "label": null,
839 "output_name": "outputFile", 863 "output_name": "outputFile",
840 "uuid": "a3dbb7a3-356a-4019-a10d-08896e990c8e" 864 "uuid": "a3dbb7a3-356a-4019-a10d-08896e990c8e"
865 }
866 ]
867 },
868 "19": {
869 "annotation": "",
870 "content_id": "__FLATTEN__",
871 "errors": null,
872 "id": 19,
873 "input_connections": {
874 "input": {
875 "id": 17,
876 "output_name": "genetrees_lists"
877 }
878 },
879 "inputs": [],
880 "label": null,
881 "name": "Flatten Collection",
882 "outputs": [
883 {
884 "name": "output",
885 "type": "input"
886 }
887 ],
888 "position": {
889 "left": 2206.984375,
890 "top": 1024.96875
891 },
892 "post_job_actions": {
893 "HideDatasetActionoutput": {
894 "action_arguments": {},
895 "action_type": "HideDatasetAction",
896 "output_name": "output"
897 }
898 },
899 "tool_id": "__FLATTEN__",
900 "tool_state": "{\"input\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"__rerun_remap_job_id__\": null, \"join_identifier\": \"\\\"_\\\"\", \"__page__\": null}",
901 "tool_version": "1.0.0",
902 "type": "tool",
903 "uuid": "5f6a95f6-1036-4a33-b610-a080b971a324",
904 "workflow_outputs": []
905 },
906 "20": {
907 "annotation": "",
908 "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/ete/ete_homology_classifier/3.1.1",
909 "errors": null,
910 "id": 20,
911 "input_connections": {
912 "genetreeFile": {
913 "id": 19,
914 "output_name": "output"
915 }
916 },
917 "inputs": [],
918 "label": null,
919 "name": "Homology Classifier and Filter",
920 "outputs": [
921 {
922 "name": "homology",
923 "type": "tabular"
924 }
925 ],
926 "position": {
927 "left": 2341.984375,
928 "top": 1160.96875
929 },
930 "post_job_actions": {},
931 "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/ete/ete_homology_classifier/3.1.1",
932 "tool_shed_repository": {
933 "changeset_revision": "6a5282f71f82",
934 "name": "ete",
935 "owner": "earlhaminst",
936 "tool_shed": "toolshed.g2.bx.psu.edu"
937 },
938 "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"genetreeFile\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"format_type\": \"{\\\"__current_case__\\\": 0, \\\"homologies\\\": [\\\"one-to-one\\\", \\\"one-to-many\\\", \\\"many-to-one\\\", \\\"many-to-many\\\", \\\"paralogs\\\"], \\\"out_format\\\": \\\"tabular\\\"}\"}",
939 "tool_version": "3.1.1",
940 "type": "tool",
941 "uuid": "427c5e21-0ed7-41b9-8e2b-447ea99e5c29",
942 "workflow_outputs": [
943 {
944 "label": null,
945 "output_name": "homology",
946 "uuid": "d20dba82-b0c5-41d7-9f2e-f67240548967"
841 } 947 }
842 ] 948 ]
843 } 949 }
844 }, 950 },
845 "tags": [], 951 "tags": [],
846 "uuid": "bbf45200-b853-41bf-a853-abb1dec8ca9d" 952 "uuid": "45eedb69-98b5-4ea2-9f17-791fa54ef823",
953 "version": 20
847 } 954 }