Mercurial > repos > peterjc > rxlr_venn_workflow

comparison rxlr_venn_workflow.ga @ 4:3c280e01b920 draft

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Uploaded v0.0.2, bump tool version numbers to fix warning about Filter1 parameter, adding link to Tool Shed in annotation. No functional changes.
author peterjc
date Wed, 21 Aug 2013 13:01:51 -0400
parents 0e7c07ff11f9
children 4726b640f221
comparison
equal deleted inserted replaced
3:1a1ab2f2b5b5 4:3c280e01b920
1 { 1 {
2 "a_galaxy_workflow": "true", 2 "a_galaxy_workflow": "true",
3 "annotation": "", 3 "annotation": "Takes a protein FASTA file, runs three different RXLR motif methods, draws a Venn diagram comparing them, and creates a FASTA file of those proteins passing all three screens.<br />\n<br />\nThis workflow is <a href=\"http://toolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow\" target=\"_blank\">available on the Galaxy Tool Shed</a> with a README file giving more information including sample data, and full citation details (Cock and Pritchard 2013).",
4 "format-version": "0.1", 4 "format-version": "0.1",
5 "name": "3 RXLR methods, Venn Diagram, overlap FASTA", 5 "name": "3 RXLR methods, Venn Diagram, overlap FASTA",
6 "steps": { 6 "steps": {
7 "0": { 7 "0": {
8 "annotation": "", 8 "annotation": "",
55 "output_name": "tabular_file" 55 "output_name": "tabular_file"
56 } 56 }
57 }, 57 },
58 "tool_errors": null, 58 "tool_errors": null,
59 "tool_id": "rxlr_motifs", 59 "tool_id": "rxlr_motifs",
60 "tool_state": "{\"__page__\": 0, \"fasta_file\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"model\": \"\\\"Whisson2007\\\"\"}", 60 "tool_state": "{\"__page__\": 0, \"fasta_file\": \"null\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"model\": \"\\\"Whisson2007\\\"\"}",
61 "tool_version": "0.0.6", 61 "tool_version": "0.0.7",
62 "type": "tool", 62 "type": "tool",
63 "user_outputs": [] 63 "user_outputs": []
64 }, 64 },
65 "2": { 65 "2": {
66 "annotation": "", 66 "annotation": "",
90 "output_name": "tabular_file" 90 "output_name": "tabular_file"
91 } 91 }
92 }, 92 },
93 "tool_errors": null, 93 "tool_errors": null,
94 "tool_id": "rxlr_motifs", 94 "tool_id": "rxlr_motifs",
95 "tool_state": "{\"__page__\": 0, \"fasta_file\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"model\": \"\\\"Win2007\\\"\"}", 95 "tool_state": "{\"__page__\": 0, \"fasta_file\": \"null\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"model\": \"\\\"Win2007\\\"\"}",
96 "tool_version": "0.0.6", 96 "tool_version": "0.0.7",
97 "type": "tool", 97 "type": "tool",
98 "user_outputs": [] 98 "user_outputs": []
99 }, 99 },
100 "3": { 100 "3": {
101 "annotation": "", 101 "annotation": "",
125 "output_name": "tabular_file" 125 "output_name": "tabular_file"
126 } 126 }
127 }, 127 },
128 "tool_errors": null, 128 "tool_errors": null,
129 "tool_id": "rxlr_motifs", 129 "tool_id": "rxlr_motifs",
130 "tool_state": "{\"__page__\": 0, \"fasta_file\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"model\": \"\\\"Bhattacharjee2006\\\"\"}", 130 "tool_state": "{\"__page__\": 0, \"fasta_file\": \"null\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"model\": \"\\\"Bhattacharjee2006\\\"\"}",
131 "tool_version": "0.0.6", 131 "tool_version": "0.0.7",
132 "type": "tool", 132 "type": "tool",
133 "user_outputs": [] 133 "user_outputs": []
134 }, 134 },
135 "4": { 135 "4": {
136 "annotation": "", 136 "annotation": "",
167 "output_name": "out_file1" 167 "output_name": "out_file1"
168 } 168 }
169 }, 169 },
170 "tool_errors": null, 170 "tool_errors": null,
171 "tool_id": "Filter1", 171 "tool_id": "Filter1",
172 "tool_state": "{\"__page__\": 0, \"cond\": \"\\\"c2=='Y'\\\"\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"input\": \"null\"}", 172 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"cond\": \"\\\"c2=='Y'\\\"\", \"input\": \"null\", \"header_lines\": \"\\\"0\\\"\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
173 "tool_version": "1.1.0", 173 "tool_version": "1.1.0",
174 "type": "tool", 174 "type": "tool",
175 "user_outputs": [] 175 "user_outputs": []
176 }, 176 },
177 "5": { 177 "5": {
209 "output_name": "out_file1" 209 "output_name": "out_file1"
210 } 210 }
211 }, 211 },
212 "tool_errors": null, 212 "tool_errors": null,
213 "tool_id": "Filter1", 213 "tool_id": "Filter1",
214 "tool_state": "{\"__page__\": 0, \"cond\": \"\\\"c2=='Y'\\\"\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"input\": \"null\"}", 214 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"cond\": \"\\\"c2=='Y'\\\"\", \"input\": \"null\", \"header_lines\": \"\\\"0\\\"\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
215 "tool_version": "1.1.0", 215 "tool_version": "1.1.0",
216 "type": "tool", 216 "type": "tool",
217 "user_outputs": [] 217 "user_outputs": []
218 }, 218 },
219 "6": { 219 "6": {
251 "output_name": "out_file1" 251 "output_name": "out_file1"
252 } 252 }
253 }, 253 },
254 "tool_errors": null, 254 "tool_errors": null,
255 "tool_id": "Filter1", 255 "tool_id": "Filter1",
256 "tool_state": "{\"__page__\": 0, \"cond\": \"\\\"c2=='Y'\\\"\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"input\": \"null\"}", 256 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"cond\": \"\\\"c2=='Y'\\\"\", \"input\": \"null\", \"header_lines\": \"\\\"0\\\"\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
257 "tool_version": "1.1.0", 257 "tool_version": "1.1.0",
258 "type": "tool", 258 "type": "tool",
259 "user_outputs": [] 259 "user_outputs": []
260 }, 260 },
261 "7": { 261 "7": {
306 "output_name": "output_pos" 306 "output_name": "output_pos"
307 } 307 }
308 }, 308 },
309 "tool_errors": null, 309 "tool_errors": null,
310 "tool_id": "seq_filter_by_id", 310 "tool_id": "seq_filter_by_id",
311 "tool_state": "{\"__page__\": 0, \"output_choice_cond\": \"{\\\"output_choice\\\": \\\"pos\\\", \\\"__current_case__\\\": 1}\", \"input_file\": \"null\", \"input_tabular\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"columns\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": [\\\"1\\\"]}\"}", 311 "tool_state": "{\"__page__\": 0, \"output_choice_cond\": \"{\\\"output_choice\\\": \\\"pos\\\", \\\"__current_case__\\\": 1}\", \"input_file\": \"null\", \"__rerun_remap_job_id__\": null, \"input_tabular\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"columns\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": [\\\"1\\\"]}\"}",
312 "tool_version": "0.0.5", 312 "tool_version": "0.0.5",
313 "type": "tool", 313 "type": "tool",
314 "user_outputs": [] 314 "user_outputs": []
315 }, 315 },
316 "8": { 316 "8": {
355 "output_name": "PDF" 355 "output_name": "PDF"
356 } 356 }
357 }, 357 },
358 "tool_errors": null, 358 "tool_errors": null,
359 "tool_id": "venn_list", 359 "tool_id": "venn_list",
360 "tool_state": "{\"__page__\": 0, \"universe\": \"{\\\"main\\\": null, \\\"type_select\\\": \\\"explicit\\\", \\\"__current_case__\\\": 0}\", \"sets\": \"[{\\\"__index__\\\": 0, \\\"set\\\": null, \\\"lab\\\": \\\"Whisson et al.\\\"}, {\\\"__index__\\\": 1, \\\"set\\\": null, \\\"lab\\\": \\\"Win et al.\\\"}, {\\\"__index__\\\": 2, \\\"set\\\": null, \\\"lab\\\": \\\"Bhattacharjee et al.\\\"}]\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"main_lab\": \"\\\"Venn Diagram comparing RXLR predictions\\\"\"}", 360 "tool_state": "{\"__page__\": 0, \"universe\": \"{\\\"main\\\": null, \\\"type_select\\\": \\\"explicit\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"main_lab\": \"\\\"Venn Diagram comparing RXLR predictions\\\"\", \"sets\": \"[{\\\"__index__\\\": 0, \\\"set\\\": null, \\\"lab\\\": \\\"Whisson et al.\\\"}, {\\\"__index__\\\": 1, \\\"set\\\": null, \\\"lab\\\": \\\"Win et al.\\\"}, {\\\"__index__\\\": 2, \\\"set\\\": null, \\\"lab\\\": \\\"Bhattacharjee et al.\\\"}]\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
361 "tool_version": "0.0.4", 361 "tool_version": "0.0.4",
362 "type": "tool", 362 "type": "tool",
363 "user_outputs": [] 363 "user_outputs": []
364 }, 364 },
365 "9": { 365 "9": {
410 "output_name": "output_pos" 410 "output_name": "output_pos"
411 } 411 }
412 }, 412 },
413 "tool_errors": null, 413 "tool_errors": null,
414 "tool_id": "seq_filter_by_id", 414 "tool_id": "seq_filter_by_id",
415 "tool_state": "{\"__page__\": 0, \"output_choice_cond\": \"{\\\"output_choice\\\": \\\"pos\\\", \\\"__current_case__\\\": 1}\", \"input_file\": \"null\", \"input_tabular\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"columns\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": [\\\"1\\\"]}\"}", 415 "tool_state": "{\"__page__\": 0, \"output_choice_cond\": \"{\\\"output_choice\\\": \\\"pos\\\", \\\"__current_case__\\\": 1}\", \"input_file\": \"null\", \"__rerun_remap_job_id__\": null, \"input_tabular\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"columns\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": [\\\"1\\\"]}\"}",
416 "tool_version": "0.0.5", 416 "tool_version": "0.0.5",
417 "type": "tool", 417 "type": "tool",
418 "user_outputs": [] 418 "user_outputs": []
419 }, 419 },
420 "10": { 420 "10": {
460 "output_name": "output_pos" 460 "output_name": "output_pos"
461 } 461 }
462 }, 462 },
463 "tool_errors": null, 463 "tool_errors": null,
464 "tool_id": "seq_filter_by_id", 464 "tool_id": "seq_filter_by_id",
465 "tool_state": "{\"__page__\": 0, \"output_choice_cond\": \"{\\\"output_choice\\\": \\\"pos\\\", \\\"__current_case__\\\": 1}\", \"input_file\": \"null\", \"input_tabular\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"columns\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": [\\\"1\\\"]}\"}", 465 "tool_state": "{\"__page__\": 0, \"output_choice_cond\": \"{\\\"output_choice\\\": \\\"pos\\\", \\\"__current_case__\\\": 1}\", \"input_file\": \"null\", \"__rerun_remap_job_id__\": null, \"input_tabular\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"columns\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": [\\\"1\\\"]}\"}",
466 "tool_version": "0.0.5", 466 "tool_version": "0.0.5",
467 "type": "tool", 467 "type": "tool",
468 "user_outputs": [] 468 "user_outputs": []
469 } 469 }
470 } 470 }