comparison Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_1-4.ga @ 3:ba15c770fd40 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
author drosofff
date Thu, 17 Nov 2016 07:27:04 -0500
parents 48b020a0d2f7
children 46614c7dd247
comparison
equal deleted inserted replaced
2:48b020a0d2f7 3:ba15c770fd40
93 }, 93 },
94 "post_job_actions": {}, 94 "post_job_actions": {},
95 "tool_errors": null, 95 "tool_errors": null,
96 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/yac_clipper/yac/1.3.6", 96 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/yac_clipper/yac/1.3.6",
97 "tool_shed_repository": { 97 "tool_shed_repository": {
98 "changeset_revision": "91cce7c1436d", 98 "changeset_revision": "a18edcf9c7ed",
99 "name": "yac_clipper", 99 "name": "yac_clipper",
100 "owner": "drosofff", 100 "owner": "drosofff",
101 "tool_shed": "toolshed.g2.bx.psu.edu" 101 "tool_shed": "toolshed.g2.bx.psu.edu"
102 }, 102 },
103 "tool_state": "{\"out_format\": \"\\\"fasta\\\"\", \"__page__\": 0, \"min\": \"\\\"18\\\"\", \"max\": \"\\\"30\\\"\", \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"459d9188801e11e5ae6af01fafdfc061\\\"\", \"clip_source\": \"{\\\"clip_source_list\\\": \\\"prebuilt\\\", \\\"clip_sequence\\\": \\\"CTGTAGGCACCATCAATCGT\\\", \\\"__current_case__\\\": 0}\", \"input\": \"null\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"Nmode\": \"\\\"reject\\\"\"}", 103 "tool_state": "{\"out_format\": \"\\\"fasta\\\"\", \"__page__\": 0, \"min\": \"\\\"18\\\"\", \"max\": \"\\\"30\\\"\", \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"459d9188801e11e5ae6af01fafdfc061\\\"\", \"clip_source\": \"{\\\"clip_source_list\\\": \\\"prebuilt\\\", \\\"clip_sequence\\\": \\\"CTGTAGGCACCATCAATCGT\\\", \\\"__current_case__\\\": 0}\", \"input\": \"null\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"Nmode\": \"\\\"reject\\\"\"}",
194 } 194 }
195 }, 195 },
196 "tool_errors": null, 196 "tool_errors": null,
197 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_fasta_tabular_converter/fasta_tabular_converter/1.1.0", 197 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_fasta_tabular_converter/fasta_tabular_converter/1.1.0",
198 "tool_shed_repository": { 198 "tool_shed_repository": {
199 "changeset_revision": "330dd8a8c31a", 199 "changeset_revision": "36388b666bfc",
200 "name": "msp_fasta_tabular_converter", 200 "name": "msp_fasta_tabular_converter",
201 "owner": "drosofff", 201 "owner": "drosofff",
202 "tool_shed": "toolshed.g2.bx.psu.edu" 202 "tool_shed": "toolshed.g2.bx.psu.edu"
203 }, 203 },
204 "tool_state": "{\"__page__\": 0, \"switch\": \"{\\\"input\\\": null, \\\"__current_case__\\\": 0, \\\"conversionType\\\": \\\"fasta2tabular\\\"}\", \"__rerun_remap_job_id__\": null}", 204 "tool_state": "{\"__page__\": 0, \"switch\": \"{\\\"input\\\": null, \\\"__current_case__\\\": 0, \\\"conversionType\\\": \\\"fasta2tabular\\\"}\", \"__rerun_remap_job_id__\": null}",
240 } 240 }
241 }, 241 },
242 "tool_errors": null, 242 "tool_errors": null,
243 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_fasta_tabular_converter/fasta_tabular_converter/1.1.0", 243 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_fasta_tabular_converter/fasta_tabular_converter/1.1.0",
244 "tool_shed_repository": { 244 "tool_shed_repository": {
245 "changeset_revision": "330dd8a8c31a", 245 "changeset_revision": "36388b666bfc",
246 "name": "msp_fasta_tabular_converter", 246 "name": "msp_fasta_tabular_converter",
247 "owner": "drosofff", 247 "owner": "drosofff",
248 "tool_shed": "toolshed.g2.bx.psu.edu" 248 "tool_shed": "toolshed.g2.bx.psu.edu"
249 }, 249 },
250 "tool_state": "{\"__page__\": 0, \"switch\": \"{\\\"input\\\": null, \\\"__current_case__\\\": 2, \\\"conversionType\\\": \\\"tabular2fastaweight\\\"}\", \"__rerun_remap_job_id__\": null}", 250 "tool_state": "{\"__page__\": 0, \"switch\": \"{\\\"input\\\": null, \\\"__current_case__\\\": 2, \\\"conversionType\\\": \\\"tabular2fastaweight\\\"}\", \"__rerun_remap_job_id__\": null}",
259 } 259 }
260 ] 260 ]
261 }, 261 },
262 "6": { 262 "6": {
263 "annotation": "", 263 "annotation": "",
264 "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.2", 264 "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.2.1",
265 "id": 6, 265 "id": 6,
266 "input_connections": { 266 "input_connections": {
267 "input": { 267 "input": {
268 "id": 5, 268 "id": 5,
269 "output_name": "output" 269 "output_name": "output"
308 "action_type": "RenameDatasetAction", 308 "action_type": "RenameDatasetAction",
309 "output_name": "unaligned" 309 "output_name": "unaligned"
310 } 310 }
311 }, 311 },
312 "tool_errors": null, 312 "tool_errors": null,
313 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.2", 313 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.2.1",
314 "tool_shed_repository": { 314 "tool_shed_repository": {
315 "changeset_revision": "c1bfa227bbb6", 315 "changeset_revision": "615d2550977f",
316 "name": "msp_sr_bowtie", 316 "name": "msp_sr_bowtie",
317 "owner": "drosofff", 317 "owner": "drosofff",
318 "tool_shed": "toolshed.g2.bx.psu.edu" 318 "tool_shed": "toolshed.g2.bx.psu.edu"
319 }, 319 },
320 "tool_state": "{\"__page__\": 0, \"output_format\": \"\\\"tabular\\\"\", \"additional_fasta\": \"\\\"unal\\\"\", \"v_mismatches\": \"\\\"2\\\"\", \"__rerun_remap_job_id__\": null, \"input\": \"null\", \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"dm6\\\", \\\"__current_case__\\\": 0}\", \"method\": \"\\\"k_option\\\"\"}", 320 "tool_state": "{\"__page__\": 0, \"output_format\": \"\\\"tabular\\\"\", \"additional_fasta\": \"\\\"unal\\\"\", \"v_mismatches\": \"\\\"2\\\"\", \"__rerun_remap_job_id__\": null, \"input\": \"null\", \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"dm6\\\", \\\"__current_case__\\\": 0}\", \"method\": \"\\\"k_option\\\"\"}",
321 "tool_version": "1.1.2", 321 "tool_version": "1.1.2.1",
322 "type": "tool", 322 "type": "tool",
323 "uuid": "e22c6843-8125-49d6-9dcd-546155536f78", 323 "uuid": "e22c6843-8125-49d6-9dcd-546155536f78",
324 "workflow_outputs": [ 324 "workflow_outputs": [
325 { 325 {
326 "label": null, 326 "label": null,
329 } 329 }
330 ] 330 ]
331 }, 331 },
332 "7": { 332 "7": {
333 "annotation": "", 333 "annotation": "",
334 "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_oases/oasesoptimiserv/1.1.4", 334 "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_oases/oasesoptimiserv/1.1.5",
335 "id": 7, 335 "id": 7,
336 "input_connections": { 336 "input_connections": {
337 "inputs_0|input": { 337 "inputs_0|input": {
338 "id": 6, 338 "id": 6,
339 "output_name": "unaligned" 339 "output_name": "unaligned"
360 "action_type": "RenameDatasetAction", 360 "action_type": "RenameDatasetAction",
361 "output_name": "transcripts" 361 "output_name": "transcripts"
362 } 362 }
363 }, 363 },
364 "tool_errors": null, 364 "tool_errors": null,
365 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_oases/oasesoptimiserv/1.1.4", 365 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_oases/oasesoptimiserv/1.1.5",
366 "tool_shed_repository": { 366 "tool_shed_repository": {
367 "changeset_revision": "f08d9c814ffb", 367 "changeset_revision": "dc684e37f668",
368 "name": "msp_oases", 368 "name": "msp_oases",
369 "owner": "drosofff", 369 "owner": "drosofff",
370 "tool_shed": "toolshed.g2.bx.psu.edu" 370 "tool_shed": "toolshed.g2.bx.psu.edu"
371 }, 371 },
372 "tool_state": "{\"__page__\": 0, \"inputs\": \"[{\\\"__index__\\\": 0, \\\"input\\\": null}]\", \"end_hash_length\": \"\\\"29\\\"\", \"__rerun_remap_job_id__\": null, \"start_hash_length\": \"\\\"13\\\"\"}", 372 "tool_state": "{\"__page__\": 0, \"inputs\": \"[{\\\"__index__\\\": 0, \\\"input\\\": null}]\", \"end_hash_length\": \"\\\"29\\\"\", \"__rerun_remap_job_id__\": null, \"start_hash_length\": \"\\\"13\\\"\"}",
373 "tool_version": "1.1.4", 373 "tool_version": "1.1.5",
374 "type": "tool", 374 "type": "tool",
375 "uuid": "4290f9b9-2ea7-4634-a639-bc008f1eb90c", 375 "uuid": "4290f9b9-2ea7-4634-a639-bc008f1eb90c",
376 "workflow_outputs": [ 376 "workflow_outputs": [
377 { 377 {
378 "label": null, 378 "label": null,
381 } 381 }
382 ] 382 ]
383 }, 383 },
384 "8": { 384 "8": {
385 "annotation": "", 385 "annotation": "",
386 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.06", 386 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.08",
387 "id": 8, 387 "id": 8,
388 "input_connections": { 388 "input_connections": {
389 "db_opts|histdb": { 389 "db_opts|histdb": {
390 "id": 1, 390 "id": 1,
391 "output_name": "output" 391 "output_name": "output"
408 "left": 1273.4895935058594, 408 "left": 1273.4895935058594,
409 "top": 800.4861679077148 409 "top": 800.4861679077148
410 }, 410 },
411 "post_job_actions": {}, 411 "post_job_actions": {},
412 "tool_errors": null, 412 "tool_errors": null,
413 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.06", 413 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.08",
414 "tool_shed_repository": { 414 "tool_shed_repository": {
415 "changeset_revision": "577d9c12411a", 415 "changeset_revision": "3034ce97dd33",
416 "name": "ncbi_blast_plus", 416 "name": "ncbi_blast_plus",
417 "owner": "devteam", 417 "owner": "devteam",
418 "tool_shed": "toolshed.g2.bx.psu.edu" 418 "tool_shed": "toolshed.g2.bx.psu.edu"
419 }, 419 },
420 "tool_state": "{\"evalue_cutoff\": \"\\\"0.001\\\"\", \"output\": \"{\\\"out_format\\\": \\\"cols\\\", \\\"std_cols\\\": [\\\"qseqid\\\", \\\"sseqid\\\", \\\"pident\\\", \\\"length\\\", \\\"mismatch\\\", \\\"gapopen\\\", \\\"qstart\\\", \\\"qend\\\", \\\"sstart\\\", \\\"send\\\", \\\"evalue\\\", \\\"bitscore\\\"], \\\"ids_cols\\\": null, \\\"tax_cols\\\": null, \\\"__current_case__\\\": 2, \\\"misc_cols\\\": null, \\\"ext_cols\\\": [\\\"slen\\\"]}\", \"adv_opts\": \"{\\\"adv_optional_id_files_opts\\\": {\\\"__current_case__\\\": 0, \\\"adv_optional_id_files_opts_selector\\\": \\\"none\\\"}, \\\"identity_cutoff\\\": \\\"0.0\\\", \\\"adv_opts_selector\\\": \\\"advanced\\\", \\\"ungapped\\\": \\\"false\\\", \\\"filter_query\\\": \\\"true\\\", \\\"word_size\\\": \\\"0\\\", \\\"__current_case__\\\": 1, \\\"parse_deflines\\\": \\\"false\\\", \\\"qcov_hsp_perc\\\": \\\"0.0\\\", \\\"strand\\\": \\\"-strand both\\\", \\\"max_hits\\\": \\\"5\\\"}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"4dd2fde8802311e5bcddf01fafdfc061\\\"\", \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"histdb\\\", \\\"subject\\\": \\\"\\\", \\\"histdb\\\": null, \\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\"}\", \"blast_type\": \"\\\"blastn\\\"\", \"query\": \"null\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 420 "tool_state": "{\"evalue_cutoff\": \"\\\"0.001\\\"\", \"output\": \"{\\\"out_format\\\": \\\"cols\\\", \\\"std_cols\\\": [\\\"qseqid\\\", \\\"sseqid\\\", \\\"pident\\\", \\\"length\\\", \\\"mismatch\\\", \\\"gapopen\\\", \\\"qstart\\\", \\\"qend\\\", \\\"sstart\\\", \\\"send\\\", \\\"evalue\\\", \\\"bitscore\\\"], \\\"ids_cols\\\": null, \\\"tax_cols\\\": null, \\\"__current_case__\\\": 2, \\\"misc_cols\\\": null, \\\"ext_cols\\\": [\\\"slen\\\"]}\", \"adv_opts\": \"{\\\"adv_optional_id_files_opts\\\": {\\\"__current_case__\\\": 0, \\\"adv_optional_id_files_opts_selector\\\": \\\"none\\\"}, \\\"identity_cutoff\\\": \\\"0.0\\\", \\\"adv_opts_selector\\\": \\\"advanced\\\", \\\"ungapped\\\": \\\"false\\\", \\\"filter_query\\\": \\\"true\\\", \\\"word_size\\\": \\\"0\\\", \\\"__current_case__\\\": 1, \\\"parse_deflines\\\": \\\"false\\\", \\\"qcov_hsp_perc\\\": \\\"0.0\\\", \\\"strand\\\": \\\"-strand both\\\", \\\"max_hits\\\": \\\"5\\\"}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"4dd2fde8802311e5bcddf01fafdfc061\\\"\", \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"histdb\\\", \\\"subject\\\": \\\"\\\", \\\"histdb\\\": null, \\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\"}\", \"blast_type\": \"\\\"blastn\\\"\", \"query\": \"null\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
421 "tool_version": "0.1.06", 421 "tool_version": "0.1.08",
422 "type": "tool", 422 "type": "tool",
423 "uuid": "bf30a0ad-4ef9-49f0-b4c7-4aae52017748", 423 "uuid": "bf30a0ad-4ef9-49f0-b4c7-4aae52017748",
424 "workflow_outputs": [ 424 "workflow_outputs": [
425 { 425 {
426 "label": null, 426 "label": null,
486 } 486 }
487 }, 487 },
488 "tool_errors": null, 488 "tool_errors": null,
489 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_blastparser_and_hits/BlastParser_and_hits/2.4.3", 489 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_blastparser_and_hits/BlastParser_and_hits/2.4.3",
490 "tool_shed_repository": { 490 "tool_shed_repository": {
491 "changeset_revision": "6dfa79a6908a", 491 "changeset_revision": "1991c830504a",
492 "name": "msp_blastparser_and_hits", 492 "name": "msp_blastparser_and_hits",
493 "owner": "drosofff", 493 "owner": "drosofff",
494 "tool_shed": "toolshed.g2.bx.psu.edu" 494 "tool_shed": "toolshed.g2.bx.psu.edu"
495 }, 495 },
496 "tool_state": "{\"__page__\": 0, \"flanking\": \"\\\"5\\\"\", \"additional_filters\": \"{\\\"__current_case__\\\": 0, \\\"use_filters\\\": \\\"no\\\"}\", \"__rerun_remap_job_id__\": null, \"mode\": \"\\\"short\\\"\", \"sequences\": \"null\", \"blast\": \"null\"}", 496 "tool_state": "{\"__page__\": 0, \"flanking\": \"\\\"5\\\"\", \"additional_filters\": \"{\\\"__current_case__\\\": 0, \\\"use_filters\\\": \\\"no\\\"}\", \"__rerun_remap_job_id__\": null, \"mode\": \"\\\"short\\\"\", \"sequences\": \"null\", \"blast\": \"null\"}",