comparison Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_1-3.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
105 } 105 }
106 }, 106 },
107 "tool_errors": null, 107 "tool_errors": null,
108 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/fetch_fasta_from_ncbi/retrieve_fasta_from_NCBI/0.9.4", 108 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/fetch_fasta_from_ncbi/retrieve_fasta_from_NCBI/0.9.4",
109 "tool_shed_repository": { 109 "tool_shed_repository": {
110 "changeset_revision": "befdb392fece", 110 "changeset_revision": "a9d8f69d59fb",
111 "name": "fetch_fasta_from_ncbi", 111 "name": "fetch_fasta_from_ncbi",
112 "owner": "drosofff", 112 "owner": "drosofff",
113 "tool_shed": "toolshed.g2.bx.psu.edu" 113 "tool_shed": "toolshed.g2.bx.psu.edu"
114 }, 114 },
115 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"queryString\": \"\\\"${ncbi_guide_ID}\\\"\", \"dbname\": \"\\\"nuccore\\\"\"}", 115 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"queryString\": \"\\\"${ncbi_guide_ID}\\\"\", \"dbname\": \"\\\"nuccore\\\"\"}",
149 }, 149 },
150 "post_job_actions": {}, 150 "post_job_actions": {},
151 "tool_errors": null, 151 "tool_errors": null,
152 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/yac_clipper/yac/1.3.6", 152 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/yac_clipper/yac/1.3.6",
153 "tool_shed_repository": { 153 "tool_shed_repository": {
154 "changeset_revision": "91cce7c1436d", 154 "changeset_revision": "a18edcf9c7ed",
155 "name": "yac_clipper", 155 "name": "yac_clipper",
156 "owner": "drosofff", 156 "owner": "drosofff",
157 "tool_shed": "toolshed.g2.bx.psu.edu" 157 "tool_shed": "toolshed.g2.bx.psu.edu"
158 }, 158 },
159 "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\\\"\"}", 159 "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\\\"\"}",
168 } 168 }
169 ] 169 ]
170 }, 170 },
171 "4": { 171 "4": {
172 "annotation": "", 172 "annotation": "",
173 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.1.06", 173 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.1.08",
174 "id": 4, 174 "id": 4,
175 "input_connections": { 175 "input_connections": {
176 "input_file": { 176 "input_file": {
177 "id": 2, 177 "id": 2,
178 "output_name": "outfilename" 178 "output_name": "outfilename"
197 "action_type": "HideDatasetAction", 197 "action_type": "HideDatasetAction",
198 "output_name": "outfile" 198 "output_name": "outfile"
199 } 199 }
200 }, 200 },
201 "tool_errors": null, 201 "tool_errors": null,
202 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.1.06", 202 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.1.08",
203 "tool_shed_repository": { 203 "tool_shed_repository": {
204 "changeset_revision": "577d9c12411a", 204 "changeset_revision": "3034ce97dd33",
205 "name": "ncbi_blast_plus", 205 "name": "ncbi_blast_plus",
206 "owner": "devteam", 206 "owner": "devteam",
207 "tool_shed": "toolshed.g2.bx.psu.edu" 207 "tool_shed": "toolshed.g2.bx.psu.edu"
208 }, 208 },
209 "tool_state": "{\"__page__\": 0, \"mask_data_file\": \"null\", \"input_file\": \"null\", \"dbtype\": \"\\\"nucl\\\"\", \"__rerun_remap_job_id__\": null, \"hash_index\": \"\\\"true\\\"\", \"tax\": \"{\\\"__current_case__\\\": 0, \\\"taxselect\\\": \\\"\\\"}\", \"__workflow_invocation_uuid__\": \"\\\"ae5b2b58802911e5808df01fafdfc061\\\"\", \"title\": \"\\\"Blastn candidate database\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"parse_seqids\": \"\\\"false\\\"\"}", 209 "tool_state": "{\"__page__\": 0, \"mask_data_file\": \"null\", \"input_file\": \"null\", \"dbtype\": \"\\\"nucl\\\"\", \"__rerun_remap_job_id__\": null, \"hash_index\": \"\\\"true\\\"\", \"tax\": \"{\\\"__current_case__\\\": 0, \\\"taxselect\\\": \\\"\\\"}\", \"__workflow_invocation_uuid__\": \"\\\"ae5b2b58802911e5808df01fafdfc061\\\"\", \"title\": \"\\\"Blastn candidate database\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"parse_seqids\": \"\\\"false\\\"\"}",
210 "tool_version": "0.1.06", 210 "tool_version": "0.1.08",
211 "type": "tool", 211 "type": "tool",
212 "uuid": "ce29cdbe-653a-4d0e-b225-0d0762c28d4d", 212 "uuid": "ce29cdbe-653a-4d0e-b225-0d0762c28d4d",
213 "workflow_outputs": [] 213 "workflow_outputs": []
214 }, 214 },
215 "5": { 215 "5": {
315 } 315 }
316 }, 316 },
317 "tool_errors": null, 317 "tool_errors": null,
318 "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/khmer_normalize_by_median/khmer_normalize_by_median/2.0.0", 318 "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/khmer_normalize_by_median/khmer_normalize_by_median/2.0.0",
319 "tool_shed_repository": { 319 "tool_shed_repository": {
320 "changeset_revision": "6d8793a4923d", 320 "changeset_revision": "ee081dc6c578",
321 "name": "khmer_normalize_by_median", 321 "name": "khmer_normalize_by_median",
322 "owner": "iuc", 322 "owner": "iuc",
323 "tool_shed": "toolshed.g2.bx.psu.edu" 323 "tool_shed": "toolshed.g2.bx.psu.edu"
324 }, 324 },
325 "tool_state": "{\"force_single_switch\": \"\\\"true\\\"\", \"cutoff\": \"\\\"20\\\"\", \"save_countgraph\": \"\\\"false\\\"\", \"parameters\": \"{\\\"type\\\": \\\"simple\\\", \\\"tablesize\\\": \\\"2e9\\\", \\\"__current_case__\\\": 0}\", \"inputs\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"paired_switch\": \"\\\"false\\\"\", \"countgraph_to_load\": \"null\", \"unpaired_reads_filename\": \"null\"}", 325 "tool_state": "{\"force_single_switch\": \"\\\"true\\\"\", \"cutoff\": \"\\\"20\\\"\", \"save_countgraph\": \"\\\"false\\\"\", \"parameters\": \"{\\\"type\\\": \\\"simple\\\", \\\"tablesize\\\": \\\"2e9\\\", \\\"__current_case__\\\": 0}\", \"inputs\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"paired_switch\": \"\\\"false\\\"\", \"countgraph_to_load\": \"null\", \"unpaired_reads_filename\": \"null\"}",
385 "uuid": "8480cd00-f3b5-4ddb-a140-370a0b6e8c99", 385 "uuid": "8480cd00-f3b5-4ddb-a140-370a0b6e8c99",
386 "workflow_outputs": [] 386 "workflow_outputs": []
387 }, 387 },
388 "8": { 388 "8": {
389 "annotation": "", 389 "annotation": "",
390 "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.2", 390 "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.2.1",
391 "id": 8, 391 "id": 8,
392 "input_connections": { 392 "input_connections": {
393 "input": { 393 "input": {
394 "id": 7, 394 "id": 7,
395 "output_name": "out_file1" 395 "output_name": "out_file1"
434 "action_type": "RenameDatasetAction", 434 "action_type": "RenameDatasetAction",
435 "output_name": "unaligned" 435 "output_name": "unaligned"
436 } 436 }
437 }, 437 },
438 "tool_errors": null, 438 "tool_errors": null,
439 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.2", 439 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.2.1",
440 "tool_shed_repository": { 440 "tool_shed_repository": {
441 "changeset_revision": "c1bfa227bbb6", 441 "changeset_revision": "615d2550977f",
442 "name": "msp_sr_bowtie", 442 "name": "msp_sr_bowtie",
443 "owner": "drosofff", 443 "owner": "drosofff",
444 "tool_shed": "toolshed.g2.bx.psu.edu" 444 "tool_shed": "toolshed.g2.bx.psu.edu"
445 }, 445 },
446 "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\\\"\"}", 446 "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\\\"\"}",
447 "tool_version": "1.1.2", 447 "tool_version": "1.1.2.1",
448 "type": "tool", 448 "type": "tool",
449 "uuid": "e22c6843-8125-49d6-9dcd-546155536f78", 449 "uuid": "e22c6843-8125-49d6-9dcd-546155536f78",
450 "workflow_outputs": [ 450 "workflow_outputs": [
451 { 451 {
452 "label": null, 452 "label": null,
455 } 455 }
456 ] 456 ]
457 }, 457 },
458 "9": { 458 "9": {
459 "annotation": "", 459 "annotation": "",
460 "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_oases/oasesoptimiserv/1.1.4", 460 "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_oases/oasesoptimiserv/1.1.5",
461 "id": 9, 461 "id": 9,
462 "input_connections": { 462 "input_connections": {
463 "inputs_0|input": { 463 "inputs_0|input": {
464 "id": 8, 464 "id": 8,
465 "output_name": "unaligned" 465 "output_name": "unaligned"
486 "action_type": "RenameDatasetAction", 486 "action_type": "RenameDatasetAction",
487 "output_name": "transcripts" 487 "output_name": "transcripts"
488 } 488 }
489 }, 489 },
490 "tool_errors": null, 490 "tool_errors": null,
491 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_oases/oasesoptimiserv/1.1.4", 491 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_oases/oasesoptimiserv/1.1.5",
492 "tool_shed_repository": { 492 "tool_shed_repository": {
493 "changeset_revision": "f08d9c814ffb", 493 "changeset_revision": "dc684e37f668",
494 "name": "msp_oases", 494 "name": "msp_oases",
495 "owner": "drosofff", 495 "owner": "drosofff",
496 "tool_shed": "toolshed.g2.bx.psu.edu" 496 "tool_shed": "toolshed.g2.bx.psu.edu"
497 }, 497 },
498 "tool_state": "{\"__page__\": 0, \"inputs\": \"[{\\\"__index__\\\": 0, \\\"input\\\": null}]\", \"end_hash_length\": \"\\\"29\\\"\", \"__rerun_remap_job_id__\": null, \"start_hash_length\": \"\\\"13\\\"\"}", 498 "tool_state": "{\"__page__\": 0, \"inputs\": \"[{\\\"__index__\\\": 0, \\\"input\\\": null}]\", \"end_hash_length\": \"\\\"29\\\"\", \"__rerun_remap_job_id__\": null, \"start_hash_length\": \"\\\"13\\\"\"}",
499 "tool_version": "1.1.4", 499 "tool_version": "1.1.5",
500 "type": "tool", 500 "type": "tool",
501 "uuid": "4290f9b9-2ea7-4634-a639-bc008f1eb90c", 501 "uuid": "4290f9b9-2ea7-4634-a639-bc008f1eb90c",
502 "workflow_outputs": [ 502 "workflow_outputs": [
503 { 503 {
504 "label": null, 504 "label": null,
507 } 507 }
508 ] 508 ]
509 }, 509 },
510 "10": { 510 "10": {
511 "annotation": "", 511 "annotation": "",
512 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.06", 512 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.08",
513 "id": 10, 513 "id": 10,
514 "input_connections": { 514 "input_connections": {
515 "db_opts|histdb": { 515 "db_opts|histdb": {
516 "id": 1, 516 "id": 1,
517 "output_name": "output" 517 "output_name": "output"
540 "action_type": "HideDatasetAction", 540 "action_type": "HideDatasetAction",
541 "output_name": "output1" 541 "output_name": "output1"
542 } 542 }
543 }, 543 },
544 "tool_errors": null, 544 "tool_errors": null,
545 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.06", 545 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.08",
546 "tool_shed_repository": { 546 "tool_shed_repository": {
547 "changeset_revision": "577d9c12411a", 547 "changeset_revision": "3034ce97dd33",
548 "name": "ncbi_blast_plus", 548 "name": "ncbi_blast_plus",
549 "owner": "devteam", 549 "owner": "devteam",
550 "tool_shed": "toolshed.g2.bx.psu.edu" 550 "tool_shed": "toolshed.g2.bx.psu.edu"
551 }, 551 },
552 "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\\\"\"}", 552 "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\\\"\"}",
553 "tool_version": "0.1.06", 553 "tool_version": "0.1.08",
554 "type": "tool", 554 "type": "tool",
555 "uuid": "bf30a0ad-4ef9-49f0-b4c7-4aae52017748", 555 "uuid": "bf30a0ad-4ef9-49f0-b4c7-4aae52017748",
556 "workflow_outputs": [] 556 "workflow_outputs": []
557 }, 557 },
558 "11": { 558 "11": {
607 } 607 }
608 }, 608 },
609 "tool_errors": null, 609 "tool_errors": null,
610 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_blastparser_and_hits/BlastParser_and_hits/2.4.3", 610 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_blastparser_and_hits/BlastParser_and_hits/2.4.3",
611 "tool_shed_repository": { 611 "tool_shed_repository": {
612 "changeset_revision": "6dfa79a6908a", 612 "changeset_revision": "1991c830504a",
613 "name": "msp_blastparser_and_hits", 613 "name": "msp_blastparser_and_hits",
614 "owner": "drosofff", 614 "owner": "drosofff",
615 "tool_shed": "toolshed.g2.bx.psu.edu" 615 "tool_shed": "toolshed.g2.bx.psu.edu"
616 }, 616 },
617 "tool_state": "{\"__page__\": 0, \"flanking\": \"\\\"5\\\"\", \"additional_filters\": \"{\\\"filter_term_out\\\": \\\"JX220408.1\\\", \\\"filter_relativeCov\\\": \\\"0.0\\\", \\\"filter_meanScore\\\": \\\"0.0\\\", \\\"use_filters\\\": \\\"yes\\\", \\\"__current_case__\\\": 1, \\\"filter_term_in\\\": \\\"Nora_virus\\\", \\\"filter_maxScore\\\": \\\"0.0\\\"}\", \"__rerun_remap_job_id__\": null, \"mode\": \"\\\"short\\\"\", \"sequences\": \"null\", \"blast\": \"null\"}", 617 "tool_state": "{\"__page__\": 0, \"flanking\": \"\\\"5\\\"\", \"additional_filters\": \"{\\\"filter_term_out\\\": \\\"JX220408.1\\\", \\\"filter_relativeCov\\\": \\\"0.0\\\", \\\"filter_meanScore\\\": \\\"0.0\\\", \\\"use_filters\\\": \\\"yes\\\", \\\"__current_case__\\\": 1, \\\"filter_term_in\\\": \\\"Nora_virus\\\", \\\"filter_maxScore\\\": \\\"0.0\\\"}\", \"__rerun_remap_job_id__\": null, \"mode\": \"\\\"short\\\"\", \"sequences\": \"null\", \"blast\": \"null\"}",
739 } 739 }
740 ] 740 ]
741 }, 741 },
742 "13": { 742 "13": {
743 "annotation": "", 743 "annotation": "",
744 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.06", 744 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.08",
745 "id": 13, 745 "id": 13,
746 "input_connections": { 746 "input_connections": {
747 "db_opts|histdb": { 747 "db_opts|histdb": {
748 "id": 4, 748 "id": 4,
749 "output_name": "outfile" 749 "output_name": "outfile"
772 "action_type": "HideDatasetAction", 772 "action_type": "HideDatasetAction",
773 "output_name": "output1" 773 "output_name": "output1"
774 } 774 }
775 }, 775 },
776 "tool_errors": null, 776 "tool_errors": null,
777 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.06", 777 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.08",
778 "tool_shed_repository": { 778 "tool_shed_repository": {
779 "changeset_revision": "577d9c12411a", 779 "changeset_revision": "3034ce97dd33",
780 "name": "ncbi_blast_plus", 780 "name": "ncbi_blast_plus",
781 "owner": "devteam", 781 "owner": "devteam",
782 "tool_shed": "toolshed.g2.bx.psu.edu" 782 "tool_shed": "toolshed.g2.bx.psu.edu"
783 }, 783 },
784 "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_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"ae5b2b58802911e5808df01fafdfc061\\\"\", \"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\\\"\"}", 784 "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_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"ae5b2b58802911e5808df01fafdfc061\\\"\", \"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\\\"\"}",
785 "tool_version": "0.1.06", 785 "tool_version": "0.1.08",
786 "type": "tool", 786 "type": "tool",
787 "uuid": "c9f9c58a-f21d-46d2-a952-9e7b7d5bf939", 787 "uuid": "c9f9c58a-f21d-46d2-a952-9e7b7d5bf939",
788 "workflow_outputs": [] 788 "workflow_outputs": []
789 }, 789 },
790 "14": { 790 "14": {
826 } 826 }
827 }, 827 },
828 "tool_errors": null, 828 "tool_errors": null,
829 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/blast_to_scaffold/blast2scaffold/0.9.0", 829 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/blast_to_scaffold/blast2scaffold/0.9.0",
830 "tool_shed_repository": { 830 "tool_shed_repository": {
831 "changeset_revision": "3288cc5a57e5", 831 "changeset_revision": "81ffa74cf96e",
832 "name": "blast_to_scaffold", 832 "name": "blast_to_scaffold",
833 "owner": "drosofff", 833 "owner": "drosofff",
834 "tool_shed": "toolshed.g2.bx.psu.edu" 834 "tool_shed": "toolshed.g2.bx.psu.edu"
835 }, 835 },
836 "tool_state": "{\"__page__\": 0, \"guideSequence\": \"null\", \"blast_tab\": \"null\", \"__rerun_remap_job_id__\": null, \"sequences\": \"null\"}", 836 "tool_state": "{\"__page__\": 0, \"guideSequence\": \"null\", \"blast_tab\": \"null\", \"__rerun_remap_job_id__\": null, \"sequences\": \"null\"}",