Mercurial > repos > drosofff > metavisitor_workflows

comparison Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_1-1.ga @ 3:ba15c770fd40 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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\\\"\"}",
154 }, 154 },
155 "post_job_actions": {}, 155 "post_job_actions": {},
156 "tool_errors": null, 156 "tool_errors": null,
157 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/yac_clipper/yac/1.3.6", 157 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/yac_clipper/yac/1.3.6",
158 "tool_shed_repository": { 158 "tool_shed_repository": {
159 "changeset_revision": "91cce7c1436d", 159 "changeset_revision": "a18edcf9c7ed",
160 "name": "yac_clipper", 160 "name": "yac_clipper",
161 "owner": "drosofff", 161 "owner": "drosofff",
162 "tool_shed": "toolshed.g2.bx.psu.edu" 162 "tool_shed": "toolshed.g2.bx.psu.edu"
163 }, 163 },
164 "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\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"Nmode\": \"\\\"reject\\\"\"}", 164 "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\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"Nmode\": \"\\\"reject\\\"\"}",
173 } 173 }
174 ] 174 ]
175 }, 175 },
176 "4": { 176 "4": {
177 "annotation": "", 177 "annotation": "",
178 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.1.06", 178 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.1.08",
179 "id": 4, 179 "id": 4,
180 "input_connections": { 180 "input_connections": {
181 "input_file": { 181 "input_file": {
182 "id": 2, 182 "id": 2,
183 "output_name": "outfilename" 183 "output_name": "outfilename"
211 "action_type": "HideDatasetAction", 211 "action_type": "HideDatasetAction",
212 "output_name": "outfile" 212 "output_name": "outfile"
213 } 213 }
214 }, 214 },
215 "tool_errors": null, 215 "tool_errors": null,
216 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.1.06", 216 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.1.08",
217 "tool_shed_repository": { 217 "tool_shed_repository": {
218 "changeset_revision": "577d9c12411a", 218 "changeset_revision": "3034ce97dd33",
219 "name": "ncbi_blast_plus", 219 "name": "ncbi_blast_plus",
220 "owner": "devteam", 220 "owner": "devteam",
221 "tool_shed": "toolshed.g2.bx.psu.edu" 221 "tool_shed": "toolshed.g2.bx.psu.edu"
222 }, 222 },
223 "tool_state": "{\"__page__\": 0, \"mask_data_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"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\\\"\"}", 223 "tool_state": "{\"__page__\": 0, \"mask_data_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"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\\\"\"}",
224 "tool_version": "0.1.06", 224 "tool_version": "0.1.08",
225 "type": "tool", 225 "type": "tool",
226 "uuid": "ce29cdbe-653a-4d0e-b225-0d0762c28d4d", 226 "uuid": "ce29cdbe-653a-4d0e-b225-0d0762c28d4d",
227 "workflow_outputs": [] 227 "workflow_outputs": []
228 }, 228 },
229 "5": { 229 "5": {
318 } 318 }
319 }, 319 },
320 "tool_errors": null, 320 "tool_errors": null,
321 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_fasta_tabular_converter/fasta_tabular_converter/1.1.0", 321 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_fasta_tabular_converter/fasta_tabular_converter/1.1.0",
322 "tool_shed_repository": { 322 "tool_shed_repository": {
323 "changeset_revision": "330dd8a8c31a", 323 "changeset_revision": "36388b666bfc",
324 "name": "msp_fasta_tabular_converter", 324 "name": "msp_fasta_tabular_converter",
325 "owner": "drosofff", 325 "owner": "drosofff",
326 "tool_shed": "toolshed.g2.bx.psu.edu" 326 "tool_shed": "toolshed.g2.bx.psu.edu"
327 }, 327 },
328 "tool_state": "{\"__page__\": 0, \"switch\": \"{\\\"input\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0, \\\"conversionType\\\": \\\"fasta2tabular\\\"}\", \"__rerun_remap_job_id__\": null}", 328 "tool_state": "{\"__page__\": 0, \"switch\": \"{\\\"input\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0, \\\"conversionType\\\": \\\"fasta2tabular\\\"}\", \"__rerun_remap_job_id__\": null}",
369 } 369 }
370 }, 370 },
371 "tool_errors": null, 371 "tool_errors": null,
372 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_fasta_tabular_converter/fasta_tabular_converter/1.1.0", 372 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_fasta_tabular_converter/fasta_tabular_converter/1.1.0",
373 "tool_shed_repository": { 373 "tool_shed_repository": {
374 "changeset_revision": "330dd8a8c31a", 374 "changeset_revision": "36388b666bfc",
375 "name": "msp_fasta_tabular_converter", 375 "name": "msp_fasta_tabular_converter",
376 "owner": "drosofff", 376 "owner": "drosofff",
377 "tool_shed": "toolshed.g2.bx.psu.edu" 377 "tool_shed": "toolshed.g2.bx.psu.edu"
378 }, 378 },
379 "tool_state": "{\"__page__\": 0, \"switch\": \"{\\\"input\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 2, \\\"conversionType\\\": \\\"tabular2fastaweight\\\"}\", \"__rerun_remap_job_id__\": null}", 379 "tool_state": "{\"__page__\": 0, \"switch\": \"{\\\"input\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 2, \\\"conversionType\\\": \\\"tabular2fastaweight\\\"}\", \"__rerun_remap_job_id__\": null}",
388 } 388 }
389 ] 389 ]
390 }, 390 },
391 "8": { 391 "8": {
392 "annotation": "", 392 "annotation": "",
393 "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.2", 393 "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.2.1",
394 "id": 8, 394 "id": 8,
395 "input_connections": { 395 "input_connections": {
396 "input": { 396 "input": {
397 "id": 7, 397 "id": 7,
398 "output_name": "output" 398 "output_name": "output"
442 "action_type": "RenameDatasetAction", 442 "action_type": "RenameDatasetAction",
443 "output_name": "unaligned" 443 "output_name": "unaligned"
444 } 444 }
445 }, 445 },
446 "tool_errors": null, 446 "tool_errors": null,
447 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.2", 447 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.2.1",
448 "tool_shed_repository": { 448 "tool_shed_repository": {
449 "changeset_revision": "c1bfa227bbb6", 449 "changeset_revision": "615d2550977f",
450 "name": "msp_sr_bowtie", 450 "name": "msp_sr_bowtie",
451 "owner": "drosofff", 451 "owner": "drosofff",
452 "tool_shed": "toolshed.g2.bx.psu.edu" 452 "tool_shed": "toolshed.g2.bx.psu.edu"
453 }, 453 },
454 "tool_state": "{\"__page__\": 0, \"output_format\": \"\\\"tabular\\\"\", \"additional_fasta\": \"\\\"unal\\\"\", \"v_mismatches\": \"\\\"2\\\"\", \"__rerun_remap_job_id__\": null, \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"dm6\\\", \\\"__current_case__\\\": 0}\", \"method\": \"\\\"k_option\\\"\"}", 454 "tool_state": "{\"__page__\": 0, \"output_format\": \"\\\"tabular\\\"\", \"additional_fasta\": \"\\\"unal\\\"\", \"v_mismatches\": \"\\\"2\\\"\", \"__rerun_remap_job_id__\": null, \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"dm6\\\", \\\"__current_case__\\\": 0}\", \"method\": \"\\\"k_option\\\"\"}",
455 "tool_version": "1.1.2", 455 "tool_version": "1.1.2.1",
456 "type": "tool", 456 "type": "tool",
457 "uuid": "e22c6843-8125-49d6-9dcd-546155536f78", 457 "uuid": "e22c6843-8125-49d6-9dcd-546155536f78",
458 "workflow_outputs": [ 458 "workflow_outputs": [
459 { 459 {
460 "label": null, 460 "label": null,
515 } 515 }
516 ] 516 ]
517 }, 517 },
518 "10": { 518 "10": {
519 "annotation": "", 519 "annotation": "",
520 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.06", 520 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.08",
521 "id": 10, 521 "id": 10,
522 "input_connections": { 522 "input_connections": {
523 "db_opts|histdb": { 523 "db_opts|histdb": {
524 "id": 1, 524 "id": 1,
525 "output_name": "output" 525 "output_name": "output"
557 "action_type": "HideDatasetAction", 557 "action_type": "HideDatasetAction",
558 "output_name": "output1" 558 "output_name": "output1"
559 } 559 }
560 }, 560 },
561 "tool_errors": null, 561 "tool_errors": null,
562 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.06", 562 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.08",
563 "tool_shed_repository": { 563 "tool_shed_repository": {
564 "changeset_revision": "577d9c12411a", 564 "changeset_revision": "3034ce97dd33",
565 "name": "ncbi_blast_plus", 565 "name": "ncbi_blast_plus",
566 "owner": "devteam", 566 "owner": "devteam",
567 "tool_shed": "toolshed.g2.bx.psu.edu" 567 "tool_shed": "toolshed.g2.bx.psu.edu"
568 }, 568 },
569 "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\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\"}\", \"blast_type\": \"\\\"blastn\\\"\", \"query\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 569 "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\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\"}\", \"blast_type\": \"\\\"blastn\\\"\", \"query\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
570 "tool_version": "0.1.06", 570 "tool_version": "0.1.08",
571 "type": "tool", 571 "type": "tool",
572 "uuid": "bf30a0ad-4ef9-49f0-b4c7-4aae52017748", 572 "uuid": "bf30a0ad-4ef9-49f0-b4c7-4aae52017748",
573 "workflow_outputs": [] 573 "workflow_outputs": []
574 }, 574 },
575 "11": { 575 "11": {
633 } 633 }
634 }, 634 },
635 "tool_errors": null, 635 "tool_errors": null,
636 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_blastparser_and_hits/BlastParser_and_hits/2.4.3", 636 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_blastparser_and_hits/BlastParser_and_hits/2.4.3",
637 "tool_shed_repository": { 637 "tool_shed_repository": {
638 "changeset_revision": "6dfa79a6908a", 638 "changeset_revision": "1991c830504a",
639 "name": "msp_blastparser_and_hits", 639 "name": "msp_blastparser_and_hits",
640 "owner": "drosofff", 640 "owner": "drosofff",
641 "tool_shed": "toolshed.g2.bx.psu.edu" 641 "tool_shed": "toolshed.g2.bx.psu.edu"
642 }, 642 },
643 "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\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"blast\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", 643 "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\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"blast\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
770 } 770 }
771 ] 771 ]
772 }, 772 },
773 "13": { 773 "13": {
774 "annotation": "", 774 "annotation": "",
775 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.06", 775 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.08",
776 "id": 13, 776 "id": 13,
777 "input_connections": { 777 "input_connections": {
778 "db_opts|histdb": { 778 "db_opts|histdb": {
779 "id": 4, 779 "id": 4,
780 "output_name": "outfile" 780 "output_name": "outfile"
812 "action_type": "HideDatasetAction", 812 "action_type": "HideDatasetAction",
813 "output_name": "output1" 813 "output_name": "output1"
814 } 814 }
815 }, 815 },
816 "tool_errors": null, 816 "tool_errors": null,
817 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.06", 817 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.08",
818 "tool_shed_repository": { 818 "tool_shed_repository": {
819 "changeset_revision": "577d9c12411a", 819 "changeset_revision": "3034ce97dd33",
820 "name": "ncbi_blast_plus", 820 "name": "ncbi_blast_plus",
821 "owner": "devteam", 821 "owner": "devteam",
822 "tool_shed": "toolshed.g2.bx.psu.edu" 822 "tool_shed": "toolshed.g2.bx.psu.edu"
823 }, 823 },
824 "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\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\"}\", \"blast_type\": \"\\\"blastn\\\"\", \"query\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 824 "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\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\"}\", \"blast_type\": \"\\\"blastn\\\"\", \"query\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
825 "tool_version": "0.1.06", 825 "tool_version": "0.1.08",
826 "type": "tool", 826 "type": "tool",
827 "uuid": "c9f9c58a-f21d-46d2-a952-9e7b7d5bf939", 827 "uuid": "c9f9c58a-f21d-46d2-a952-9e7b7d5bf939",
828 "workflow_outputs": [] 828 "workflow_outputs": []
829 }, 829 },
830 "14": { 830 "14": {
879 } 879 }
880 }, 880 },
881 "tool_errors": null, 881 "tool_errors": null,
882 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/blast_to_scaffold/blast2scaffold/0.9.0", 882 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/blast_to_scaffold/blast2scaffold/0.9.0",
883 "tool_shed_repository": { 883 "tool_shed_repository": {
884 "changeset_revision": "3288cc5a57e5", 884 "changeset_revision": "81ffa74cf96e",
885 "name": "blast_to_scaffold", 885 "name": "blast_to_scaffold",
886 "owner": "drosofff", 886 "owner": "drosofff",
887 "tool_shed": "toolshed.g2.bx.psu.edu" 887 "tool_shed": "toolshed.g2.bx.psu.edu"
888 }, 888 },
889 "tool_state": "{\"__page__\": 0, \"guideSequence\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"blast_tab\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"sequences\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", 889 "tool_state": "{\"__page__\": 0, \"guideSequence\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"blast_tab\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"sequences\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",