comparison Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_1-3.ga @ 2:48b020a0d2f7 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit d5feabb3309f2da09ba15b5fe818d0a7b30f3266
author drosofff
date Fri, 13 May 2016 05:46:40 -0400
parents 4a47903bb4df
children ba15c770fd40
comparison
equal deleted inserted replaced
1:3d8eb2c065c7 2:48b020a0d2f7
104 "output_name": "outfilename" 104 "output_name": "outfilename"
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": {
110 "changeset_revision": "befdb392fece",
111 "name": "fetch_fasta_from_ncbi",
112 "owner": "drosofff",
113 "tool_shed": "toolshed.g2.bx.psu.edu"
114 },
109 "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\\\"\"}",
110 "tool_version": "0.9.4", 116 "tool_version": "0.9.4",
111 "type": "tool", 117 "type": "tool",
112 "uuid": "7858036a-2e5d-4dc3-8ce4-819c746c742c", 118 "uuid": "7858036a-2e5d-4dc3-8ce4-819c746c742c",
113 "workflow_outputs": [ 119 "workflow_outputs": [
142 "top": 292.50001525878906 148 "top": 292.50001525878906
143 }, 149 },
144 "post_job_actions": {}, 150 "post_job_actions": {},
145 "tool_errors": null, 151 "tool_errors": null,
146 "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": {
154 "changeset_revision": "91cce7c1436d",
155 "name": "yac_clipper",
156 "owner": "drosofff",
157 "tool_shed": "toolshed.g2.bx.psu.edu"
158 },
147 "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\\\"\"}",
148 "tool_version": "1.3.6", 160 "tool_version": "1.3.6",
149 "type": "tool", 161 "type": "tool",
150 "uuid": "69611c78-3f25-4471-abf7-426ec35fd2db", 162 "uuid": "69611c78-3f25-4471-abf7-426ec35fd2db",
151 "workflow_outputs": [ 163 "workflow_outputs": [
186 "output_name": "outfile" 198 "output_name": "outfile"
187 } 199 }
188 }, 200 },
189 "tool_errors": null, 201 "tool_errors": null,
190 "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/0.1.06",
191 "tool_state": "{\"__page__\": 0, \"mask_data_file\": \"null\", \"input_file\": \"null\", \"dbtype\": \"\\\"nucl\\\"\", \"__rerun_remap_job_id__\": null, \"hash_index\": \"\\\"True\\\"\", \"tax\": \"{\\\"taxselect\\\": \\\"\\\", \\\"__current_case__\\\": 0}\", \"__workflow_invocation_uuid__\": \"\\\"ae5b2b58802911e5808df01fafdfc061\\\"\", \"title\": \"\\\"Blastn candidate database\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"parse_seqids\": \"\\\"False\\\"\"}", 203 "tool_shed_repository": {
204 "changeset_revision": "577d9c12411a",
205 "name": "ncbi_blast_plus",
206 "owner": "devteam",
207 "tool_shed": "toolshed.g2.bx.psu.edu"
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\\\"\"}",
192 "tool_version": "0.1.06", 210 "tool_version": "0.1.06",
193 "type": "tool", 211 "type": "tool",
194 "uuid": "ce29cdbe-653a-4d0e-b225-0d0762c28d4d", 212 "uuid": "ce29cdbe-653a-4d0e-b225-0d0762c28d4d",
195 "workflow_outputs": [] 213 "workflow_outputs": []
196 }, 214 },
226 "output_name": "out_file1" 244 "output_name": "out_file1"
227 } 245 }
228 }, 246 },
229 "tool_errors": null, 247 "tool_errors": null,
230 "tool_id": "toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2", 248 "tool_id": "toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2",
249 "tool_shed_repository": {
250 "changeset_revision": "201c568972c3",
251 "name": "concatenate_multiple_datasets",
252 "owner": "mvdbeek",
253 "tool_shed": "toolshed.g2.bx.psu.edu"
254 },
231 "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", 255 "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
232 "tool_version": "0.2", 256 "tool_version": "0.2",
233 "type": "tool", 257 "type": "tool",
234 "uuid": "6be696ec-ca89-4e64-ad39-7d0e7fb4401a", 258 "uuid": "6be696ec-ca89-4e64-ad39-7d0e7fb4401a",
235 "workflow_outputs": [ 259 "workflow_outputs": [
290 "output_name": "report" 314 "output_name": "report"
291 } 315 }
292 }, 316 },
293 "tool_errors": null, 317 "tool_errors": null,
294 "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",
295 "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\"}", 319 "tool_shed_repository": {
320 "changeset_revision": "6d8793a4923d",
321 "name": "khmer_normalize_by_median",
322 "owner": "iuc",
323 "tool_shed": "toolshed.g2.bx.psu.edu"
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\"}",
296 "tool_version": "2.0.0", 326 "tool_version": "2.0.0",
297 "type": "tool", 327 "type": "tool",
298 "uuid": "834cfd60-e0df-40e3-9d01-ecfa4296960b", 328 "uuid": "834cfd60-e0df-40e3-9d01-ecfa4296960b",
299 "workflow_outputs": [ 329 "workflow_outputs": [
300 { 330 {
341 "output_name": "out_file1" 371 "output_name": "out_file1"
342 } 372 }
343 }, 373 },
344 "tool_errors": null, 374 "tool_errors": null,
345 "tool_id": "toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2", 375 "tool_id": "toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2",
376 "tool_shed_repository": {
377 "changeset_revision": "201c568972c3",
378 "name": "concatenate_multiple_datasets",
379 "owner": "mvdbeek",
380 "tool_shed": "toolshed.g2.bx.psu.edu"
381 },
346 "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", 382 "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
347 "tool_version": "0.2", 383 "tool_version": "0.2",
348 "type": "tool", 384 "type": "tool",
349 "uuid": "8480cd00-f3b5-4ddb-a140-370a0b6e8c99", 385 "uuid": "8480cd00-f3b5-4ddb-a140-370a0b6e8c99",
350 "workflow_outputs": [] 386 "workflow_outputs": []
399 "output_name": "unaligned" 435 "output_name": "unaligned"
400 } 436 }
401 }, 437 },
402 "tool_errors": null, 438 "tool_errors": null,
403 "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",
440 "tool_shed_repository": {
441 "changeset_revision": "c1bfa227bbb6",
442 "name": "msp_sr_bowtie",
443 "owner": "drosofff",
444 "tool_shed": "toolshed.g2.bx.psu.edu"
445 },
404 "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\\\"\"}",
405 "tool_version": "1.1.2", 447 "tool_version": "1.1.2",
406 "type": "tool", 448 "type": "tool",
407 "uuid": "e22c6843-8125-49d6-9dcd-546155536f78", 449 "uuid": "e22c6843-8125-49d6-9dcd-546155536f78",
408 "workflow_outputs": [ 450 "workflow_outputs": [
445 "output_name": "transcripts" 487 "output_name": "transcripts"
446 } 488 }
447 }, 489 },
448 "tool_errors": null, 490 "tool_errors": null,
449 "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/1.1.4",
492 "tool_shed_repository": {
493 "changeset_revision": "f08d9c814ffb",
494 "name": "msp_oases",
495 "owner": "drosofff",
496 "tool_shed": "toolshed.g2.bx.psu.edu"
497 },
450 "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\\\"\"}",
451 "tool_version": "1.1.4", 499 "tool_version": "1.1.4",
452 "type": "tool", 500 "type": "tool",
453 "uuid": "4290f9b9-2ea7-4634-a639-bc008f1eb90c", 501 "uuid": "4290f9b9-2ea7-4634-a639-bc008f1eb90c",
454 "workflow_outputs": [ 502 "workflow_outputs": [
493 "output_name": "output1" 541 "output_name": "output1"
494 } 542 }
495 }, 543 },
496 "tool_errors": null, 544 "tool_errors": null,
497 "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/0.1.06",
498 "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\\\": {\\\"adv_optional_id_files_opts_selector\\\": \\\"none\\\", \\\"__current_case__\\\": 0}, \\\"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\\\"\"}", 546 "tool_shed_repository": {
547 "changeset_revision": "577d9c12411a",
548 "name": "ncbi_blast_plus",
549 "owner": "devteam",
550 "tool_shed": "toolshed.g2.bx.psu.edu"
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\\\"\"}",
499 "tool_version": "0.1.06", 553 "tool_version": "0.1.06",
500 "type": "tool", 554 "type": "tool",
501 "uuid": "bf30a0ad-4ef9-49f0-b4c7-4aae52017748", 555 "uuid": "bf30a0ad-4ef9-49f0-b4c7-4aae52017748",
502 "workflow_outputs": [] 556 "workflow_outputs": []
503 }, 557 },
552 "output_name": "un_sequences" 606 "output_name": "un_sequences"
553 } 607 }
554 }, 608 },
555 "tool_errors": null, 609 "tool_errors": null,
556 "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": {
612 "changeset_revision": "6dfa79a6908a",
613 "name": "msp_blastparser_and_hits",
614 "owner": "drosofff",
615 "tool_shed": "toolshed.g2.bx.psu.edu"
616 },
557 "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\"}",
558 "tool_version": "2.4.3", 618 "tool_version": "2.4.3",
559 "type": "tool", 619 "type": "tool",
560 "uuid": "84989771-81db-4d86-bff6-cfda892b1959", 620 "uuid": "84989771-81db-4d86-bff6-cfda892b1959",
561 "workflow_outputs": [ 621 "workflow_outputs": [
659 "output_name": "singlets" 719 "output_name": "singlets"
660 } 720 }
661 }, 721 },
662 "tool_errors": null, 722 "tool_errors": null,
663 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_cap3/cap3/1.2.0", 723 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_cap3/cap3/1.2.0",
724 "tool_shed_repository": {
725 "changeset_revision": "ddb463fdf57e",
726 "name": "msp_cap3",
727 "owner": "drosofff",
728 "tool_shed": "toolshed.g2.bx.psu.edu"
729 },
664 "tool_state": "{\"__page__\": 0, \"inputSequences\": \"null\", \"overlaplength\": \"\\\"40\\\"\", \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"ae5b2b58802911e5808df01fafdfc061\\\"\", \"overlapidentity\": \"\\\"90\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 730 "tool_state": "{\"__page__\": 0, \"inputSequences\": \"null\", \"overlaplength\": \"\\\"40\\\"\", \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"ae5b2b58802911e5808df01fafdfc061\\\"\", \"overlapidentity\": \"\\\"90\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
665 "tool_version": "1.2.0", 731 "tool_version": "1.2.0",
666 "type": "tool", 732 "type": "tool",
667 "uuid": "1d6dcdba-8f89-453b-ae30-6bb8aee06360", 733 "uuid": "1d6dcdba-8f89-453b-ae30-6bb8aee06360",
668 "workflow_outputs": [ 734 "workflow_outputs": [
707 "output_name": "output1" 773 "output_name": "output1"
708 } 774 }
709 }, 775 },
710 "tool_errors": null, 776 "tool_errors": null,
711 "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/0.1.06",
778 "tool_shed_repository": {
779 "changeset_revision": "577d9c12411a",
780 "name": "ncbi_blast_plus",
781 "owner": "devteam",
782 "tool_shed": "toolshed.g2.bx.psu.edu"
783 },
712 "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\\\"\"}",
713 "tool_version": "0.1.06", 785 "tool_version": "0.1.06",
714 "type": "tool", 786 "type": "tool",
715 "uuid": "c9f9c58a-f21d-46d2-a952-9e7b7d5bf939", 787 "uuid": "c9f9c58a-f21d-46d2-a952-9e7b7d5bf939",
716 "workflow_outputs": [] 788 "workflow_outputs": []
753 "output_name": "output" 825 "output_name": "output"
754 } 826 }
755 }, 827 },
756 "tool_errors": null, 828 "tool_errors": null,
757 "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": {
831 "changeset_revision": "3288cc5a57e5",
832 "name": "blast_to_scaffold",
833 "owner": "drosofff",
834 "tool_shed": "toolshed.g2.bx.psu.edu"
835 },
758 "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\"}",
759 "tool_version": "0.9.0", 837 "tool_version": "0.9.0",
760 "type": "tool", 838 "type": "tool",
761 "uuid": "031fbacb-303d-421d-84ee-24c9474c26d2", 839 "uuid": "031fbacb-303d-421d-84ee-24c9474c26d2",
762 "workflow_outputs": [] 840 "workflow_outputs": []
800 "output_name": "out_file1" 878 "output_name": "out_file1"
801 } 879 }
802 }, 880 },
803 "tool_errors": null, 881 "tool_errors": null,
804 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/regex_find_replace/regex1/0.1.0", 882 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/regex_find_replace/regex1/0.1.0",
883 "tool_shed_repository": {
884 "changeset_revision": "9ea374bb0350",
885 "name": "regex_find_replace",
886 "owner": "jjohnson",
887 "tool_shed": "toolshed.g2.bx.psu.edu"
888 },
805 "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"checks\": \"[{\\\"__index__\\\": 0, \\\"replacement\\\": \\\">Nora_Median-Norm-reads\\\", \\\"pattern\\\": \\\">.+\\\"}]\", \"__page__\": 0}", 889 "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"checks\": \"[{\\\"__index__\\\": 0, \\\"replacement\\\": \\\">Nora_Median-Norm-reads\\\", \\\"pattern\\\": \\\">.+\\\"}]\", \"__page__\": 0}",
806 "tool_version": "0.1.0", 890 "tool_version": "0.1.0",
807 "type": "tool", 891 "type": "tool",
808 "uuid": "d804abd4-ad4e-4382-a81d-b592bec797cf", 892 "uuid": "d804abd4-ad4e-4382-a81d-b592bec797cf",
809 "workflow_outputs": [ 893 "workflow_outputs": [