Mercurial > repos > drosofff > metavisitor_workflows
diff 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 |
line wrap: on
line diff
--- a/Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_1-3.ga Fri May 13 05:46:40 2016 -0400 +++ b/Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_1-3.ga Thu Nov 17 07:27:04 2016 -0500 @@ -107,7 +107,7 @@ "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/fetch_fasta_from_ncbi/retrieve_fasta_from_NCBI/0.9.4", "tool_shed_repository": { - "changeset_revision": "befdb392fece", + "changeset_revision": "a9d8f69d59fb", "name": "fetch_fasta_from_ncbi", "owner": "drosofff", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -151,7 +151,7 @@ "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/yac_clipper/yac/1.3.6", "tool_shed_repository": { - "changeset_revision": "91cce7c1436d", + "changeset_revision": "a18edcf9c7ed", "name": "yac_clipper", "owner": "drosofff", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -170,7 +170,7 @@ }, "4": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.1.06", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.1.08", "id": 4, "input_connections": { "input_file": { @@ -199,15 +199,15 @@ } }, "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.1.06", + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.1.08", "tool_shed_repository": { - "changeset_revision": "577d9c12411a", + "changeset_revision": "3034ce97dd33", "name": "ncbi_blast_plus", "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, "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\\\"\"}", - "tool_version": "0.1.06", + "tool_version": "0.1.08", "type": "tool", "uuid": "ce29cdbe-653a-4d0e-b225-0d0762c28d4d", "workflow_outputs": [] @@ -317,7 +317,7 @@ "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/khmer_normalize_by_median/khmer_normalize_by_median/2.0.0", "tool_shed_repository": { - "changeset_revision": "6d8793a4923d", + "changeset_revision": "ee081dc6c578", "name": "khmer_normalize_by_median", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -387,7 +387,7 @@ }, "8": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.2", + "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.2.1", "id": 8, "input_connections": { "input": { @@ -436,15 +436,15 @@ } }, "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.2.1", "tool_shed_repository": { - "changeset_revision": "c1bfa227bbb6", + "changeset_revision": "615d2550977f", "name": "msp_sr_bowtie", "owner": "drosofff", "tool_shed": "toolshed.g2.bx.psu.edu" }, "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\\\"\"}", - "tool_version": "1.1.2", + "tool_version": "1.1.2.1", "type": "tool", "uuid": "e22c6843-8125-49d6-9dcd-546155536f78", "workflow_outputs": [ @@ -457,7 +457,7 @@ }, "9": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_oases/oasesoptimiserv/1.1.4", + "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_oases/oasesoptimiserv/1.1.5", "id": 9, "input_connections": { "inputs_0|input": { @@ -488,15 +488,15 @@ } }, "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_oases/oasesoptimiserv/1.1.4", + "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_oases/oasesoptimiserv/1.1.5", "tool_shed_repository": { - "changeset_revision": "f08d9c814ffb", + "changeset_revision": "dc684e37f668", "name": "msp_oases", "owner": "drosofff", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__page__\": 0, \"inputs\": \"[{\\\"__index__\\\": 0, \\\"input\\\": null}]\", \"end_hash_length\": \"\\\"29\\\"\", \"__rerun_remap_job_id__\": null, \"start_hash_length\": \"\\\"13\\\"\"}", - "tool_version": "1.1.4", + "tool_version": "1.1.5", "type": "tool", "uuid": "4290f9b9-2ea7-4634-a639-bc008f1eb90c", "workflow_outputs": [ @@ -509,7 +509,7 @@ }, "10": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.06", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.08", "id": 10, "input_connections": { "db_opts|histdb": { @@ -542,15 +542,15 @@ } }, "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.06", + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.08", "tool_shed_repository": { - "changeset_revision": "577d9c12411a", + "changeset_revision": "3034ce97dd33", "name": "ncbi_blast_plus", "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, "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\\\"\"}", - "tool_version": "0.1.06", + "tool_version": "0.1.08", "type": "tool", "uuid": "bf30a0ad-4ef9-49f0-b4c7-4aae52017748", "workflow_outputs": [] @@ -609,7 +609,7 @@ "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_blastparser_and_hits/BlastParser_and_hits/2.4.3", "tool_shed_repository": { - "changeset_revision": "6dfa79a6908a", + "changeset_revision": "1991c830504a", "name": "msp_blastparser_and_hits", "owner": "drosofff", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -741,7 +741,7 @@ }, "13": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.06", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.08", "id": 13, "input_connections": { "db_opts|histdb": { @@ -774,15 +774,15 @@ } }, "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.06", + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.08", "tool_shed_repository": { - "changeset_revision": "577d9c12411a", + "changeset_revision": "3034ce97dd33", "name": "ncbi_blast_plus", "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, "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\\\"\"}", - "tool_version": "0.1.06", + "tool_version": "0.1.08", "type": "tool", "uuid": "c9f9c58a-f21d-46d2-a952-9e7b7d5bf939", "workflow_outputs": [] @@ -828,7 +828,7 @@ "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/blast_to_scaffold/blast2scaffold/0.9.0", "tool_shed_repository": { - "changeset_revision": "3288cc5a57e5", + "changeset_revision": "81ffa74cf96e", "name": "blast_to_scaffold", "owner": "drosofff", "tool_shed": "toolshed.g2.bx.psu.edu"