Mercurial > repos > artbio > metavisitor_2_workflows
diff Galaxy-Workflow-Metavisitor__Workflow_for_nucleic_vir2_generation.ga @ 0:c375489bbcb0 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows/metavisitor_2_workflows commit ecf95caa7d5e9ab001a75cbf5fb306e7ecd3def3
author | artbio |
---|---|
date | Sun, 21 Jul 2019 19:22:52 -0400 |
parents | |
children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Galaxy-Workflow-Metavisitor__Workflow_for_nucleic_vir2_generation.ga Sun Jul 21 19:22:52 2019 -0400 @@ -0,0 +1,318 @@ +{ + "a_galaxy_workflow": "true", + "uuid": "742e3aa8-0dc5-440d-8120-3b10f4e7308d", + "tags": [], + "format-version": "0.1", + "version": 1, + "steps": { + "1": { + "tool_id": "toolshed.g2.bx.psu.edu/repos/artbio/fetch_fasta_from_ncbi/retrieve_fasta_from_NCBI/2.3.0", + "errors": null, + "uuid": "25b4eea6-c049-4432-9ebb-5b7c7a17e24b", + "tool_version": "2.3.0", + "outputs": [ + { + "type": "fasta", + "name": "outfile" + }, + { + "type": "txt", + "name": "logfile" + } + ], + "post_job_actions": {}, + "workflow_outputs": [ + { + "output_name": "outfile", + "uuid": "b5b6d8a1-5d12-4df9-97e3-f82124301e24", + "label": null + }, + { + "output_name": "logfile", + "uuid": "8243ff90-8e45-4d12-b9d0-ea17ee0dd3c0", + "label": null + } + ], + "annotation": "sequences > 10 000bp", + "content_id": "toolshed.g2.bx.psu.edu/repos/artbio/fetch_fasta_from_ncbi/retrieve_fasta_from_NCBI/2.3.0", + "input_connections": {}, + "inputs": [], + "position": { + "top": 563, + "left": 200 + }, + "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"queryString\": \"\\\"txid10239[Organism] NOT txid131567[Organism] NOT phage[All Fields] NOT patent[All Fields] NOT chimeric[Title] NOT vector[Title] NOT method[Title] NOT X174[All Fields] AND 10001:1300000[Sequence length]\\\"\", \"dbname\": \"\\\"nuccore\\\"\", \"dry_run\": \"\\\"false\\\"\"}", + "label": "Get long sequences", + "type": "tool", + "id": 1, + "tool_shed_repository": { + "owner": "artbio", + "changeset_revision": "c667d0ee39f5", + "name": "fetch_fasta_from_ncbi", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "name": "Retrieve FASTA from NCBI" + }, + "0": { + "tool_id": "toolshed.g2.bx.psu.edu/repos/artbio/fetch_fasta_from_ncbi/retrieve_fasta_from_NCBI/2.3.0", + "errors": null, + "uuid": "9c3e474c-3e57-4378-a5cc-ef9c6b7b092a", + "tool_version": "2.3.0", + "outputs": [ + { + "type": "fasta", + "name": "outfile" + }, + { + "type": "txt", + "name": "logfile" + } + ], + "post_job_actions": {}, + "workflow_outputs": [ + { + "output_name": "outfile", + "uuid": "f1d297ff-bf05-41ac-b262-4901674827a2", + "label": null + }, + { + "output_name": "logfile", + "uuid": "b27a01c2-0d64-4aae-941d-946dd21e6bd2", + "label": null + } + ], + "annotation": "sequences <= 10 000bp", + "content_id": "toolshed.g2.bx.psu.edu/repos/artbio/fetch_fasta_from_ncbi/retrieve_fasta_from_NCBI/2.3.0", + "input_connections": {}, + "inputs": [], + "position": { + "top": 241, + "left": 213 + }, + "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"queryString\": \"\\\"txid10239[Organism] NOT txid131567[Organism] NOT phage[All Fields] NOT patent[All Fields] NOT chimeric[Title] NOT vector[Title] NOT method[Title] NOT X174[All Fields] AND 301:10000[Sequence length]\\\"\", \"dbname\": \"\\\"nuccore\\\"\", \"dry_run\": \"\\\"false\\\"\"}", + "label": "Get short sequences", + "type": "tool", + "id": 0, + "tool_shed_repository": { + "owner": "artbio", + "changeset_revision": "c667d0ee39f5", + "name": "fetch_fasta_from_ncbi", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "name": "Retrieve FASTA from NCBI" + }, + "3": { + "tool_id": "toolshed.g2.bx.psu.edu/repos/artbio/concatenate_multiple_datasets/cat_multi_datasets/1.4.1", + "errors": null, + "uuid": "94beda09-1785-4da8-84ec-70773fa6eddd", + "tool_version": "1.4.1", + "outputs": [ + { + "type": "input", + "name": "paired_output" + }, + { + "type": "input", + "name": "list_output" + }, + { + "type": "input", + "name": "out_file1" + }, + { + "type": "_sniff_", + "name": "paired_out_file" + } + ], + "post_job_actions": { + "HideDatasetActionpaired_out_file": { + "output_name": "paired_out_file", + "action_type": "HideDatasetAction", + "action_arguments": {} + }, + "RenameDatasetActionout_file1": { + "output_name": "out_file1", + "action_type": "RenameDatasetAction", + "action_arguments": { + "newname": "Vir2" + } + }, + "HideDatasetActionpaired_output": { + "output_name": "paired_output", + "action_type": "HideDatasetAction", + "action_arguments": {} + }, + "HideDatasetActionout_file1": { + "output_name": "out_file1", + "action_type": "HideDatasetAction", + "action_arguments": {} + }, + "HideDatasetActionlist_output": { + "output_name": "list_output", + "action_type": "HideDatasetAction", + "action_arguments": {} + } + }, + "workflow_outputs": [], + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/artbio/concatenate_multiple_datasets/cat_multi_datasets/1.4.1", + "input_connections": { + "global_condition|inputs": [ + { + "output_name": "centroids", + "id": 2 + }, + { + "output_name": "outfile", + "id": 1 + } + ] + }, + "inputs": [ + { + "name": "global_condition", + "description": "runtime parameter for tool Concatenate multiple datasets" + } + ], + "position": { + "top": 571.5, + "left": 735 + }, + "tool_state": "{\"dataset_names\": \"\\\"false\\\"\", \"headers\": \"\\\"0\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"global_condition\": \"{\\\"__current_case__\\\": 0, \\\"input_type\\\": \\\"singles\\\", \\\"inputs\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\"}", + "label": "Vir2", + "type": "tool", + "id": 3, + "tool_shed_repository": { + "owner": "artbio", + "changeset_revision": "55cf9d9defd1", + "name": "concatenate_multiple_datasets", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "name": "Concatenate multiple datasets" + }, + "2": { + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_clustering/2.8.3.0", + "errors": null, + "uuid": "6fddbef5-bc89-4574-a0cf-335aee053e4c", + "tool_version": "2.8.3.0", + "outputs": [ + { + "type": "fasta", + "name": "msaout" + }, + { + "type": "fasta", + "name": "consout" + }, + { + "type": "fasta", + "name": "centroids" + }, + { + "type": "fasta", + "name": "alnout" + }, + { + "type": "fasta", + "name": "notmatched" + }, + { + "type": "fasta", + "name": "matched" + }, + { + "type": "tabular", + "name": "blast6out" + }, + { + "type": "fasta", + "name": "fastapairs" + }, + { + "type": "tabular", + "name": "uc_outfile" + } + ], + "post_job_actions": { + "HideDatasetActionfastapairs": { + "output_name": "fastapairs", + "action_type": "HideDatasetAction", + "action_arguments": {} + }, + "HideDatasetActionconsout": { + "output_name": "consout", + "action_type": "HideDatasetAction", + "action_arguments": {} + }, + "HideDatasetActionmsaout": { + "output_name": "msaout", + "action_type": "HideDatasetAction", + "action_arguments": {} + }, + "HideDatasetActionalnout": { + "output_name": "alnout", + "action_type": "HideDatasetAction", + "action_arguments": {} + }, + "HideDatasetActionblast6out": { + "output_name": "blast6out", + "action_type": "HideDatasetAction", + "action_arguments": {} + }, + "HideDatasetActionuc_outfile": { + "output_name": "uc_outfile", + "action_type": "HideDatasetAction", + "action_arguments": {} + }, + "HideDatasetActionnotmatched": { + "output_name": "notmatched", + "action_type": "HideDatasetAction", + "action_arguments": {} + }, + "HideDatasetActionmatched": { + "output_name": "matched", + "action_type": "HideDatasetAction", + "action_arguments": {} + } + }, + "workflow_outputs": [ + { + "output_name": "centroids", + "uuid": "091f386f-32e1-4270-8754-9da84c187b82", + "label": null + } + ], + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_clustering/2.8.3.0", + "input_connections": { + "infile": { + "output_name": "outfile", + "id": 0 + } + }, + "inputs": [ + { + "name": "infile", + "description": "runtime parameter for tool VSearch clustering" + } + ], + "position": { + "top": 232, + "left": 463.5 + }, + "tool_state": "{\"sizein\": \"\\\"false\\\"\", \"cons_truncate\": \"\\\"false\\\"\", \"__page__\": null, \"maxrejects\": \"\\\"32\\\"\", \"usersort\": \"\\\"false\\\"\", \"qmask\": \"\\\"dust\\\"\", \"iddef\": \"\\\"2\\\"\", \"__rerun_remap_job_id__\": null, \"clustering_mode\": \"{\\\"__current_case__\\\": 0, \\\"clustering_mode_select\\\": \\\"cluster_fast\\\"}\", \"id\": \"\\\"0.95\\\"\", \"sizeout\": \"\\\"false\\\"\", \"strand\": \"\\\"plus\\\"\", \"outputs\": \"[\\\"--centroids\\\"]\", \"maxaccepts\": \"\\\"1\\\"\", \"infile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"uc\": \"\\\"false\\\"\"}", + "label": "Get centroids", + "type": "tool", + "id": 2, + "tool_shed_repository": { + "owner": "iuc", + "changeset_revision": "b3c7199d8786", + "name": "vsearch", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "name": "VSearch clustering" + } + }, + "annotation": "", + "name": "Metavisitor: Workflow for nucleic vir2 generation" +}