Mercurial > repos > earlhaminst > geneseqtofamily
diff swissprot.ga @ 0:b92f5ab6d127 draft
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
author | earlhaminst |
---|---|
date | Mon, 09 Jan 2017 15:06:04 -0500 |
parents | |
children | 06470b2e491f |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/swissprot.ga Mon Jan 09 15:06:04 2017 -0500 @@ -0,0 +1,555 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "", + "format-version": "0.1", + "name": "SwisProt scratch", + "steps": { + "0": { + "annotation": "", + "content_id": null, + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "CDS" + } + ], + "label": null, + "name": "Input dataset", + "outputs": [], + "position": { + "left": 163.95219802856445, + "top": 290.93748664855957 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"CDS\"}", + "tool_version": null, + "type": "data_input", + "uuid": "4fb3c053-8997-48fe-a31b-e5ae64617009", + "workflow_outputs": [] + }, + "1": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: transeq101/5.0.0", + "id": 1, + "input_connections": { + "input1": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool transeq", + "name": "input1" + } + ], + "label": null, + "name": "transeq", + "outputs": [ + { + "name": "out_file1", + "type": "fasta" + } + ], + "position": { + "left": 500.90070724487305, + "top": 199.963228225708 + }, + "post_job_actions": { + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: transeq101/5.0.0", + "tool_shed_repository": { + "changeset_revision": "511429456d3c", + "name": "emboss_5", + "owner": "devteam", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"trim\": \"\\\"no\\\"\", \"__page__\": 0, \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"out_format1\": \"\\\"fasta\\\"\", \"frame\": \"\\\"1\\\"\", \"regions\": \"\\\"\\\"\", \"clean\": \"\\\"no\\\"\", \"table\": \"\\\"0\\\"\", \"alternative\": \"\\\"no\\\"\", \"__rerun_remap_job_id__\": null}", + "tool_version": "5.0.0", + "type": "tool", + "uuid": "bd77191a-7c1a-4f0e-be8e-0116b7d8b321", + "workflow_outputs": [] + }, + "2": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.1.08", + "id": 2, + "input_connections": { + "query": { + "id": 1, + "output_name": "out_file1" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool NCBI BLAST+ blastp", + "name": "query" + } + ], + "label": null, + "name": "NCBI BLAST+ blastp", + "outputs": [ + { + "name": "output1", + "type": "tabular" + } + ], + "position": { + "left": 760.4779167175293, + "top": 292.49998664855957 + }, + "post_job_actions": { + "HideDatasetActionoutput1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output1" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.1.08", + "tool_shed_repository": { + "changeset_revision": "3034ce97dd33", + "name": "ncbi_blast_plus", + "owner": "devteam", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"evalue_cutoff\": \"\\\"0.001\\\"\", \"__page__\": 0, \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"blast_type\": \"\\\"blastp\\\"\", \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"db\\\", \\\"subject\\\": \\\"\\\", \\\"histdb\\\": \\\"\\\", \\\"__current_case__\\\": 0, \\\"database\\\": [\\\"swissprot\\\"]}\", \"output\": \"{\\\"out_format\\\": \\\"ext\\\", \\\"__current_case__\\\": 1}\", \"query\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", + "tool_version": "0.1.08", + "type": "tool", + "uuid": "c751b0ee-57ca-4aef-bbf5-d201a6b799a3", + "workflow_outputs": [] + }, + "3": { + "annotation": "", + "content_id": "Cut1", + "id": 3, + "input_connections": { + "input": { + "id": 2, + "output_name": "output1" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool Cut", + "name": "input" + } + ], + "label": null, + "name": "Cut", + "outputs": [ + { + "name": "out_file1", + "type": "tabular" + } + ], + "position": { + "left": 973.9337882995605, + "top": 572.8860034942627 + }, + "post_job_actions": { + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + } + }, + "tool_errors": null, + "tool_id": "Cut1", + "tool_state": "{\"columnList\": \"\\\"c2\\\"\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"delimiter\": \"\\\"T\\\"\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", + "tool_version": "1.0.2", + "type": "tool", + "uuid": "f866ff7f-7ad1-46f5-bf80-c2d9ff778afe", + "workflow_outputs": [] + }, + "4": { + "annotation": "", + "content_id": "Cut1", + "id": 4, + "input_connections": { + "input": { + "id": 3, + "output_name": "out_file1" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool Cut", + "name": "input" + } + ], + "label": null, + "name": "Cut", + "outputs": [ + { + "name": "out_file1", + "type": "tabular" + } + ], + "position": { + "left": 983.9337882995605, + "top": 728.970537185669 + }, + "post_job_actions": { + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + } + }, + "tool_errors": null, + "tool_id": "Cut1", + "tool_state": "{\"columnList\": \"\\\"c2\\\"\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"delimiter\": \"\\\"P\\\"\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", + "tool_version": "1.0.2", + "type": "tool", + "uuid": "e4e8e4fc-6ba4-49f6-9be8-c54bc5502ac3", + "workflow_outputs": [] + }, + "5": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/uniprot_rest_interface/uniprot/0.1", + "id": 5, + "input_connections": { + "infile": { + "id": 4, + "output_name": "out_file1" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool UniProt", + "name": "infile" + } + ], + "label": null, + "name": "UniProt", + "outputs": [ + { + "name": "outfile_retrieve_fasta", + "type": "fasta" + }, + { + "name": "outfile_retrieve_gff", + "type": "gff" + }, + { + "name": "outfile_retrieve_txt", + "type": "txt" + }, + { + "name": "outfile_map", + "type": "tabular" + } + ], + "position": { + "left": 1315.9558219909668, + "top": 405.4779224395752 + }, + "post_job_actions": { + "HideDatasetActionoutfile_map": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "outfile_map" + }, + "HideDatasetActionoutfile_retrieve_fasta": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "outfile_retrieve_fasta" + }, + "HideDatasetActionoutfile_retrieve_gff": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "outfile_retrieve_gff" + }, + "HideDatasetActionoutfile_retrieve_txt": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "outfile_retrieve_txt" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/uniprot_rest_interface/uniprot/0.1", + "tool_shed_repository": { + "changeset_revision": "cd2a41c65447", + "name": "uniprot_rest_interface", + "owner": "bgruening", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"__page__\": 0, \"tool\": \"{\\\"to\\\": {\\\"db_GenomeAnnotationDB\\\": \\\"ENSEMBL_TRS_ID\\\", \\\"__current_case__\\\": 9, \\\"category_TO\\\": \\\"GenomeAnnotationDB\\\"}, \\\"from\\\": {\\\"category_FROM\\\": \\\"uniprot\\\", \\\"db_uniprot_FROM\\\": \\\"ACC+ID\\\", \\\"__current_case__\\\": 0}, \\\"__current_case__\\\": 0, \\\"tool_choice\\\": \\\"map\\\"}\", \"__rerun_remap_job_id__\": null, \"id_column\": \"\\\"1\\\"\", \"infile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", + "tool_version": "0.1", + "type": "tool", + "uuid": "8802d99a-7699-4c13-8d53-ea2c22280808", + "workflow_outputs": [] + }, + "6": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/uniprot_rest_interface/uniprot/0.1", + "id": 6, + "input_connections": { + "infile": { + "id": 4, + "output_name": "out_file1" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool UniProt", + "name": "infile" + } + ], + "label": null, + "name": "UniProt", + "outputs": [ + { + "name": "outfile_retrieve_fasta", + "type": "fasta" + }, + { + "name": "outfile_retrieve_gff", + "type": "gff" + }, + { + "name": "outfile_retrieve_txt", + "type": "txt" + }, + { + "name": "outfile_map", + "type": "tabular" + } + ], + "position": { + "left": 1326.9484977722168, + "top": 817.9227466583252 + }, + "post_job_actions": { + "HideDatasetActionoutfile_map": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "outfile_map" + }, + "HideDatasetActionoutfile_retrieve_fasta": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "outfile_retrieve_fasta" + }, + "HideDatasetActionoutfile_retrieve_gff": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "outfile_retrieve_gff" + }, + "HideDatasetActionoutfile_retrieve_txt": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "outfile_retrieve_txt" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/uniprot_rest_interface/uniprot/0.1", + "tool_shed_repository": { + "changeset_revision": "cd2a41c65447", + "name": "uniprot_rest_interface", + "owner": "bgruening", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"__page__\": 0, \"tool\": \"{\\\"to\\\": {\\\"db_GenomeAnnotationDB\\\": \\\"P_ENTREZGENEID\\\", \\\"__current_case__\\\": 9, \\\"category_TO\\\": \\\"GenomeAnnotationDB\\\"}, \\\"from\\\": {\\\"category_FROM\\\": \\\"uniprot\\\", \\\"db_uniprot_FROM\\\": \\\"ACC+ID\\\", \\\"__current_case__\\\": 0}, \\\"__current_case__\\\": 0, \\\"tool_choice\\\": \\\"map\\\"}\", \"__rerun_remap_job_id__\": null, \"id_column\": \"\\\"1\\\"\", \"infile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", + "tool_version": "0.1", + "type": "tool", + "uuid": "011b53a7-1aae-4bf1-af40-2df13c2cf41b", + "workflow_outputs": [] + }, + "7": { + "annotation": "", + "content_id": "Cut1", + "id": 7, + "input_connections": { + "input": { + "id": 5, + "output_name": "outfile_map" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool Cut", + "name": "input" + } + ], + "label": null, + "name": "Cut", + "outputs": [ + { + "name": "out_file1", + "type": "tabular" + } + ], + "position": { + "left": 1619.9815788269043, + "top": 493.40071296691895 + }, + "post_job_actions": { + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + } + }, + "tool_errors": null, + "tool_id": "Cut1", + "tool_state": "{\"columnList\": \"\\\"c2\\\"\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"delimiter\": \"\\\"P\\\"\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", + "tool_version": "1.0.2", + "type": "tool", + "uuid": "65a8eef6-7ae8-466f-8be0-57fb24546996", + "workflow_outputs": [] + }, + "8": { + "annotation": "", + "content_id": "Cut1", + "id": 8, + "input_connections": { + "input": { + "id": 6, + "output_name": "outfile_map" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool Cut", + "name": "input" + } + ], + "label": null, + "name": "Cut", + "outputs": [ + { + "name": "out_file1", + "type": "tabular" + } + ], + "position": { + "left": 1621.9668083190918, + "top": 869.908037185669 + }, + "post_job_actions": { + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + } + }, + "tool_errors": null, + "tool_id": "Cut1", + "tool_state": "{\"columnList\": \"\\\"c2\\\"\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"delimiter\": \"\\\"T\\\"\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", + "tool_version": "1.0.2", + "type": "tool", + "uuid": "9bf2d387-d452-41dc-974a-14fc8d5b1dae", + "workflow_outputs": [] + }, + "9": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/ensembl_get_sequences/get_sequences/0.1.2", + "id": 9, + "input_connections": { + "input": { + "id": 7, + "output_name": "out_file1" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool Get sequences by Ensembl ID", + "name": "input" + } + ], + "label": null, + "name": "Get sequences by Ensembl ID", + "outputs": [ + { + "name": "output", + "type": "fasta" + } + ], + "position": { + "left": 1935.5881462097168, + "top": 501.12129402160645 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/ensembl_get_sequences/get_sequences/0.1.2", + "tool_shed_repository": { + "changeset_revision": "4b7261f484bb", + "name": "ensembl_get_sequences", + "owner": "earlhaminst", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"__page__\": 0, \"species_selector\": \"\\\"ensembl\\\"\", \"__rerun_remap_job_id__\": null, \"expand_3prime\": \"\\\"0\\\"\", \"type_selector\": \"\\\"genomic\\\"\", \"expand_5prime\": \"\\\"0\\\"\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", + "tool_version": "0.1.2", + "type": "tool", + "uuid": "1ad6ced1-1875-41d3-a075-f6b7049badc9", + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "de004541-64cd-4953-a822-dbc8a004e081" + } + ] + }, + "10": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/ensembl_get_feature_info/get_feature_info/0.1.2", + "id": 10, + "input_connections": { + "input": { + "id": 8, + "output_name": "out_file1" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool Get features by Ensembl ID", + "name": "input" + } + ], + "label": null, + "name": "Get features by Ensembl ID", + "outputs": [ + { + "name": "output", + "type": "json" + } + ], + "position": { + "left": 1935.1285514831543, + "top": 894.0808277130127 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/ensembl_get_feature_info/get_feature_info/0.1.2", + "tool_shed_repository": { + "changeset_revision": "840ea71e6318", + "name": "ensembl_get_feature_info", + "owner": "earlhaminst", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"__page__\": 0, \"species_selector\": \"\\\"ensembl\\\"\", \"__rerun_remap_job_id__\": null, \"format_selector\": \"\\\"full\\\"\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"expand\": \"\\\"false\\\"\"}", + "tool_version": "0.1.2", + "type": "tool", + "uuid": "29de2a25-3a3d-42b5-aa68-994f8eeb8820", + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "caa4c8d9-8487-4d6c-8284-ea63ab9ca3d4" + } + ] + } + }, + "uuid": "2aedea24-8fdc-4b58-b8b3-752b0ceba3e9" +} \ No newline at end of file