Mercurial > repos > bgruening > find_genes_located_nearby_workflow
view find_genes_located_nearby.ga @ 2:38b08a771e7e draft default tip
Uploaded
author | bgruening |
---|---|
date | Tue, 17 Mar 2015 13:34:31 -0400 |
parents | db68266f7364 |
children |
line wrap: on
line source
{ "a_galaxy_workflow": "true", "annotation": "Input are two protein genes in FASTA format. They will be blasted with tblastn against the NCBI NR database. Both results are compared and hits are returned that are close to each other.", "format-version": "0.1", "name": "Finding 2 genes close to each other", "steps": { "0": { "annotation": "", "id": 0, "input_connections": {}, "inputs": [ { "description": "", "name": "Protein in FASTA format" } ], "name": "Input dataset", "outputs": [], "position": { "left": 248, "top": 311 }, "tool_errors": null, "tool_id": null, "tool_state": "{\"name\": \"Protein in FASTA format\"}", "tool_version": null, "type": "data_input", "user_outputs": [] }, "1": { "annotation": "", "id": 1, "input_connections": {}, "inputs": [ { "description": "", "name": "Protein in FASTA format" } ], "name": "Input dataset", "outputs": [], "position": { "left": 250, "top": 386 }, "tool_errors": null, "tool_id": null, "tool_state": "{\"name\": \"Protein in FASTA format\"}", "tool_version": null, "type": "data_input", "user_outputs": [] }, "2": { "annotation": "", "id": 2, "input_connections": { "query": { "id": 0, "output_name": "output" } }, "inputs": [], "name": "NCBI BLAST+ tblastn", "outputs": [ { "name": "output1", "type": "tabular" } ], "position": { "left": 380.6166687011719, "top": 224.61666870117188 }, "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_tblastn_wrapper/0.1.01", "tool_state": "{\"__page__\": 0, \"evalue_cutoff\": \"\\\"0.001\\\"\", \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"db\\\", \\\"subject\\\": \\\"\\\", \\\"histdb\\\": \\\"\\\", \\\"__current_case__\\\": 0, \\\"database\\\": \\\"nt_28-09-14\\\"}\", \"output\": \"{\\\"out_format\\\": \\\"cols\\\", \\\"std_cols\\\": [\\\"sseqid\\\", \\\"sstart\\\", \\\"send\\\", \\\"bitscore\\\"], \\\"ids_cols\\\": null, \\\"tax_cols\\\": null, \\\"__current_case__\\\": 2, \\\"misc_cols\\\": null, \\\"ext_cols\\\": null}\", \"query\": \"null\"}", "tool_version": "0.1.01", "type": "tool", "user_outputs": [] }, "3": { "annotation": "", "id": 3, "input_connections": { "query": { "id": 1, "output_name": "output" } }, "inputs": [], "name": "NCBI BLAST+ tblastn", "outputs": [ { "name": "output1", "type": "tabular" } ], "position": { "left": 393.6166687011719, "top": 444.6166687011719 }, "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_tblastn_wrapper/0.1.01", "tool_state": "{\"__page__\": 0, \"evalue_cutoff\": \"\\\"0.001\\\"\", \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"db\\\", \\\"subject\\\": \\\"\\\", \\\"histdb\\\": \\\"\\\", \\\"__current_case__\\\": 0, \\\"database\\\": \\\"nt_28-09-14\\\"}\", \"output\": \"{\\\"out_format\\\": \\\"cols\\\", \\\"std_cols\\\": [\\\"sseqid\\\", \\\"sstart\\\", \\\"send\\\", \\\"bitscore\\\"], \\\"ids_cols\\\": null, \\\"tax_cols\\\": null, \\\"__current_case__\\\": 2, \\\"misc_cols\\\": null, \\\"ext_cols\\\": null}\", \"query\": \"null\"}", "tool_version": "0.1.01", "type": "tool", "user_outputs": [] }, "4": { "annotation": "", "id": 4, "input_connections": { "input": { "id": 2, "output_name": "output1" } }, "inputs": [], "name": "Filter", "outputs": [ { "name": "out_file1", "type": "input" } ], "position": { "left": 656.5, "top": 190.5 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "Filter1", "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"header_lines\": \"\\\"0\\\"\", \"cond\": \"\\\"c4>150\\\"\", \"__page__\": 0}", "tool_version": "1.1.0", "type": "tool", "user_outputs": [] }, "5": { "annotation": "", "id": 5, "input_connections": { "input": { "id": 3, "output_name": "output1" } }, "inputs": [], "name": "Filter", "outputs": [ { "name": "out_file1", "type": "input" } ], "position": { "left": 609.5, "top": 349.5 }, "post_job_actions": { "HideDatasetActionout_file1": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "out_file1" } }, "tool_errors": null, "tool_id": "Filter1", "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"header_lines\": \"\\\"0\\\"\", \"cond\": \"\\\"c4>150\\\"\", \"__page__\": 0}", "tool_version": "1.1.0", "type": "tool", "user_outputs": [] }, "6": { "annotation": "", "id": 6, "input_connections": { "input": { "id": 4, "output_name": "out_file1" } }, "inputs": [], "name": "Compute", "outputs": [ { "name": "out_file1", "type": "input" } ], "position": { "left": 715, "top": 224 }, "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/column_maker/Add_a_column1/1.1.0", "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"cond\": \"\\\"max(c3,c2)\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"round\": \"\\\"yes\\\"\"}", "tool_version": "1.1.0", "type": "tool", "user_outputs": [] }, "7": { "annotation": "", "id": 7, "input_connections": { "input": { "id": 5, "output_name": "out_file1" } }, "inputs": [], "name": "Compute", "outputs": [ { "name": "out_file1", "type": "input" } ], "position": { "left": 661.5, "top": 381.5 }, "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/column_maker/Add_a_column1/1.1.0", "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"cond\": \"\\\"min(c3,c2)\\\"\", \"round\": \"\\\"yes\\\"\", \"__page__\": 0}", "tool_version": "1.1.0", "type": "tool", "user_outputs": [] }, "8": { "annotation": "", "id": 8, "input_connections": { "input": { "id": 6, "output_name": "out_file1" } }, "inputs": [], "name": "Compute", "outputs": [ { "name": "out_file1", "type": "input" } ], "position": { "left": 767, "top": 260 }, "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/column_maker/Add_a_column1/1.1.0", "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"cond\": \"\\\"min(c3,c2)\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"round\": \"\\\"yes\\\"\"}", "tool_version": "1.1.0", "type": "tool", "user_outputs": [] }, "9": { "annotation": "", "id": 9, "input_connections": { "input": { "id": 7, "output_name": "out_file1" } }, "inputs": [], "name": "Compute", "outputs": [ { "name": "out_file1", "type": "input" } ], "position": { "left": 714.5, "top": 416.5 }, "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/column_maker/Add_a_column1/1.1.0", "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"cond\": \"\\\"max(c3,c2)\\\"\", \"round\": \"\\\"yes\\\"\", \"__page__\": 0}", "tool_version": "1.1.0", "type": "tool", "user_outputs": [] }, "10": { "annotation": "", "id": 10, "input_connections": { "input": { "id": 8, "output_name": "out_file1" } }, "inputs": [], "name": "Cut", "outputs": [ { "name": "out_file1", "type": "tabular" } ], "position": { "left": 957, "top": 271 }, "post_job_actions": { "ChangeDatatypeActionout_file1": { "action_arguments": { "newtype": "interval" }, "action_type": "ChangeDatatypeAction", "output_name": "out_file1" } }, "tool_errors": null, "tool_id": "Cut1", "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"delimiter\": \"\\\"T\\\"\", \"columnList\": \"\\\"c1,c6,c5\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", "tool_version": "1.0.2", "type": "tool", "user_outputs": [] }, "11": { "annotation": "", "id": 11, "input_connections": { "input": { "id": 9, "output_name": "out_file1" } }, "inputs": [], "name": "Compute", "outputs": [ { "name": "out_file1", "type": "input" } ], "position": { "left": 768.5, "top": 452.5 }, "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/column_maker/Add_a_column1/1.1.0", "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"cond\": \"\\\"max(c5-10000,1)\\\"\", \"round\": \"\\\"yes\\\"\", \"__page__\": 0}", "tool_version": "1.1.0", "type": "tool", "user_outputs": [] }, "12": { "annotation": "", "id": 12, "input_connections": { "input": { "id": 11, "output_name": "out_file1" } }, "inputs": [], "name": "Compute", "outputs": [ { "name": "out_file1", "type": "input" } ], "position": { "left": 819.5, "top": 489.5 }, "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/column_maker/Add_a_column1/1.1.0", "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"cond\": \"\\\"c6+10000\\\"\", \"round\": \"\\\"yes\\\"\", \"__page__\": 0}", "tool_version": "1.1.0", "type": "tool", "user_outputs": [] }, "13": { "annotation": "", "id": 13, "input_connections": { "input": { "id": 12, "output_name": "out_file1" } }, "inputs": [], "name": "Cut", "outputs": [ { "name": "out_file1", "type": "tabular" } ], "position": { "left": 953.5, "top": 392.5 }, "post_job_actions": { "ChangeDatatypeActionout_file1": { "action_arguments": { "newtype": "interval" }, "action_type": "ChangeDatatypeAction", "output_name": "out_file1" } }, "tool_errors": null, "tool_id": "Cut1", "tool_state": "{\"columnList\": \"\\\"c1,c7,c8\\\"\", \"input\": \"null\", \"delimiter\": \"\\\"T\\\"\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", "tool_version": "1.0.2", "type": "tool", "user_outputs": [] }, "14": { "annotation": "", "id": 14, "input_connections": { "input1": { "id": 10, "output_name": "out_file1" }, "input2": { "id": 13, "output_name": "out_file1" } }, "inputs": [], "name": "Intersect", "outputs": [ { "name": "output", "type": "input" } ], "position": { "left": 1160.9166870117188, "top": 325.91668701171875 }, "post_job_actions": { "HideDatasetActionoutput": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output" } }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/intersect/gops_intersect_1/1.0.0", "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"input1\": \"null\", \"min\": \"\\\"1\\\"\", \"__rerun_remap_job_id__\": null, \"returntype\": \"\\\"\\\"\"}", "tool_version": "1.0.0", "type": "tool", "user_outputs": [] }, "15": { "annotation": "", "id": 15, "input_connections": { "input": { "id": 14, "output_name": "output" } }, "inputs": [], "name": "Sort", "outputs": [ { "name": "out_file1", "type": "input" } ], "position": { "left": 1154.9166870117188, "top": 458.91668701171875 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "sort1", "tool_state": "{\"__page__\": 0, \"style\": \"\\\"alpha\\\"\", \"column\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"1\\\"}\", \"__rerun_remap_job_id__\": null, \"order\": \"\\\"DESC\\\"\", \"input\": \"null\", \"column_set\": \"[{\\\"other_order\\\": \\\"DESC\\\", \\\"__index__\\\": 0, \\\"other_column\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"2\\\"}, \\\"other_style\\\": \\\"num\\\"}]\"}", "tool_version": "1.0.3", "type": "tool", "user_outputs": [] }, "16": { "annotation": "", "id": 16, "input_connections": { "input1": { "id": 15, "output_name": "out_file1" } }, "inputs": [], "name": "Group", "outputs": [ { "name": "out_file1", "type": "tabular" } ], "position": { "left": 1352.5, "top": 399 }, "post_job_actions": { "RenameDatasetActionout_file1": { "action_arguments": { "newname": "Counting hits per genome" }, "action_type": "RenameDatasetAction", "output_name": "out_file1" } }, "tool_errors": null, "tool_id": "Grouping1", "tool_state": "{\"operations\": \"[{\\\"opcol\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"1\\\"}, \\\"__index__\\\": 0, \\\"optype\\\": \\\"length\\\", \\\"opround\\\": \\\"no\\\"}]\", \"__page__\": 0, \"input1\": \"null\", \"ignorelines\": \"null\", \"groupcol\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"1\\\"}\", \"__rerun_remap_job_id__\": null, \"ignorecase\": \"\\\"False\\\"\"}", "tool_version": "2.1.0", "type": "tool", "user_outputs": [] } }, "uuid": "12fe8ac4-30db-4db4-b8f9-7c44e0cc0788" }