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Commit message:
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 2c7c545579169dda723cd7d91d9ccef1c5061fed |
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modified:
readme.md swissprot.ga |
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added:
GeneFamilies_GeneSeqToFamily.ga |
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| diff -r cc5419f7dff7 -r 06470b2e491f GeneFamilies_GeneSeqToFamily.ga --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/GeneFamilies_GeneSeqToFamily.ga Mon Jun 25 18:50:55 2018 -0400 |
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| b'@@ -0,0 +1,303 @@\n+{\n+ "a_galaxy_workflow": "true", \n+ "annotation": "", \n+ "format-version": "0.1", \n+ "name": "GeneFamilies_GeneSeqToFamily", \n+ "steps": {\n+ "0": {\n+ "annotation": "", \n+ "content_id": null, \n+ "errors": null, \n+ "id": 0, \n+ "input_connections": {}, \n+ "inputs": [\n+ {\n+ "description": "", \n+ "name": "CDS"\n+ }\n+ ], \n+ "label": "CDS", \n+ "name": "Input dataset", \n+ "outputs": [], \n+ "position": {\n+ "left": 200, \n+ "top": 390.5\n+ }, \n+ "tool_id": null, \n+ "tool_state": "{\\"name\\": \\"CDS\\"}", \n+ "tool_version": null, \n+ "type": "data_input", \n+ "uuid": "d2777a78-6429-47f6-9567-cb15140ace8d", \n+ "workflow_outputs": [\n+ {\n+ "label": null, \n+ "output_name": "output", \n+ "uuid": "7eedd485-b41e-4b55-9359-9f7e56d84f54"\n+ }\n+ ]\n+ }, \n+ "1": {\n+ "annotation": "", \n+ "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: transeq101/5.0.0", \n+ "errors": null, \n+ "id": 1, \n+ "input_connections": {\n+ "input1": {\n+ 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"tool_shed": "toolshed.g2.bx.psu.edu"\n+ }, \n+ "tool_state": "{\\"__page__\\": null, \\"__rerun_remap_job_id__\\": null, \\"c_conditional\\": \\"{\\\\\\"c\\\\\\": \\\\\\"\\\\\\", \\\\\\"b\\\\\\": \\\\\\"0.1\\\\\\", \\\\\\"m\\\\\\": \\\\\\"500\\\\\\", \\\\\\"C\\\\\\": {\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}, \\\\\\"O\\\\\\": {\\\\\\"O_selector\\\\\\": \\\\\\"\\\\\\", \\\\\\"__current_case__\\\\\\": 1}, \\\\\\"L\\\\\\": \\\\\\"2\\\\\\", \\\\\\"s\\\\\\": \\\\\\"0.34\\\\\\", \\\\\\"__current_case__\\\\\\": 1}\\", \\"w\\": \\"\\\\\\"0\\\\\\"\\", \\"inputFile\\": \\"{\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}\\"}", \n+ "tool_version": "0.5.1.1", \n+ "type": "tool", \n+ "uuid": "d2b2ba89-b47d-4241-8adf-0d780f834412", \n+ "workflow_outputs": []\n+ }\n+ }, \n+ "tags": [], \n+ "uuid": "5bad18ae-08f1-4da5-b375-5a43d0440616"\n+}\n' |
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| diff -r cc5419f7dff7 -r 06470b2e491f readme.md --- a/readme.md Mon Nov 27 11:04:05 2017 -0500 +++ b/readme.md Mon Jun 25 18:50:55 2018 -0400 |
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| @@ -67,6 +67,11 @@ The Aequatus.js plugin provides an interactive visual representation of the phylogenetic and structural relationships among the homologous genes, using a shared colour scheme for coding regions to represent homology in internal gene structure alongside their corresponding gene trees. It is also able to indicate insertions and deletions in homologous genes with respect to shared ancestors. +## Citation information: + +If you are using GeneSeqToFamily for any kind of research purpose, please cite the following paper: + +Anil S. Thanki, Nicola Soranzo, Wilfried Haerty, Robert P. Davey (2018) [GeneSeqToFamily: a Galaxy workflow to find gene families based on the Ensembl Compara GeneTrees pipeline](https://doi.org/10.1093/gigascience/giy005) *GigaScience* 7(3), giy005, doi: 10.1093/gigascience/giy005 ## References @@ -74,9 +79,6 @@ 1. Vilella AJ, Severin J, Ureta-Vidal A, Heng L, Durbin R, Birney E (2009) [EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates.](http://genome.cshlp.org/content/19/2/327) *Genome Res.* 19(2):327–335, doi: 10.1101/gr.073585.107 2. Thanki AS, Ayling S, Herrero J, Davey RP (2016) [Aequatus: An open-source homology browser.](http://biorxiv.org/content/early/2016/06/01/055632) *bioRxiv*, doi: 10.1101/055632 -## Pre-print - -Pre-print for this work can be found at [bioRxiv server](http://biorxiv.org/content/early/2017/04/19/096529) ## Project contacts: @@ -84,4 +86,4 @@ * Nicola Soranzo <Nicola.Soranzo@earlham.ac.uk> * Robert Davey <Robert.Davey@earlham.ac.uk> -Copyright © 2016-2017 Earlham Institute, Norwich, UK +Copyright © 2016-2018 Earlham Institute, Norwich, UK |
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| diff -r cc5419f7dff7 -r 06470b2e491f swissprot.ga --- a/swissprot.ga Mon Nov 27 11:04:05 2017 -0500 +++ b/swissprot.ga Mon Jun 25 18:50:55 2018 -0400 |
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| b'@@ -2,11 +2,12 @@\n "a_galaxy_workflow": "true", \n "annotation": "", \n "format-version": "0.1", \n- "name": "SwisProt scratch", \n+ "name": "SwissProt", \n "steps": {\n "0": {\n "annotation": "", \n "content_id": null, \n+ "errors": null, \n "id": 0, \n "input_connections": {}, \n "inputs": [\n@@ -15,24 +16,30 @@\n "name": "CDS"\n }\n ], \n- "label": null, \n+ "label": "CDS", \n "name": "Input dataset", \n "outputs": [], \n "position": {\n- "left": 163.95219802856445, \n- "top": 290.93748664855957\n+ "left": 163.9375, \n+ "top": 290.9375\n }, \n- "tool_errors": null, \n "tool_id": null, \n "tool_state": "{\\"name\\": \\"CDS\\"}", \n "tool_version": null, \n "type": "data_input", \n "uuid": "4fb3c053-8997-48fe-a31b-e5ae64617009", \n- "workflow_outputs": []\n+ "workflow_outputs": [\n+ {\n+ "label": null, \n+ "output_name": "output", \n+ "uuid": "81633688-02fb-4a42-a785-b784ffe3ee0e"\n+ }\n+ ]\n }, \n "1": {\n "annotation": "", \n "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: transeq101/5.0.0", \n+ "errors": null, \n "id": 1, \n "input_connections": {\n "input1": {\n@@ -55,8 +62,8 @@\n }\n ], \n "position": {\n- "left": 500.90070724487305, \n- "top": 199.963228225708\n+ "left": 500.890625, \n+ "top": 199.953125\n }, \n "post_job_actions": {\n "HideDatasetActionout_file1": {\n@@ -65,10 +72,9 @@\n "output_name": "out_file1"\n }\n }, \n- "tool_errors": null, \n "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: transeq101/5.0.0", \n "tool_shed_repository": {\n- "changeset_revision": "511429456d3c", \n+ "changeset_revision": "1b6538ec8b56", \n "name": "emboss_5", \n "owner": "devteam", \n "tool_shed": "toolshed.g2.bx.psu.edu"\n@@ -82,6 +88,7 @@\n "2": {\n "annotation": "", \n "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.1.08", \n+ "errors": null, \n "id": 2, \n "input_connections": {\n "query": {\n@@ -104,8 +111,8 @@\n }\n ], \n "position": {\n- 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"content_id": "Cut1", \n+ "errors": null, \n "id": 8, \n "input_connections": {\n "input": {\n@@ -434,8 +441,8 @@\n }\n ], \n "position": {\n- "left": 1621.9668083190918, \n- "top": 869.908037185669\n+ "left": 1621.953125, \n+ "top": 869.90625\n }, \n "post_job_actions": {\n "HideDatasetActionout_file1": {\n@@ -444,7 +451,6 @@\n "output_name": "out_file1"\n }\n }, \n- "tool_errors": null, \n "tool_id": "Cut1", \n "tool_state": "{\\"columnList\\": \\"\\\\\\"c2\\\\\\"\\", \\"input\\": \\"{\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}\\", \\"delimiter\\": \\"\\\\\\"T\\\\\\"\\", \\"__rerun_remap_job_id__\\": null, \\"__page__\\": 0}", \n "tool_version": "1.0.2", \n@@ -455,6 +461,7 @@\n "9": {\n "annotation": "", \n "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/ensembl_get_sequences/get_sequences/0.1.2", \n+ "errors": null, \n "id": 9, \n "input_connections": {\n "input": {\n@@ -477,19 +484,18 @@\n }\n ], \n "position": {\n- "left": 1935.5881462097168, \n- "top": 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