# HG changeset patch # User bgruening # Date 1373485079 14400 # Node ID 03f5132065e28c0915b498b3609c9d4069239179 Uploaded diff -r 000000000000 -r 03f5132065e2 glimmer3_with_trainingset.ga --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/glimmer3_with_trainingset.ga Wed Jul 10 15:37:59 2013 -0400 @@ -0,0 +1,153 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "", + "format-version": "0.1", + "name": "Glimmer gene calling with trainingset.", + "steps": { + "0": { + "annotation": "The set of genes is used to train the gene calling of glimmer.", + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "The set of genes is used to train the gene calling of glimmer.", + "name": "Set of Genes" + } + ], + "name": "Input dataset", + "outputs": [], + "position": { + "left": 283, + "top": 376 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"Set of Genes\"}", + "tool_version": null, + "type": "data_input", + "user_outputs": [] + }, + "1": { + "annotation": "", + "id": 1, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Input Genomic Sequence" + } + ], + "name": "Input dataset", + "outputs": [], + "position": { + "left": 443, + "top": 232 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"Input Genomic Sequence\"}", + "tool_version": null, + "type": "data_input", + "user_outputs": [] + }, + "2": { + "annotation": "", + "id": 2, + "input_connections": { + "infile": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "name": "Glimmer ICM builder", + "outputs": [ + { + "name": "outfile", + "type": "data" + } + ], + "position": { + "left": 503, + "top": 486 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/glimmer/glimmer_build-icm/0.2", + "tool_state": "{\"__page__\": 0, \"depth\": \"\\\"7\\\"\", \"period\": \"\\\"3\\\"\", \"width\": \"\\\"12\\\"\", \"stop_codon_opts\": \"{\\\"genbank_gencode\\\": \\\"11\\\", \\\"__current_case__\\\": 0, \\\"stop_codon_opts_selector\\\": \\\"gb\\\"}\", \"no_stops\": \"\\\"False\\\"\", \"chromInfo\": \"\\\"/home/bag/projects/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"infile\": \"null\"}", + "tool_version": "0.2", + "type": "tool", + "user_outputs": [] + }, + "3": { + "annotation": "", + "id": 3, + "input_connections": { + "icm_input": { + "id": 2, + "output_name": "outfile" + }, + "seq_input": { + "id": 1, + "output_name": "output" + } + }, + "inputs": [], + "name": "Glimmer3", + "outputs": [ + { + "name": "genes_output", + "type": "fasta" + }, + { + "name": "report_output", + "type": "txt" + }, + { + "name": "detailed_output", + "type": "txt" + } + ], + "position": { + "left": 674, + "top": 319 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/glimmer/glimmer_knowlegde-based/0.2", + "tool_state": "{\"extend\": \"\\\"False\\\"\", \"__page__\": 0, \"linear\": \"\\\"True\\\"\", \"detailed_report\": \"\\\"False\\\"\", \"seq_input\": \"null\", \"gc_percent\": \"\\\"0.0\\\"\", \"start_codons\": \"\\\"atg,gtg,ttg\\\"\", \"threshold\": \"\\\"30\\\"\", \"stop_codon_opts\": \"{\\\"genbank_gencode\\\": \\\"11\\\", \\\"__current_case__\\\": 0, \\\"stop_codon_opts_selector\\\": \\\"gb\\\"}\", \"max_olap\": \"\\\"50\\\"\", \"no_indep\": \"\\\"False\\\"\", \"gene_len\": \"\\\"90\\\"\", \"report\": \"\\\"False\\\"\", \"chromInfo\": \"\\\"/home/bag/projects/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"icm_input\": \"null\"}", + "tool_version": "0.2", + "type": "tool", + "user_outputs": [] + }, + "4": { + "annotation": "", + "id": 4, + "input_connections": { + "input1": { + "id": 3, + "output_name": "genes_output" + } + }, + "inputs": [], + "name": "transeq", + "outputs": [ + { + "name": "out_file1", + "type": "fasta" + } + ], + "position": { + "left": 988, + "top": 351 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: transeq101/5.0.0", + "tool_state": "{\"trim\": \"\\\"no\\\"\", \"__page__\": 0, \"input1\": \"null\", \"out_format1\": \"\\\"fasta\\\"\", \"frame\": \"\\\"1\\\"\", \"regions\": \"\\\"\\\"\", \"clean\": \"\\\"no\\\"\", \"table\": \"\\\"11\\\"\", \"alternative\": \"\\\"no\\\"\"}", + "tool_version": "5.0.0", + "type": "tool", + "user_outputs": [] + } + } +} diff -r 000000000000 -r 03f5132065e2 readme.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readme.rst Wed Jul 10 15:37:59 2013 -0400 @@ -0,0 +1,28 @@ +============================== +Glimmer3 gene calling workflow +============================== + +This Tool Shed Repository contains a workflow for the gene prediction of from a given nucleotide FASTA file. + +At first an interpolated context model (ICM) is build from a know set of genes, preferable from the closest relative available organism(s). In a following step this ICM model is used to predict genes on the second input. The output is a FASTA file with nucleotide sequences that is further converted to proteins sequences. + +To run that worflow glimmer_ und the EMBOSS_ suite is required. Both can be installed from the Tool Shed. + +.. _glimmer: http://www.cbcb.umd.edu/software/glimmer/ +.. _EMBOSS: http://emboss.sourceforge.net/ + +| A. L. Delcher, K.A. Bratke, E.C. Powers, and S.L. Salzberg. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics (Advance online version) (2007). + +EMBOSS: The European Molecular Biology Open Software Suite (2000) +Rice,P. Longden,I. and Bleasby,A. +Trends in Genetics 16, (6) pp276--277 + +************ +Availability +************ + +This workflow is available on the main Galaxy Tool Shed: +http://toolshed.g2.bx.psu.edu/view/bgruening/glimmer_gene_calling_workflow + +Development is being done here: +https://github.com/bgruening/galaxytools/workflows/glimmer3/ diff -r 000000000000 -r 03f5132065e2 repository_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Wed Jul 10 15:37:59 2013 -0400 @@ -0,0 +1,5 @@ + + + + +