--- /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": []
+        }
+    }
+}

--- /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/

--- /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 @@
+<?xml version="1.0"?>
+<repositories description="This requires the glimmer3 repository and the emboss5 tool suite.">
+    <repository name="glimmer" owner="bgruening" toolshed="http://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="c159a6ded912" name="emboss_5" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
+</repositories>