--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Galaxy-Workflow-Glimmer.ga	Mon Sep 09 12:16:17 2013 -0400
@@ -0,0 +1,175 @@
+{
+    "a_galaxy_workflow": "true", 
+    "annotation": "glimmer-from-scratch", 
+    "format-version": "0.1", 
+    "name": "Glimmer", 
+    "steps": {
+        "0": {
+            "annotation": "", 
+            "id": 0, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "Genome sequence"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 158, 
+                "top": 200
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"Genome sequence\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "1": {
+            "annotation": "", 
+            "id": 1, 
+            "input_connections": {
+                "loSequence": {
+                    "id": 0, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Long-ORFs", 
+            "outputs": [
+                {
+                    "name": "logfile", 
+                    "type": "txt"
+                }, 
+                {
+                    "name": "loOutput", 
+                    "type": "glimmer_coords"
+                }
+            ], 
+            "position": {
+                "left": 248, 
+                "top": 336
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "long-orfs_wrapper", 
+            "tool_state": "{\"loFixed\": \"\\\"False\\\"\", \"__page__\": 0, \"loMaxOverlap\": \"\\\"\\\"\", \"loMinLen\": \"\\\"\\\"\", \"loStartCodons\": \"\\\"\\\"\", \"loTransTable\": \"\\\"\\\"\", \"loNoHeader\": \"\\\"False\\\"\", \"loLengthOpt\": \"\\\"False\\\"\", \"loCutoff\": \"\\\"\\\"\", \"loStopCodons\": \"\\\"\\\"\", \"loLinear\": \"\\\"False\\\"\", \"loWithoutStops\": \"\\\"False\\\"\", \"loEntropy\": \"null\", \"loSequence\": \"null\"}", 
+            "tool_version": "0.2", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "2": {
+            "annotation": "", 
+            "id": 2, 
+            "input_connections": {
+                "exCoords": {
+                    "id": 1, 
+                    "output_name": "loOutput"
+                }, 
+                "exSequence": {
+                    "id": 0, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Extract", 
+            "outputs": [
+                {
+                    "name": "logfile", 
+                    "type": "txt"
+                }, 
+                {
+                    "name": "exOutput", 
+                    "type": "fasta"
+                }
+            ], 
+            "position": {
+                "left": 659, 
+                "top": 231
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "extract_wrapper", 
+            "tool_state": "{\"__page__\": 0, \"exSequence\": \"null\", \"exCoords\": \"null\", \"exDir\": \"\\\"False\\\"\", \"exNoStop\": \"\\\"False\\\"\", \"exNoStart\": \"\\\"False\\\"\", \"exNoWrap\": \"\\\"False\\\"\", \"exMinLen\": \"\\\"\\\"\", \"ex2Fields\": \"\\\"False\\\"\"}", 
+            "tool_version": "0.2", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "3": {
+            "annotation": "", 
+            "id": 3, 
+            "input_connections": {
+                "biSequence": {
+                    "id": 2, 
+                    "output_name": "exOutput"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Build-ICM", 
+            "outputs": [
+                {
+                    "name": "logfile", 
+                    "type": "txt"
+                }, 
+                {
+                    "name": "biIcm", 
+                    "type": "glimmer_icm"
+                }
+            ], 
+            "position": {
+                "left": 177, 
+                "top": 715
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "build-icm_wrapper", 
+            "tool_state": "{\"__page__\": 0, \"biStopCodons\": \"\\\"\\\"\", \"biPeriod\": \"\\\"3\\\"\", \"biTransTable\": \"\\\"\\\"\", \"biNoStops\": \"\\\"False\\\"\", \"biDepth\": \"\\\"7\\\"\", \"biReverse\": \"\\\"False\\\"\", \"biSequence\": \"null\", \"biWidth\": \"\\\"12\\\"\"}", 
+            "tool_version": "0.2", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "4": {
+            "annotation": "", 
+            "id": 4, 
+            "input_connections": {
+                "glIcm": {
+                    "id": 3, 
+                    "output_name": "biIcm"
+                }, 
+                "glSequence": {
+                    "id": 0, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Glimmer3", 
+            "outputs": [
+                {
+                    "name": "logfile", 
+                    "type": "txt"
+                }, 
+                {
+                    "name": "glDetail", 
+                    "type": "txt"
+                }, 
+                {
+                    "name": "glPredict", 
+                    "type": "txt"
+                }
+            ], 
+            "position": {
+                "left": 508, 
+                "top": 715
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "glimmer3_wrapper", 
+            "tool_state": "{\"__page__\": 0, \"glFirstCodon\": \"\\\"False\\\"\", \"glNoIndep\": \"\\\"False\\\"\", \"glIcm\": \"null\", \"glRbsPwm\": \"null\", \"glEntropy\": \"null\", \"glSeparateGenes\": \"\\\"False\\\"\", \"glOrfCoords\": \"null\", \"glMaxOverlap\": \"\\\"\\\"\", \"glIgnoreScoreLen\": \"\\\"\\\"\", \"glGcPercent\": \"\\\"\\\"\", \"glSequence\": \"null\", \"glGeneLen\": \"\\\"\\\"\", \"glStopCodons\": \"\\\"\\\"\", \"glExtend\": \"\\\"False\\\"\", \"glLinear\": \"\\\"False\\\"\", \"glTransTable\": \"\\\"\\\"\", \"glThreshold\": \"\\\"\\\"\", \"glStartCodons\": \"\\\"\\\"\", \"glStartProbs\": \"\\\"\\\"\"}", 
+            "tool_version": "0.2", 
+            "type": "tool", 
+            "user_outputs": []
+        }
+    }
+}