# HG changeset patch
# User fcaramia
# Date 1357689108 18000
# Node ID 4eeda563e6c160027cdda9facf875c7eb2694d1b
# Parent  109dcafe9aa6c8d89659301c0f2d1554e723e70b
Uploaded

diff -r 109dcafe9aa6 -r 4eeda563e6c1 Galaxy-Workflow-Differential_Methylation_Bismark.ga
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Galaxy-Workflow-Differential_Methylation_Bismark.ga	Tue Jan 08 18:51:48 2013 -0500
@@ -0,0 +1,229 @@
+{
+    "a_galaxy_workflow": "true", 
+    "annotation": "Compare Methylation levels of 2 samples", 
+    "format-version": "0.1", 
+    "name": "Differential_Methylation_Bismark", 
+    "steps": {
+        "0": {
+            "annotation": "", 
+            "id": 0, 
+            "input_connections": {}, 
+            "inputs": [], 
+            "name": "Bismark", 
+            "outputs": [
+                {
+                    "name": "summary", 
+                    "type": "txt"
+                }, 
+                {
+                    "name": "output", 
+                    "type": "bam"
+                }
+            ], 
+            "position": {
+                "left": 198, 
+                "top": 200
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/fcaramia/methylation_analysis_bismark/bismark_tool/0.7.6", 
+            "tool_state": "{\"__page__\": 0, \"format_option\": \"\\\"fastq\\\"\", \"genome\": \"\\\"bismark.dm3.BDGP5.25.62\\\"\", \"option_input\": \"{\\\"input_option\\\": \\\"mates\\\", \\\"file_mate1\\\": null, \\\"__current_case__\\\": 0, \\\"file_mate2\\\": null}\", \"non_directional\": \"\\\"ON\\\"\"}", 
+            "tool_version": "0.7.6", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "1": {
+            "annotation": "", 
+            "id": 1, 
+            "input_connections": {}, 
+            "inputs": [], 
+            "name": "Bismark", 
+            "outputs": [
+                {
+                    "name": "summary", 
+                    "type": "txt"
+                }, 
+                {
+                    "name": "output", 
+                    "type": "bam"
+                }
+            ], 
+            "position": {
+                "left": 200, 
+                "top": 375
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/fcaramia/methylation_analysis_bismark/bismark_tool/0.7.6", 
+            "tool_state": "{\"__page__\": 0, \"format_option\": \"\\\"fastq\\\"\", \"genome\": \"\\\"bismark.dm3.BDGP5.25.62\\\"\", \"option_input\": \"{\\\"input_option\\\": \\\"mates\\\", \\\"file_mate1\\\": null, \\\"__current_case__\\\": 0, \\\"file_mate2\\\": null}\", \"non_directional\": \"\\\"ON\\\"\"}", 
+            "tool_version": "0.7.6", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "2": {
+            "annotation": "", 
+            "id": 2, 
+            "input_connections": {
+                "bamfile": {
+                    "id": 0, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Methylation Extractor", 
+            "outputs": [
+                {
+                    "name": "output", 
+                    "type": "bedgraph"
+                }, 
+                {
+                    "name": "summary", 
+                    "type": "txt"
+                }
+            ], 
+            "position": {
+                "left": 432.5, 
+                "top": 218
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/fcaramia/methylation_analysis_bismark/methyation_extractor_tool/0.7.6", 
+            "tool_state": "{\"__page__\": 0, \"bamfile\": \"null\", \"ending\": \"\\\"paired\\\"\", \"no_overlap\": \"\\\"ON\\\"\", \"genome\": \"\\\"bismark.dm3.BDGP5.25.62\\\"\", \"report\": \"\\\"ON\\\"\"}", 
+            "tool_version": "0.7.6", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "3": {
+            "annotation": "", 
+            "id": 3, 
+            "input_connections": {
+                "bamfile": {
+                    "id": 1, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Methylation Extractor", 
+            "outputs": [
+                {
+                    "name": "output", 
+                    "type": "bedgraph"
+                }, 
+                {
+                    "name": "summary", 
+                    "type": "txt"
+                }
+            ], 
+            "position": {
+                "left": 432.5, 
+                "top": 394
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/fcaramia/methylation_analysis_bismark/methyation_extractor_tool/0.7.6", 
+            "tool_state": "{\"__page__\": 0, \"bamfile\": \"null\", \"ending\": \"\\\"paired\\\"\", \"no_overlap\": \"\\\"ON\\\"\", \"genome\": \"\\\"bismark.dm3.BDGP5.25.62\\\"\", \"report\": \"\\\"ON\\\"\"}", 
+            "tool_version": "0.7.6", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "4": {
+            "annotation": "", 
+            "id": 4, 
+            "input_connections": {
+                "bedgraph": {
+                    "id": 2, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Methylation by Region Converter", 
+            "outputs": [
+                {
+                    "name": "output", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "summary", 
+                    "type": "txt"
+                }
+            ], 
+            "position": {
+                "left": 673, 
+                "top": 221
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/fcaramia/methylation_analysis_bismark/methyation_by_region_tool/0.1.1", 
+            "tool_state": "{\"sample\": \"\\\"None\\\"\", \"__page__\": 0, \"refBedSource\": \"{\\\"index\\\": \\\"bismark.bed.agilent.human\\\", \\\"__current_case__\\\": 0, \\\"bedSource\\\": \\\"indexed\\\"}\", \"bedgraph\": \"null\"}", 
+            "tool_version": "0.1.1", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "5": {
+            "annotation": "", 
+            "id": 5, 
+            "input_connections": {
+                "bedgraph": {
+                    "id": 3, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Methylation by Region Converter", 
+            "outputs": [
+                {
+                    "name": "output", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "summary", 
+                    "type": "txt"
+                }
+            ], 
+            "position": {
+                "left": 674, 
+                "top": 397
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/fcaramia/methylation_analysis_bismark/methyation_by_region_tool/0.1.1", 
+            "tool_state": "{\"sample\": \"\\\"None\\\"\", \"__page__\": 0, \"refBedSource\": \"{\\\"index\\\": \\\"bismark.bed.agilent.human\\\", \\\"__current_case__\\\": 0, \\\"bedSource\\\": \\\"indexed\\\"}\", \"bedgraph\": \"null\"}", 
+            "tool_version": "0.1.1", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "6": {
+            "annotation": "", 
+            "id": 6, 
+            "input_connections": {
+                "seg1": {
+                    "id": 4, 
+                    "output_name": "output"
+                }, 
+                "seg2": {
+                    "id": 5, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Differential Methylation", 
+            "outputs": [
+                {
+                    "name": "output", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 993, 
+                "top": 308
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/fcaramia/methylation_analysis_bismark/differential_methylation_tool/1.0.0", 
+            "tool_state": "{\"__page__\": 0, \"seg1\": \"null\", \"annot\": \"\\\"both\\\"\", \"seg2\": \"null\", \"fdr\": \"\\\"none\\\"\", \"genome\": \"\\\"bismark.dm3.BDGP5.25.62\\\"\"}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }
+    }
+}
\ No newline at end of file