changeset 2:ea2117a7b363

Uploaded CAPS marker design workflow for 454 Data
author john-mccallum
date Sun, 09 Sep 2012 23:16:56 -0400
parents a0689dc29b7f
children 402c3f0fe807
files Galaxy-Workflow-CAPS_Marker_Development_from_454_Read_Mapping.ga
diffstat 1 files changed, 401 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Galaxy-Workflow-CAPS_Marker_Development_from_454_Read_Mapping.ga	Sun Sep 09 23:16:56 2012 -0400
@@ -0,0 +1,401 @@
+{
+    "a_galaxy_workflow": "true", 
+    "annotation": "", 
+    "format-version": "0.1", 
+    "name": "CAPS Marker Development from 454 Read Mapping", 
+    "steps": {
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+            "annotation": "", 
+            "id": 0, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "Reference sequences"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
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+            "tool_state": "{\"name\": \"Reference sequences\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "1": {
+            "annotation": "Reads to map", 
+            "id": 1, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "Reads to map", 
+                    "name": "SFF File "
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
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+                "top": 313.95454406738281
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+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "2": {
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+            "id": 2, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "barcode, vector or adapter sequences to trim", 
+                    "name": "Trimming file"
+                }
+            ], 
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+            "type": "data_input", 
+            "user_outputs": []
+        }, 
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+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "runMapping", 
+            "outputs": [
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+                    "type": "txt"
+                }, 
+                {
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+                    "type": "tabular"
+                }, 
+                {
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+                    "type": "fasta"
+                }, 
+                {
+                    "name": "trimmed_reads_qual", 
+                    "type": "qual454"
+                }, 
+                {
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+                    "type": "tabular"
+                }, 
+                {
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+                    "type": "fasta"
+                }, 
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+                    "type": "qual454"
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+                {
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+                }, 
+                {
+                    "name": "large_contigs_fasta", 
+                    "type": "fasta"
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+                    "type": "qual454"
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+                {
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+                    "type": "tabular"
+                }, 
+                {
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+                    "type": "txt"
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+                {
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+                    "type": "tabular"
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+                    "type": "tabular"
+                }, 
+                {
+                    "name": "all_struct_vars", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "hc_diff", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "hc_struct_vars", 
+                    "type": "tabular"
+                }, 
+                {
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+                    "type": "tabular"
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+                {
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+                    "type": "xls"
+                }, 
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+                    "type": "tabular"
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+            "type": "tool", 
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+                    "type": "gff3"
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+            "inputs": [], 
+            "name": "CAPS Detection", 
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+                    "type": "interval"
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+                    "type": "tabular"
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+            "name": "Design primers to features", 
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+                    "type": "tabular"
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+}
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