# HG changeset patch
# User mzeidler
# Date 1380192617 14400
# Node ID 335fcf29f08a11614e7ecbd07e434a7b2dd72cb0
# Parent  7a3a6d023ef1d39ba3e9b03dfc3f740aa2301f34
Uploaded

diff -r 7a3a6d023ef1 -r 335fcf29f08a Galaxy-Workflow-Virana.ga
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Galaxy-Workflow-Virana.ga	Thu Sep 26 06:50:17 2013 -0400
@@ -0,0 +1,170 @@
+{
+    "a_galaxy_workflow": "true", 
+    "annotation": "simple virana test workflow", 
+    "format-version": "0.1", 
+    "name": "Virana", 
+    "steps": {
+        "0": {
+            "annotation": "", 
+            "id": 0, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "Input Dataset"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 200, 
+                "top": 200
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"Input Dataset\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "1": {
+            "annotation": "", 
+            "id": 1, 
+            "input_connections": {}, 
+            "inputs": [], 
+            "name": "Virana References", 
+            "outputs": [
+                {
+                    "name": "output", 
+                    "type": "fasta"
+                }
+            ], 
+            "position": {
+                "left": 200, 
+                "top": 283
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "testtoolshed.g2.bx.psu.edu/repos/mzeidler/virana_main/vref_fasta/1.0.0", 
+            "tool_state": "{\"__page__\": 0, \"refseq\": \"null\", \"zipped\": \"\\\"False\\\"\"}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "2": {
+            "annotation": "", 
+            "id": 2, 
+            "input_connections": {
+                "input": {
+                    "id": 1, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Virana DNAIndex", 
+            "outputs": [
+                {
+                    "name": "output", 
+                    "type": "bwa_index"
+                }
+            ], 
+            "position": {
+                "left": 434, 
+                "top": 200
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "testtoolshed.g2.bx.psu.edu/repos/mzeidler/virana_main/vmap_dnaindex/1.0.0", 
+            "tool_state": "{\"input\": \"null\", \"__page__\": 0}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "3": {
+            "annotation": "", 
+            "id": 3, 
+            "input_connections": {
+                "index": {
+                    "id": 2, 
+                    "output_name": "output"
+                }, 
+                "reads": {
+                    "id": 0, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Virana DNAMap", 
+            "outputs": [
+                {
+                    "name": "hit_output", 
+                    "type": "hit_bz2"
+                }, 
+                {
+                    "name": "bam_output", 
+                    "type": "bam"
+                }, 
+                {
+                    "name": "sam_output", 
+                    "type": "sam"
+                }, 
+                {
+                    "name": "qual_output", 
+                    "type": "qual"
+                }, 
+                {
+                    "name": "tax_output", 
+                    "type": "tax"
+                }
+            ], 
+            "position": {
+                "left": 668, 
+                "top": 200
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "testtoolshed.g2.bx.psu.edu/repos/mzeidler/virana_main/vmap_dnamap/1.0.0", 
+            "tool_state": "{\"index\": \"null\", \"sam\": \"\\\"False\\\"\", \"sensitive\": \"\\\"False\\\"\", \"__page__\": 0, \"tax\": \"\\\"False\\\"\", \"qual\": \"\\\"False\\\"\", \"reads\": \"null\", \"sample_id\": \"\\\"None\\\"\", \"output_type\": \"{\\\"hit\\\": \\\"False\\\", \\\"__current_case__\\\": 1}\", \"refseq\": \"null\", \"bam\": \"\\\"False\\\"\", \"paired\": \"{\\\"select_paired\\\": \\\"single\\\", \\\"__current_case__\\\": 1}\"}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "4": {
+            "annotation": "", 
+            "id": 4, 
+            "input_connections": {
+                "references": {
+                    "id": 1, 
+                    "output_name": "output"
+                }, 
+                "virana_hits": {
+                    "id": 3, 
+                    "output_name": "hit_output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Virana Homologous Groups", 
+            "outputs": [
+                {
+                    "name": "hom_output", 
+                    "type": "hom_reg"
+                }, 
+                {
+                    "name": "stat_output", 
+                    "type": "reg_stats"
+                }
+            ], 
+            "position": {
+                "left": 902, 
+                "top": 200
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "testtoolshed.g2.bx.psu.edu/repos/mzeidler/virana_main/vhom_region/1.1.1", 
+            "tool_state": "{\"max_gap_length\": \"\\\"25\\\"\", \"__page__\": 0, \"virana_hits\": \"null\", \"filter\": \"[]\", \"reference_database_filter\": \"null\", \"word_length\": \"\\\"7\\\"\", \"references\": \"null\", \"ambiguity_cutoff\": \"\\\"0.3\\\"\", \"min_read_number\": \"\\\"5\\\"\", \"min_region_length\": \"\\\"50\\\"\", \"cdna\": \"null\"}", 
+            "tool_version": "1.1.1", 
+            "type": "tool", 
+            "user_outputs": []
+        }
+    }
+}
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