--- a/rapsodyn/Galaxy-Workflow-rapsosnp_v1.20_-_10x_-_sam.ga	Tue Oct 07 10:34:34 2014 -0400
+++ b/rapsodyn/Galaxy-Workflow-rapsosnp_v1.20_-_10x_-_sam.ga	Fri Oct 10 07:05:36 2014 -0400
@@ -2,7 +2,7 @@
     "a_galaxy_workflow": "true", 
     "annotation": "", 
     "format-version": "0.1", 
-    "name": "rapsosnp v1.20 - 1x - sam", 
+    "name": "rapsosnp v1.20 - 10x - sam", 
     "steps": {
         "0": {
             "annotation": "", 
@@ -285,14 +285,14 @@
                 }
             ], 
             "position": {
-                "left": 936.93310546875, 
+                "left": 936.933349609375, 
                 "top": 338.43333435058594
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "PrepareFastqLight", 
-            "tool_state": "{\"__page__\": 0, \"quality_type\": \"\\\"illumina\\\"\", \"min_length\": \"\\\"30\\\"\", \"__rerun_remap_job_id__\": null, \"min_quality\": \"\\\"30\\\"\", \"input_read1_file\": \"null\", \"input_read2_file\": \"null\"}", 
-            "tool_version": "1.01", 
+            "tool_state": "{\"__page__\": 0, \"quality_type\": \"\\\"auto\\\"\", \"min_length\": \"\\\"30\\\"\", \"__rerun_remap_job_id__\": null, \"min_quality\": \"\\\"30\\\"\", \"input_read1_file\": \"null\", \"input_read2_file\": \"null\"}", 
+            "tool_version": "1.03", 
             "type": "tool", 
             "user_outputs": []
         }, 
@@ -326,14 +326,14 @@
                 }
             ], 
             "position": {
-                "left": 943.93310546875, 
+                "left": 943.933349609375, 
                 "top": 585.4333343505859
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "PrepareFastqLight", 
-            "tool_state": "{\"__page__\": 0, \"quality_type\": \"\\\"illumina\\\"\", \"min_length\": \"\\\"30\\\"\", \"__rerun_remap_job_id__\": null, \"min_quality\": \"\\\"30\\\"\", \"input_read1_file\": \"null\", \"input_read2_file\": \"null\"}", 
-            "tool_version": "1.01", 
+            "tool_state": "{\"__page__\": 0, \"quality_type\": \"\\\"auto\\\"\", \"min_length\": \"\\\"30\\\"\", \"__rerun_remap_job_id__\": null, \"min_quality\": \"\\\"30\\\"\", \"input_read1_file\": \"null\", \"input_read2_file\": \"null\"}", 
+            "tool_version": "1.03", 
             "type": "tool", 
             "user_outputs": []
         }, 
@@ -367,14 +367,14 @@
                 }
             ], 
             "position": {
-                "left": 947.93310546875, 
+                "left": 947.933349609375, 
                 "top": 812.433349609375
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "PrepareFastqLight", 
-            "tool_state": "{\"__page__\": 0, \"quality_type\": \"\\\"illumina\\\"\", \"min_length\": \"\\\"30\\\"\", \"__rerun_remap_job_id__\": null, \"min_quality\": \"\\\"30\\\"\", \"input_read1_file\": \"null\", \"input_read2_file\": \"null\"}", 
-            "tool_version": "1.01", 
+            "tool_state": "{\"__page__\": 0, \"quality_type\": \"\\\"auto\\\"\", \"min_length\": \"\\\"30\\\"\", \"__rerun_remap_job_id__\": null, \"min_quality\": \"\\\"30\\\"\", \"input_read1_file\": \"null\", \"input_read2_file\": \"null\"}", 
+            "tool_version": "1.03", 
             "type": "tool", 
             "user_outputs": []
         }, 
@@ -408,14 +408,14 @@
                 }
             ], 
             "position": {
-                "left": 1267.93310546875, 
+                "left": 1267.933349609375, 
                 "top": 343.43333435058594
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "PrepareFastqLight", 
-            "tool_state": "{\"__page__\": 0, \"quality_type\": \"\\\"illumina\\\"\", \"min_length\": \"\\\"30\\\"\", \"__rerun_remap_job_id__\": null, \"min_quality\": \"\\\"30\\\"\", \"input_read1_file\": \"null\", \"input_read2_file\": \"null\"}", 
-            "tool_version": "1.01", 
+            "tool_state": "{\"__page__\": 0, \"quality_type\": \"\\\"auto\\\"\", \"min_length\": \"\\\"30\\\"\", \"__rerun_remap_job_id__\": null, \"min_quality\": \"\\\"30\\\"\", \"input_read1_file\": \"null\", \"input_read2_file\": \"null\"}", 
+            "tool_version": "1.03", 
             "type": "tool", 
             "user_outputs": []
         }, 
@@ -449,14 +449,14 @@
                 }
             ], 
             "position": {
-                "left": 1261.93310546875, 
+                "left": 1261.933349609375, 
                 "top": 587.4333343505859
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "PrepareFastqLight", 
-            "tool_state": "{\"__page__\": 0, \"quality_type\": \"\\\"illumina\\\"\", \"min_length\": \"\\\"30\\\"\", \"__rerun_remap_job_id__\": null, \"min_quality\": \"\\\"30\\\"\", \"input_read1_file\": \"null\", \"input_read2_file\": \"null\"}", 
-            "tool_version": "1.01", 
+            "tool_state": "{\"__page__\": 0, \"quality_type\": \"\\\"auto\\\"\", \"min_length\": \"\\\"30\\\"\", \"__rerun_remap_job_id__\": null, \"min_quality\": \"\\\"30\\\"\", \"input_read1_file\": \"null\", \"input_read2_file\": \"null\"}", 
+            "tool_version": "1.03", 
             "type": "tool", 
             "user_outputs": []
         }, 
@@ -490,14 +490,14 @@
                 }
             ], 
             "position": {
-                "left": 954.93310546875, 
+                "left": 954.933349609375, 
                 "top": 1044.433349609375
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "PrepareFastqLight", 
-            "tool_state": "{\"__page__\": 0, \"quality_type\": \"\\\"illumina\\\"\", \"min_length\": \"\\\"30\\\"\", \"__rerun_remap_job_id__\": null, \"min_quality\": \"\\\"30\\\"\", \"input_read1_file\": \"null\", \"input_read2_file\": \"null\"}", 
-            "tool_version": "1.01", 
+            "tool_state": "{\"__page__\": 0, \"quality_type\": \"\\\"auto\\\"\", \"min_length\": \"\\\"30\\\"\", \"__rerun_remap_job_id__\": null, \"min_quality\": \"\\\"30\\\"\", \"input_read1_file\": \"null\", \"input_read2_file\": \"null\"}", 
+            "tool_version": "1.03", 
             "type": "tool", 
             "user_outputs": []
         }, 
@@ -531,14 +531,14 @@
                 }
             ], 
             "position": {
-                "left": 1265.93310546875, 
+                "left": 1265.933349609375, 
                 "top": 815.433349609375
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "PrepareFastqLight", 
-            "tool_state": "{\"__page__\": 0, \"quality_type\": \"\\\"illumina\\\"\", \"min_length\": \"\\\"30\\\"\", \"__rerun_remap_job_id__\": null, \"min_quality\": \"\\\"30\\\"\", \"input_read1_file\": \"null\", \"input_read2_file\": \"null\"}", 
-            "tool_version": "1.01", 
+            "tool_state": "{\"__page__\": 0, \"quality_type\": \"\\\"auto\\\"\", \"min_length\": \"\\\"30\\\"\", \"__rerun_remap_job_id__\": null, \"min_quality\": \"\\\"30\\\"\", \"input_read1_file\": \"null\", \"input_read2_file\": \"null\"}", 
+            "tool_version": "1.03", 
             "type": "tool", 
             "user_outputs": []
         }, 
@@ -572,14 +572,14 @@
                 }
             ], 
             "position": {
-                "left": 953.93310546875, 
+                "left": 953.933349609375, 
                 "top": 1282.433349609375
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "PrepareFastqLight", 
-            "tool_state": "{\"__page__\": 0, \"quality_type\": \"\\\"illumina\\\"\", \"min_length\": \"\\\"30\\\"\", \"__rerun_remap_job_id__\": null, \"min_quality\": \"\\\"30\\\"\", \"input_read1_file\": \"null\", \"input_read2_file\": \"null\"}", 
-            "tool_version": "1.01", 
+            "tool_state": "{\"__page__\": 0, \"quality_type\": \"\\\"auto\\\"\", \"min_length\": \"\\\"30\\\"\", \"__rerun_remap_job_id__\": null, \"min_quality\": \"\\\"30\\\"\", \"input_read1_file\": \"null\", \"input_read2_file\": \"null\"}", 
+            "tool_version": "1.03", 
             "type": "tool", 
             "user_outputs": []
         }, 
@@ -613,14 +613,14 @@
                 }
             ], 
             "position": {
-                "left": 1265.93310546875, 
+                "left": 1265.933349609375, 
                 "top": 1043.433349609375
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "PrepareFastqLight", 
-            "tool_state": "{\"__page__\": 0, \"quality_type\": \"\\\"illumina\\\"\", \"min_length\": \"\\\"30\\\"\", \"__rerun_remap_job_id__\": null, \"min_quality\": \"\\\"30\\\"\", \"input_read1_file\": \"null\", \"input_read2_file\": \"null\"}", 
-            "tool_version": "1.01", 
+            "tool_state": "{\"__page__\": 0, \"quality_type\": \"\\\"auto\\\"\", \"min_length\": \"\\\"30\\\"\", \"__rerun_remap_job_id__\": null, \"min_quality\": \"\\\"30\\\"\", \"input_read1_file\": \"null\", \"input_read2_file\": \"null\"}", 
+            "tool_version": "1.03", 
             "type": "tool", 
             "user_outputs": []
         }, 
@@ -654,14 +654,14 @@
                 }
             ], 
             "position": {
-                "left": 1270.93310546875, 
+                "left": 1270.933349609375, 
                 "top": 1281.433349609375
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "PrepareFastqLight", 
-            "tool_state": "{\"__page__\": 0, \"quality_type\": \"\\\"illumina\\\"\", \"min_length\": \"\\\"30\\\"\", \"__rerun_remap_job_id__\": null, \"min_quality\": \"\\\"30\\\"\", \"input_read1_file\": \"null\", \"input_read2_file\": \"null\"}", 
-            "tool_version": "1.01", 
+            "tool_state": "{\"__page__\": 0, \"quality_type\": \"\\\"auto\\\"\", \"min_length\": \"\\\"30\\\"\", \"__rerun_remap_job_id__\": null, \"min_quality\": \"\\\"30\\\"\", \"input_read1_file\": \"null\", \"input_read2_file\": \"null\"}", 
+            "tool_version": "1.03", 
             "type": "tool", 
             "user_outputs": []
         }, 
@@ -1400,15 +1400,27 @@
             "input_connections": {
                 "input_files": [
                     {
-                        "id": 37, 
+                        "id": 28, 
+                        "output_name": "output_sam_file"
+                    }, 
+                    {
+                        "id": 29, 
                         "output_name": "output_sam_file"
                     }, 
                     {
-                        "id": 36, 
+                        "id": 30, 
                         "output_name": "output_sam_file"
                     }, 
                     {
-                        "id": 35, 
+                        "id": 31, 
+                        "output_name": "output_sam_file"
+                    }, 
+                    {
+                        "id": 32, 
+                        "output_name": "output_sam_file"
+                    }, 
+                    {
+                        "id": 33, 
                         "output_name": "output_sam_file"
                     }, 
                     {
@@ -1416,27 +1428,15 @@
                         "output_name": "output_sam_file"
                     }, 
                     {
-                        "id": 33, 
-                        "output_name": "output_sam_file"
-                    }, 
-                    {
-                        "id": 32, 
+                        "id": 35, 
                         "output_name": "output_sam_file"
                     }, 
                     {
-                        "id": 31, 
+                        "id": 36, 
                         "output_name": "output_sam_file"
                     }, 
                     {
-                        "id": 30, 
-                        "output_name": "output_sam_file"
-                    }, 
-                    {
-                        "id": 29, 
-                        "output_name": "output_sam_file"
-                    }, 
-                    {
-                        "id": 28, 
+                        "id": 37, 
                         "output_name": "output_sam_file"
                     }
                 ]
@@ -2702,15 +2702,27 @@
             "input_connections": {
                 "input_files": [
                     {
-                        "id": 64, 
+                        "id": 69, 
+                        "output_name": "output_variant_file"
+                    }, 
+                    {
+                        "id": 73, 
                         "output_name": "output_variant_file"
                     }, 
                     {
-                        "id": 65, 
+                        "id": 72, 
                         "output_name": "output_variant_file"
                     }, 
                     {
-                        "id": 66, 
+                        "id": 71, 
+                        "output_name": "output_variant_file"
+                    }, 
+                    {
+                        "id": 70, 
+                        "output_name": "output_variant_file"
+                    }, 
+                    {
+                        "id": 68, 
                         "output_name": "output_variant_file"
                     }, 
                     {
@@ -2718,27 +2730,15 @@
                         "output_name": "output_variant_file"
                     }, 
                     {
-                        "id": 68, 
-                        "output_name": "output_variant_file"
-                    }, 
-                    {
-                        "id": 70, 
+                        "id": 66, 
                         "output_name": "output_variant_file"
                     }, 
                     {
-                        "id": 71, 
+                        "id": 65, 
                         "output_name": "output_variant_file"
                     }, 
                     {
-                        "id": 72, 
-                        "output_name": "output_variant_file"
-                    }, 
-                    {
-                        "id": 73, 
-                        "output_name": "output_variant_file"
-                    }, 
-                    {
-                        "id": 69, 
+                        "id": 64, 
                         "output_name": "output_variant_file"
                     }
                 ]
@@ -2802,63 +2802,71 @@
             "input_connections": {
                 "input_files": [
                     {
-                        "id": 7, 
+                        "id": 75, 
                         "output_name": "log_file"
                     }, 
                     {
-                        "id": 8, 
+                        "id": 69, 
                         "output_name": "log_file"
                     }, 
                     {
-                        "id": 9, 
+                        "id": 73, 
                         "output_name": "log_file"
                     }, 
                     {
-                        "id": 12, 
+                        "id": 72, 
+                        "output_name": "log_file"
+                    }, 
+                    {
+                        "id": 71, 
                         "output_name": "log_file"
                     }, 
                     {
-                        "id": 14, 
+                        "id": 70, 
                         "output_name": "log_file"
                     }, 
                     {
-                        "id": 10, 
+                        "id": 68, 
                         "output_name": "log_file"
                     }, 
                     {
-                        "id": 11, 
+                        "id": 67, 
                         "output_name": "log_file"
                     }, 
                     {
-                        "id": 13, 
+                        "id": 66, 
                         "output_name": "log_file"
                     }, 
                     {
-                        "id": 15, 
+                        "id": 65, 
                         "output_name": "log_file"
                     }, 
                     {
-                        "id": 16, 
+                        "id": 64, 
+                        "output_name": "log_file"
+                    }, 
+                    {
+                        "id": 42, 
                         "output_name": "log_file"
                     }, 
                     {
-                        "id": 28, 
+                        "id": 41, 
                         "output_name": "log_file"
                     }, 
                     {
-                        "id": 29, 
+                        "id": 37, 
                         "output_name": "log_file"
                     }, 
                     {
-                        "id": 30, 
+                        "id": 36, 
                         "output_name": "log_file"
                     }, 
                     {
-                        "id": 33, 
+                        "id": 34, 
                         "output_name": "log_file"
                     }, 
                     {
-                        "id": 35, 
+                        "id": 32, 
                         "output_name": "log_file"
                     }, 
                     {
@@ -2866,71 +2874,63 @@
                         "output_name": "log_file"
                     }, 
                     {
-                        "id": 32, 
+                        "id": 35, 
                         "output_name": "log_file"
                     }, 
                     {
-                        "id": 34, 
+                        "id": 33, 
                         "output_name": "log_file"
                     }, 
                     {
-                        "id": 36, 
+                        "id": 30, 
                         "output_name": "log_file"
                     }, 
                     {
-                        "id": 37, 
-                        "output_name": "log_file"
-                    }, 
-                    {
-                        "id": 41, 
+                        "id": 29, 
                         "output_name": "log_file"
                     }, 
                     {
-                        "id": 42, 
+                        "id": 28, 
                         "output_name": "log_file"
                     }, 
                     {
-                        "id": 64, 
+                        "id": 16, 
                         "output_name": "log_file"
                     }, 
                     {
-                        "id": 65, 
+                        "id": 15, 
                         "output_name": "log_file"
                     }, 
                     {
-                        "id": 66, 
+                        "id": 13, 
                         "output_name": "log_file"
                     }, 
                     {
-                        "id": 67, 
+                        "id": 11, 
                         "output_name": "log_file"
                     }, 
                     {
-                        "id": 68, 
-                        "output_name": "log_file"
-                    }, 
-                    {
-                        "id": 70, 
+                        "id": 10, 
                         "output_name": "log_file"
                     }, 
                     {
-                        "id": 71, 
+                        "id": 14, 
                         "output_name": "log_file"
                     }, 
                     {
-                        "id": 72, 
+                        "id": 12, 
                         "output_name": "log_file"
                     }, 
                     {
-                        "id": 73, 
+                        "id": 9, 
                         "output_name": "log_file"
                     }, 
                     {
-                        "id": 69, 
+                        "id": 8, 
                         "output_name": "log_file"
                     }, 
                     {
-                        "id": 75, 
+                        "id": 7, 
                         "output_name": "log_file"
                     }
                 ]