--- a/Galaxy-Workflow-MiModD_example_workflow_2.ga	Wed Feb 11 10:06:13 2015 -0500
+++ b/Galaxy-Workflow-MiModD_example_workflow_2.ga	Thu Jun 04 18:19:52 2015 +0200
@@ -2,7 +2,7 @@
     "a_galaxy_workflow": "true", 
     "annotation": "", 
     "format-version": "0.1", 
-    "name": "MiModD example workflow 3", 
+    "name": "MiModD example workflow 2", 
     "steps": {
         "0": {
             "annotation": "", 
@@ -14,6 +14,7 @@
                     "name": "Input Dataset"
                 }
             ], 
+            "label": null, 
             "name": "Input dataset", 
             "outputs": [], 
             "position": {
@@ -25,7 +26,8 @@
             "tool_state": "{\"name\": \"Input Dataset\"}", 
             "tool_version": null, 
             "type": "data_input", 
-            "user_outputs": []
+            "user_outputs": [], 
+            "uuid": "None"
         }, 
         "1": {
             "annotation": "", 
@@ -37,6 +39,7 @@
                 }
             }, 
             "inputs": [], 
+            "label": null, 
             "name": "SNAP Read Alignment", 
             "outputs": [
                 {
@@ -51,10 +54,11 @@
             "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "read_alignment", 
-            "tool_state": "{\"__page__\": 0, \"datasets\": \"[{\\\"__index__\\\": 0, \\\"mode_choose\\\": {\\\"input\\\": {\\\"header\\\": null, \\\"ifile\\\": null, \\\"iformat\\\": \\\"bam\\\", \\\"__current_case__\\\": 0}, \\\"mode\\\": \\\"paired\\\", \\\"__current_case__\\\": 1}}, {\\\"__index__\\\": 1, \\\"mode_choose\\\": {\\\"input\\\": {\\\"header\\\": null, \\\"ifile\\\": null, \\\"iformat\\\": \\\"bam\\\", \\\"__current_case__\\\": 0}, \\\"mode\\\": \\\"paired\\\", \\\"__current_case__\\\": 1}}, {\\\"__index__\\\": 2, \\\"mode_choose\\\": {\\\"input\\\": {\\\"header\\\": null, \\\"ifile\\\": null, \\\"iformat\\\": \\\"bam\\\", \\\"__current_case__\\\": 0}, \\\"mode\\\": \\\"paired\\\", \\\"__current_case__\\\": 1}}]\", \"__rerun_remap_job_id__\": null, \"set\": \"{\\\"sort\\\": \\\"0\\\", \\\"__current_case__\\\": 0, \\\"clipping\\\": \\\"++\\\", \\\"filter_output\\\": \\\"off\\\", \\\"confadpt\\\": \\\"7\\\", \\\"slack\\\": \\\"0.3\\\", \\\"maxdist\\\": \\\"8\\\", \\\"maxseeds\\\": \\\"25\\\", \\\"maxhits\\\": \\\"250\\\", \\\"max_mate_overlap\\\": \\\"0\\\", \\\"selectivity\\\": \\\"off\\\", \\\"settings_mode\\\": \\\"default\\\", \\\"sp_min\\\": \\\"100\\\", \\\"sp_max\\\": \\\"10000\\\", \\\"seedsize\\\": \\\"20\\\", \\\"mmatch_notation\\\": \\\"general\\\", \\\"confdiff\\\": \\\"2\\\"}\", \"oformat\": \"\\\"bam\\\"\", \"ref_genome\": \"null\"}", 
+            "tool_state": "{\"__page__\": 0, \"datasets\": \"[{\\\"__index__\\\": 0, \\\"mode_choose\\\": {\\\"input\\\": {\\\"header\\\": null, \\\"ifile\\\": null, \\\"iformat\\\": \\\"bam\\\", \\\"__current_case__\\\": 0}, \\\"mode\\\": \\\"paired\\\", \\\"__current_case__\\\": 1}}, {\\\"__index__\\\": 1, \\\"mode_choose\\\": {\\\"input\\\": {\\\"header\\\": null, \\\"ifile\\\": null, \\\"iformat\\\": \\\"bam\\\", \\\"__current_case__\\\": 0}, \\\"mode\\\": \\\"paired\\\", \\\"__current_case__\\\": 1}}, {\\\"__index__\\\": 2, \\\"mode_choose\\\": {\\\"input\\\": {\\\"header\\\": null, \\\"ifile\\\": null, \\\"iformat\\\": \\\"bam\\\", \\\"__current_case__\\\": 0}, \\\"mode\\\": \\\"paired\\\", \\\"__current_case__\\\": 1}}]\", \"__rerun_remap_job_id__\": null, \"set\": \"{\\\"sort\\\": \\\"0\\\", \\\"__current_case__\\\": 0, \\\"clipping\\\": \\\"++\\\", \\\"filter_output\\\": \\\"off\\\", \\\"confadpt\\\": \\\"7\\\", \\\"slack\\\": \\\"0.3\\\", \\\"maxdist\\\": \\\"8\\\", \\\"maxseeds\\\": \\\"25\\\", \\\"discard_overlapping_mates\\\": \\\"\\\", \\\"maxhits\\\": \\\"250\\\", \\\"selectivity\\\": \\\"off\\\", \\\"settings_mode\\\": \\\"default\\\", \\\"sp_min\\\": \\\"100\\\", \\\"sp_max\\\": \\\"10000\\\", \\\"seedsize\\\": \\\"20\\\", \\\"mmatch_notation\\\": \\\"general\\\", \\\"confdiff\\\": \\\"2\\\"}\", \"oformat\": \"\\\"bam\\\"\", \"ref_genome\": \"null\"}", 
             "tool_version": "1.0.0", 
             "type": "tool", 
-            "user_outputs": []
+            "user_outputs": [], 
+            "uuid": "None"
         }, 
         "2": {
             "annotation": "", 
@@ -70,6 +74,7 @@
                 }
             }, 
             "inputs": [], 
+            "label": null, 
             "name": "Variant Calling", 
             "outputs": [
                 {
@@ -84,10 +89,11 @@
             "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "variant_calling", 
-            "tool_state": "{\"__page__\": 0, \"group_by_id\": \"\\\"True\\\"\", \"__rerun_remap_job_id__\": null, \"depth\": \"\\\"250\\\"\", \"list_input\": \"[{\\\"__index__\\\": 0, \\\"inputfile\\\": null}]\", \"ref_genome\": \"null\", \"no_md5_check\": \"\\\"False\\\"\"}", 
+            "tool_state": "{\"__page__\": 0, \"group_by_id\": \"\\\"False\\\"\", \"__rerun_remap_job_id__\": null, \"depth\": \"\\\"250\\\"\", \"list_input\": \"[{\\\"__index__\\\": 0, \\\"inputfile\\\": null}]\", \"ref_genome\": \"null\", \"no_md5_check\": \"\\\"False\\\"\"}", 
             "tool_version": "1.0.0", 
             "type": "tool", 
-            "user_outputs": []
+            "user_outputs": [], 
+            "uuid": "None"
         }, 
         "3": {
             "annotation": "", 
@@ -99,6 +105,7 @@
                 }
             }, 
             "inputs": [], 
+            "label": null, 
             "name": "Extract Variant Sites", 
             "outputs": [
                 {
@@ -116,7 +123,8 @@
             "tool_state": "{\"__page__\": 0, \"ifile\": \"null\", \"keep_alts\": \"\\\"False\\\"\", \"sitesinfo\": \"[]\", \"__rerun_remap_job_id__\": null}", 
             "tool_version": "1.0.0", 
             "type": "tool", 
-            "user_outputs": []
+            "user_outputs": [], 
+            "uuid": "None"
         }, 
         "4": {
             "annotation": "", 
@@ -128,6 +136,7 @@
                 }
             }, 
             "inputs": [], 
+            "label": null, 
             "name": "Coverage Statistics", 
             "outputs": [
                 {
@@ -145,7 +154,8 @@
             "tool_state": "{\"__page__\": 0, \"ifile\": \"null\", \"__rerun_remap_job_id__\": null}", 
             "tool_version": "1.0.0", 
             "type": "tool", 
-            "user_outputs": []
+            "user_outputs": [], 
+            "uuid": "None"
         }, 
         "5": {
             "annotation": "", 
@@ -161,6 +171,7 @@
                 }
             }, 
             "inputs": [], 
+            "label": null, 
             "name": "Deletion Prediction for paired-end data", 
             "outputs": [
                 {
@@ -175,10 +186,12 @@
             "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "deletion_prediction", 
-            "tool_state": "{\"__page__\": 0, \"group_by_id\": \"\\\"True\\\"\", \"__rerun_remap_job_id__\": null, \"min_size\": \"\\\"100\\\"\", \"list_input\": \"[{\\\"__index__\\\": 0, \\\"bamfile\\\": null}]\", \"include_uncovered\": \"\\\"False\\\"\", \"covfile\": \"null\", \"max_cov\": \"\\\"4\\\"\"}", 
+            "tool_state": "{\"__page__\": 0, \"group_by_id\": \"\\\"False\\\"\", \"__rerun_remap_job_id__\": null, \"min_size\": \"\\\"100\\\"\", \"list_input\": \"[{\\\"__index__\\\": 0, \\\"bamfile\\\": null}]\", \"include_uncovered\": \"\\\"False\\\"\", \"covfile\": \"null\", \"max_cov\": \"\\\"4\\\"\"}", 
             "tool_version": "1.0.0", 
             "type": "tool", 
-            "user_outputs": []
+            "user_outputs": [], 
+            "uuid": "None"
         }
-    }
+    }, 
+    "uuid": "ebf4ae7e-e823-4b67-a0aa-2a0e70b48db8"
 }
\ No newline at end of file