diff Galaxy-Workflow-MiModD_example_workflow_3.ga @ 1:87bfe31ce878 default tip

workflows for MiModD 0.1.6

--- a/Galaxy-Workflow-MiModD_example_workflow_3.ga	Wed Feb 11 10:06:13 2015 -0500
+++ b/Galaxy-Workflow-MiModD_example_workflow_3.ga	Thu Jun 04 18:19:52 2015 +0200
@@ -11,25 +11,52 @@
             "inputs": [
                 {
                     "description": "", 
-                    "name": "Input Dataset"
+                    "name": "Reference Genome"
                 }
             ], 
+            "label": null, 
             "name": "Input dataset", 
             "outputs": [], 
             "position": {
-                "left": 172, 
-                "top": 176
+                "left": 200, 
+                "top": 391
             }, 
             "tool_errors": null, 
             "tool_id": null, 
-            "tool_state": "{\"name\": \"Input Dataset\"}", 
+            "tool_state": "{\"name\": \"Reference Genome\"}", 
             "tool_version": null, 
             "type": "data_input", 
-            "user_outputs": []
+            "user_outputs": [], 
+            "uuid": "None"
         }, 
         "1": {
             "annotation": "", 
             "id": 1, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "Hawaiian strain variants file"
+                }
+            ], 
+            "label": null, 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 707.5, 
+                "top": 335
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"Hawaiian strain variants file\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": [], 
+            "uuid": "80c25284-13aa-4172-bb52-2e8adee43626"
+        }, 
+        "2": {
+            "annotation": "", 
+            "id": 2, 
             "input_connections": {
                 "ref_genome": {
                     "id": 0, 
@@ -37,6 +64,7 @@
                 }
             }, 
             "inputs": [], 
+            "label": null, 
             "name": "SNAP Read Alignment", 
             "outputs": [
                 {
@@ -45,23 +73,24 @@
                 }
             ], 
             "position": {
-                "left": 359, 
-                "top": 368
+                "left": 334, 
+                "top": 607
             }, 
             "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}}]\", \"__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\\\": \\\"single\\\", \\\"__current_case__\\\": 0}}]\", \"__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": {
+        "3": {
             "annotation": "", 
-            "id": 2, 
+            "id": 3, 
             "input_connections": {
                 "list_input_0|inputfile": {
-                    "id": 1, 
+                    "id": 2, 
                     "output_name": "outputfile"
                 }, 
                 "ref_genome": {
@@ -70,6 +99,7 @@
                 }
             }, 
             "inputs": [], 
+            "label": null, 
             "name": "Variant Calling", 
             "outputs": [
                 {
@@ -78,27 +108,33 @@
                 }
             ], 
             "position": {
-                "left": 708, 
-                "top": 364
+                "left": 692, 
+                "top": 607
             }, 
             "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": {
+        "4": {
             "annotation": "", 
-            "id": 3, 
+            "id": 4, 
             "input_connections": {
                 "ifile": {
-                    "id": 2, 
+                    "id": 3, 
                     "output_name": "output_vcf"
+                }, 
+                "sitesinfo_0|pre_vcf": {
+                    "id": 1, 
+                    "output_name": "output"
                 }
             }, 
             "inputs": [], 
+            "label": null, 
             "name": "Extract Variant Sites", 
             "outputs": [
                 {
@@ -107,27 +143,29 @@
                 }
             ], 
             "position": {
-                "left": 1104.5, 
-                "top": 227
+                "left": 973.5, 
+                "top": 483
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "extract_variants", 
-            "tool_state": "{\"__page__\": 0, \"ifile\": \"null\", \"keep_alts\": \"\\\"False\\\"\", \"sitesinfo\": \"[]\", \"__rerun_remap_job_id__\": null}", 
+            "tool_state": "{\"__page__\": 0, \"ifile\": \"null\", \"keep_alts\": \"\\\"False\\\"\", \"sitesinfo\": \"[{\\\"__index__\\\": 0, \\\"pre_vcf\\\": null}]\", \"__rerun_remap_job_id__\": null}", 
             "tool_version": "1.0.0", 
             "type": "tool", 
-            "user_outputs": []
+            "user_outputs": [], 
+            "uuid": "None"
         }, 
-        "4": {
+        "5": {
             "annotation": "", 
-            "id": 4, 
+            "id": 5, 
             "input_connections": {
                 "ifile": {
-                    "id": 2, 
+                    "id": 3, 
                     "output_name": "output_vcf"
                 }
             }, 
             "inputs": [], 
+            "label": null, 
             "name": "Coverage Statistics", 
             "outputs": [
                 {
@@ -136,8 +174,8 @@
                 }
             ], 
             "position": {
-                "left": 1133, 
-                "top": 455
+                "left": 1054, 
+                "top": 726
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
@@ -145,40 +183,57 @@
             "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": {
+        "6": {
             "annotation": "", 
-            "id": 5, 
+            "id": 6, 
             "input_connections": {
-                "covfile": {
-                    "id": 2, 
+                "ifile": {
+                    "id": 4, 
                     "output_name": "output_vcf"
-                }, 
-                "list_input_0|bamfile": {
-                    "id": 1, 
-                    "output_name": "outputfile"
                 }
             }, 
-            "inputs": [], 
-            "name": "Deletion Prediction for paired-end data", 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Prepare variant data for mapping", 
+                    "name": "sample"
+                }, 
+                {
+                    "description": "runtime parameter for tool Prepare variant data for mapping", 
+                    "name": "run"
+                }, 
+                {
+                    "description": "runtime parameter for tool Prepare variant data for mapping", 
+                    "name": "run"
+                }
+            ], 
+            "label": null, 
+            "name": "Prepare variant data for mapping", 
             "outputs": [
                 {
-                    "name": "outputfile", 
-                    "type": "gff"
+                    "name": "ofile", 
+                    "type": "vcf"
+                }, 
+                {
+                    "name": "dictfile", 
+                    "type": "tabular"
                 }
             ], 
             "position": {
-                "left": 1064, 
-                "top": 667
+                "left": 1209.5, 
+                "top": 200
             }, 
             "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_id": "cloudmap_prepare", 
+            "tool_state": "{\"__page__\": 0, \"ifile\": \"null\", \"run\": \"{\\\"infer_missing\\\": \\\"False\\\", \\\"related_parent_sample\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"mode\\\": \\\"VAF\\\", \\\"__current_case__\\\": 1, \\\"unrelated_parent_sample\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"__rerun_remap_job_id__\": null, \"seqdict\": \"\\\"True\\\"\", \"sample\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", 
             "tool_version": "1.0.0", 
             "type": "tool", 
-            "user_outputs": []
+            "user_outputs": [], 
+            "uuid": "6225f501-6db8-4c83-ad42-59a8f1330a55"
         }
-    }
-}
+    }, 
+    "uuid": "0a619835-3d93-489f-8d0d-93a567536404"
+}
\ No newline at end of file