Mercurial > repos > dcorreia > phylogeny_tools

changeset 17:886d136b8e1a draft

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Uploaded
author dcorreia
date Mon, 30 May 2016 10:08:22 -0400
parents 55bf08c57673
children 514b89b62e78
files workflows/Oneclick_FastME_workflow.ga
diffstat 1 files changed, 104 insertions(+), 30 deletions(-) [+]
line wrap: on
line diff
--- a/workflows/Oneclick_FastME_workflow.ga	Mon May 02 09:23:33 2016 -0400
+++ b/workflows/Oneclick_FastME_workflow.ga	Mon May 30 10:08:22 2016 -0400
@@ -27,12 +27,12 @@
             "tool_state": "{\"name\": \"Input Dataset\"}", 
             "tool_version": null, 
             "type": "data_input", 
-            "uuid": "3c6c9c92-0d91-45d2-8bbd-64005ef779ed", 
+            "uuid": "2bb237ac-ba9e-45b1-a220-b504c47b21e2", 
             "workflow_outputs": [
                 {
                     "label": null, 
                     "output_name": "output", 
-                    "uuid": "6988a34d-271d-47b1-b9ca-3e6257f5ee49"
+                    "uuid": "b384f9a6-aaa9-4217-9ee2-8d06fc4a50e0"
                 }
             ]
         }, 
@@ -46,7 +46,12 @@
                     "output_name": "output"
                 }
             }, 
-            "inputs": [], 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool MAFFT", 
+                    "name": "inputSequences"
+                }
+            ], 
             "label": null, 
             "name": "MAFFT", 
             "outputs": [
@@ -60,26 +65,32 @@
                 }
             ], 
             "position": {
-                "left": 420, 
-                "top": 200
+                "left": 440, 
+                "top": 185.5
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "testtoolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.221.3", 
-            "tool_state": "{\"__page__\": 0, \"outputFormat\": \"\\\"\\\"\", \"getTree\": \"\\\"False\\\"\", \"inputSequences\": \"null\", \"datatype\": \"\\\"\\\"\", \"cond_flavour\": \"{\\\"flavourType\\\": \\\"mafft-fftns\\\", \\\"__current_case__\\\": 0}\", \"matrix_condition\": \"{\\\"matrix\\\": \\\"\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"adjustdirection\": \"\\\" \\\"\", \"ep\": \"\\\"0.123\\\"\", \"reorder\": \"\\\"False\\\"\", \"op\": \"\\\"1.53\\\"\"}", 
+            "tool_shed_repository": {
+                "changeset_revision": "c9affca9656a", 
+                "name": "mafft", 
+                "owner": "rnateam", 
+                "tool_shed": "testtoolshed.g2.bx.psu.edu"
+            }, 
+            "tool_state": "{\"__page__\": 0, \"outputFormat\": \"\\\"\\\"\", \"getTree\": \"\\\"false\\\"\", \"inputSequences\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"datatype\": \"\\\"\\\"\", \"cond_flavour\": \"{\\\"flavourType\\\": \\\"mafft-fftns\\\", \\\"__current_case__\\\": 0}\", \"matrix_condition\": \"{\\\"matrix\\\": \\\"\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"adjustdirection\": \"\\\" \\\"\", \"ep\": \"\\\"0.123\\\"\", \"reorder\": \"\\\"false\\\"\", \"op\": \"\\\"1.53\\\"\"}", 
             "tool_version": "7.221.3", 
             "type": "tool", 
-            "uuid": "a32bc078-ccf9-4f55-8b0d-6ec0df697ef2", 
+            "uuid": "8da821be-52ef-405f-a782-3a39fb54cbcd", 
             "workflow_outputs": [
                 {
                     "label": null, 
-                    "output_name": "outputAlignment", 
-                    "uuid": "314687d4-48f5-4ec5-9625-8c18b6bf87d1"
+                    "output_name": "outputTree", 
+                    "uuid": "3159b3b0-a844-4093-a4a2-d5e700a5aed3"
                 }, 
                 {
                     "label": null, 
-                    "output_name": "outputTree", 
-                    "uuid": "989b1ed9-d052-4106-8b4c-136207ca5f59"
+                    "output_name": "outputAlignment", 
+                    "uuid": "a75a58d9-9030-4ff5-9cb5-8ef87253b098"
                 }
             ]
         }, 
@@ -93,7 +104,12 @@
                     "output_name": "output"
                 }
             }, 
-            "inputs": [], 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Sequence type detection", 
+                    "name": "input"
+                }
+            ], 
             "label": null, 
             "name": "Sequence type detection", 
             "outputs": [
@@ -115,10 +131,16 @@
             }, 
             "tool_errors": null, 
             "tool_id": "testtoolshed.g2.bx.psu.edu/repos/dcorreia/phylogeny_tools/seqtypedetect/1.0", 
-            "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", 
+            "tool_shed_repository": {
+                "changeset_revision": "55bf08c57673", 
+                "name": "phylogeny_tools", 
+                "owner": "dcorreia", 
+                "tool_shed": "testtoolshed.g2.bx.psu.edu"
+            }, 
+            "tool_state": "{\"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", 
             "tool_version": "1.0", 
             "type": "tool", 
-            "uuid": "4e5b5fa3-4f80-4dcf-b9ce-fd607b1fdb7f", 
+            "uuid": "551e493d-ce9b-4621-9a12-b84a19ade098", 
             "workflow_outputs": []
         }, 
         "3": {
@@ -135,7 +157,16 @@
                     "output_name": "output"
                 }
             }, 
-            "inputs": [], 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Noisy", 
+                    "name": "sequence"
+                }, 
+                {
+                    "description": "runtime parameter for tool Noisy", 
+                    "name": "input"
+                }
+            ], 
             "label": null, 
             "name": "Noisy", 
             "outputs": [
@@ -170,15 +201,21 @@
             }, 
             "tool_errors": null, 
             "tool_id": "testtoolshed.g2.bx.psu.edu/repos/dcorreia/noisy/noisy/1.5.12.1", 
-            "tool_state": "{\"cutoff\": \"\\\"0.4\\\"\", \"orderingmethode\": \"{\\\"ordering\\\": \\\"nnet\\\", \\\"__current_case__\\\": 0}\", \"constant\": \"\\\"True\\\"\", \"missingchar\": \"{\\\"setmissingchar\\\": \\\"False\\\", \\\"__current_case__\\\": 0}\", \"sequence\": \"{\\\"input_info\\\": null, \\\"seqtype\\\": \\\"cfg\\\", \\\"__current_case__\\\": 3}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"smooth\": \"\\\"1\\\"\", \"gap\": \"\\\"True\\\"\", \"shuffles\": \"\\\"1000\\\"\", \"input\": \"null\", \"usematrix\": \"{\\\"matrix\\\": \\\"False\\\", \\\"__current_case__\\\": 0}\", \"distance\": \"\\\"HAMMING\\\"\"}", 
+            "tool_shed_repository": {
+                "changeset_revision": "dc60058d559e", 
+                "name": "noisy", 
+                "owner": "dcorreia", 
+                "tool_shed": "testtoolshed.g2.bx.psu.edu"
+            }, 
+            "tool_state": "{\"cutoff\": \"\\\"0.4\\\"\", \"orderingmethode\": \"{\\\"ordering\\\": \\\"nnet\\\", \\\"__current_case__\\\": 0}\", \"constant\": \"\\\"true\\\"\", \"missingchar\": \"{\\\"setmissingchar\\\": \\\"false\\\", \\\"__current_case__\\\": 0}\", \"sequence\": \"{\\\"input_info\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"seqtype\\\": \\\"cfg\\\", \\\"__current_case__\\\": 3}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"smooth\": \"\\\"1\\\"\", \"gap\": \"\\\"true\\\"\", \"shuffles\": \"\\\"1000\\\"\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"usematrix\": \"{\\\"matrix\\\": \\\"false\\\", \\\"__current_case__\\\": 0}\", \"distance\": \"\\\"HAMMING\\\"\"}", 
             "tool_version": "1.5.12.1", 
             "type": "tool", 
-            "uuid": "5ceb2522-01a7-4cf5-a85c-5d0c516b7d63", 
+            "uuid": "ff555b68-1f3c-4be6-928f-cbb219d94c9f", 
             "workflow_outputs": [
                 {
                     "label": null, 
                     "output_name": "output1", 
-                    "uuid": "43650c9e-6d12-4823-babe-641c1b268a5b"
+                    "uuid": "826919f2-e2cc-4bdc-ab29-f41ff907beb3"
                 }
             ]
         }, 
@@ -192,7 +229,12 @@
                     "output_name": "output1"
                 }
             }, 
-            "inputs": [], 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Fasta to Phylip", 
+                    "name": "input"
+                }
+            ], 
             "label": null, 
             "name": "Fasta to Phylip", 
             "outputs": [
@@ -214,10 +256,16 @@
             }, 
             "tool_errors": null, 
             "tool_id": "testtoolshed.g2.bx.psu.edu/repos/dcorreia/phylogeny_tools/fasta_to_phylip/1.0.0", 
-            "tool_state": "{\"__page__\": 0, \"input\": \"null\", \"__rerun_remap_job_id__\": null, \"format\": \"\\\"\\\"\"}", 
+            "tool_shed_repository": {
+                "changeset_revision": "55bf08c57673", 
+                "name": "phylogeny_tools", 
+                "owner": "dcorreia", 
+                "tool_shed": "testtoolshed.g2.bx.psu.edu"
+            }, 
+            "tool_state": "{\"__page__\": 0, \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"format\": \"\\\"\\\"\"}", 
             "tool_version": "1.0.0", 
             "type": "tool", 
-            "uuid": "e47321fd-5d3e-4386-8c1e-8c0b0692c924", 
+            "uuid": "57d2ddb4-a946-47e3-9670-f2aaf1f67e9f", 
             "workflow_outputs": []
         }, 
         "5": {
@@ -234,7 +282,16 @@
                     "output_name": "output"
                 }
             }, 
-            "inputs": [], 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool FastME", 
+                    "name": "input"
+                }, 
+                {
+                    "description": "runtime parameter for tool FastME", 
+                    "name": "typeChoice"
+                }
+            ], 
             "label": null, 
             "name": "FastME", 
             "outputs": [
@@ -285,15 +342,21 @@
             }, 
             "tool_errors": null, 
             "tool_id": "testtoolshed.g2.bx.psu.edu/repos/gandres/fastme/fastme/2.1.4.2", 
-            "tool_state": "{\"distance\": \"\\\"--method=I\\\"\", \"__page__\": 0, \"equilibrium\": \"\\\"False\\\"\", \"__rerun_remap_job_id__\": null, \"bootChoice\": \"{\\\"boot\\\": \\\"false\\\", \\\"__current_case__\\\": 0}\", \"gammaChoice\": \"{\\\"rate\\\": \\\"1.0\\\", \\\"gamma\\\": \\\"true\\\", \\\"__current_case__\\\": 0}\", \"treeRefinement\": \"\\\"--spr\\\"\", \"fileout_label\": \"\\\"Newick tree\\\"\", \"input\": \"null\", \"typeChoice\": \"{\\\"datatype\\\": \\\"cfg\\\", \\\"input_info\\\": null, \\\"__current_case__\\\": 3}\", \"removeGap\": \"null\"}", 
+            "tool_shed_repository": {
+                "changeset_revision": "5f6da08745cd", 
+                "name": "fastme", 
+                "owner": "gandres", 
+                "tool_shed": "testtoolshed.g2.bx.psu.edu"
+            }, 
+            "tool_state": "{\"distance\": \"\\\"--method=I\\\"\", \"__page__\": 0, \"equilibrium\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null, \"bootChoice\": \"{\\\"boot\\\": \\\"false\\\", \\\"__current_case__\\\": 0}\", \"gammaChoice\": \"{\\\"rate\\\": \\\"1.0\\\", \\\"__current_case__\\\": 0, \\\"gamma\\\": \\\"true\\\"}\", \"treeRefinement\": \"\\\"--spr\\\"\", \"fileout_label\": \"\\\"Newick tree\\\"\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"typeChoice\": \"{\\\"datatype\\\": \\\"cfg\\\", \\\"input_info\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 3}\", \"removeGap\": \"\\\"\\\"\"}", 
             "tool_version": "2.1.4.2", 
             "type": "tool", 
-            "uuid": "ec00afbd-0b74-4946-b36e-d391453fb1a9", 
+            "uuid": "78e28129-1192-4c0f-8bde-5ef93e40b706", 
             "workflow_outputs": [
                 {
                     "label": null, 
                     "output_name": "outputTree", 
-                    "uuid": "7a0e2140-00fc-41a3-b015-463e1ff3644c"
+                    "uuid": "501fa44d-16bb-403a-a7d6-233503c88b15"
                 }
             ]
         }, 
@@ -307,7 +370,12 @@
                     "output_name": "outputTree"
                 }
             }, 
-            "inputs": [], 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Newick Display", 
+                    "name": "fileNewick"
+                }
+            ], 
             "label": null, 
             "name": "Newick Display", 
             "outputs": [
@@ -323,18 +391,24 @@
             "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "testtoolshed.g2.bx.psu.edu/repos/dcorreia/newick_display/nwdisplay/1", 
-            "tool_state": "{\"__page__\": 0, \"condbranchlength\": \"{\\\"branchlength\\\": \\\"false\\\", \\\"__current_case__\\\": 1}\", \"leafPolice\": \"\\\"sans-serif\\\"\", \"scalebar\": \"\\\"True\\\"\", \"__rerun_remap_job_id__\": null, \"width\": \"\\\"800\\\"\", \"leafSize\": \"\\\"10px\\\"\", \"radial\": \"\\\"False\\\"\", \"fileNewick\": \"null\", \"condbranchsupport\": \"{\\\"branchsupport\\\": \\\"false\\\", \\\"__current_case__\\\": 1}\", \"legend\": \"\\\"\\\"\"}", 
+            "tool_shed_repository": {
+                "changeset_revision": "ceba45fbfcb8", 
+                "name": "newick_display", 
+                "owner": "dcorreia", 
+                "tool_shed": "testtoolshed.g2.bx.psu.edu"
+            }, 
+            "tool_state": "{\"__page__\": 0, \"condbranchlength\": \"{\\\"branchlength\\\": \\\"false\\\", \\\"__current_case__\\\": 1}\", \"leafPolice\": \"\\\"sans-serif\\\"\", \"scalebar\": \"\\\"true\\\"\", \"__rerun_remap_job_id__\": null, \"width\": \"\\\"800\\\"\", \"leafSize\": \"\\\"10px\\\"\", \"radial\": \"\\\"false\\\"\", \"fileNewick\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"condbranchsupport\": \"{\\\"branchsupport\\\": \\\"false\\\", \\\"__current_case__\\\": 1}\", \"legend\": \"\\\"\\\"\"}", 
             "tool_version": "1", 
             "type": "tool", 
-            "uuid": "81ba3d82-c684-4e41-8366-625b240b2d3f", 
+            "uuid": "a7c685e5-910a-4a40-a7ba-15f8a57d6276", 
             "workflow_outputs": [
                 {
                     "label": null, 
                     "output_name": "output", 
-                    "uuid": "315742d7-e9e3-450e-b9ee-e26f96dee822"
+                    "uuid": "214c8ce2-2e41-40a7-bd31-ed0a6f1dc2c9"
                 }
             ]
         }
     }, 
-    "uuid": "17a16b44-5977-4861-b46d-d04f4e2e5876"
+    "uuid": "8d73f7e7-aeac-4965-b941-8c516b9a80f5"
 }
\ No newline at end of file