Mercurial > repos > chrisd > amrplusplus_workflow

changeset 8:0eae27b15aa0 draft default tip

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planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 5e58b41d1ef7243f07d32905bd822d0a13876344-dirty
author chrisd
date Thu, 14 Jul 2016 19:04:32 -0400
parents 0b7210ad9187
children
files amrplusplus_workflow.ga repository_dependencies.xml
diffstat 2 files changed, 88 insertions(+), 92 deletions(-) [+]
line wrap: on
line diff
--- a/amrplusplus_workflow.ga	Sat Jun 25 17:17:42 2016 -0400
+++ b/amrplusplus_workflow.ga	Thu Jul 14 19:04:32 2016 -0400
@@ -2,7 +2,7 @@
     "a_galaxy_workflow": "true", 
     "annotation": "", 
     "format-version": "0.1", 
-    "name": "amrplusplus workflow", 
+    "name": "amrplusplus workflow (imported from uploaded file)", 
     "steps": {
         "0": {
             "annotation": "", 
@@ -237,8 +237,61 @@
         }, 
         "5": {
             "annotation": "", 
+            "content_id": "toolshed.g2.bx.psu.edu/repos/chrisd/metasnp/metasnp/0.1.0", 
+            "id": 5, 
+            "input_connections": {
+                "reference": {
+                    "id": 3, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool MetaSNP", 
+                    "name": "sam_type"
+                }, 
+                {
+                    "description": "runtime parameter for tool MetaSNP", 
+                    "name": "reference"
+                }
+            ], 
+            "label": null, 
+            "name": "MetaSNP", 
+            "outputs": [
+                {
+                    "name": "output", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 1447, 
+                "top": 543
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/chrisd/metasnp/metasnp/0.1.0", 
+            "tool_shed_repository": {
+                "changeset_revision": "a3d1f2a85806", 
+                "name": "metasnp", 
+                "owner": "chrisd", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "tool_state": "{\"sam_type\": \"{\\\"best\\\": \\\"false\\\", \\\"sampe_input\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"mode\\\": \\\"paired_end\\\", \\\"__current_case__\\\": 1}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"reference\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", 
+            "tool_version": "0.1.0", 
+            "type": "tool", 
+            "uuid": "f126b5ac-a201-4478-8336-cdc6d70c54ca", 
+            "workflow_outputs": [
+                {
+                    "label": null, 
+                    "output_name": "output", 
+                    "uuid": "2a7f2c96-ce1d-4ce0-b8cb-ba31df13bdb6"
+                }
+            ]
+        }, 
+        "6": {
+            "annotation": "", 
             "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.12.1", 
-            "id": 5, 
+            "id": 6, 
             "input_connections": {
                 "input_type|fastq_input1": {
                     "id": 4, 
@@ -300,13 +353,13 @@
                 }
             ]
         }, 
-        "6": {
+        "7": {
             "annotation": "", 
             "content_id": "toolshed.g2.bx.psu.edu/repos/brenninc/samtools_flag_filter_1_2/samtools_flag_filter/0.1", 
-            "id": 6, 
+            "id": 7, 
             "input_connections": {
                 "input": {
-                    "id": 5, 
+                    "id": 6, 
                     "output_name": "bam_output"
                 }
             }, 
@@ -349,13 +402,13 @@
                 }
             ]
         }, 
-        "7": {
+        "8": {
             "annotation": "", 
             "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.12.1", 
-            "id": 7, 
+            "id": 8, 
             "input_connections": {
                 "input_type|bam_input": {
-                    "id": 6, 
+                    "id": 7, 
                     "output_name": "output"
                 }, 
                 "reference_source|ref_file": {
@@ -406,13 +459,13 @@
                 }
             ]
         }, 
-        "8": {
+        "9": {
             "annotation": "", 
             "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0", 
-            "id": 8, 
+            "id": 9, 
             "input_connections": {
                 "input1": {
-                    "id": 7, 
+                    "id": 8, 
                     "output_name": "bam_output"
                 }
             }, 
@@ -455,13 +508,13 @@
                 }
             ]
         }, 
-        "9": {
+        "10": {
             "annotation": "", 
             "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0", 
-            "id": 9, 
+            "id": 10, 
             "input_connections": {
                 "input1": {
-                    "id": 8, 
+                    "id": 9, 
                     "output_name": "output1"
                 }
             }, 
@@ -504,120 +557,63 @@
                 }
             ]
         }, 
-        "10": {
-            "annotation": "", 
-            "content_id": "toolshed.g2.bx.psu.edu/repos/chrisd/snipfinder/snp_caller/0.1.0", 
-            "id": 10, 
-            "input_connections": {
-                "input1": {
-                    "id": 3, 
-                    "output_name": "output"
-                }, 
-                "sam_type|sampe_input2": {
-                    "id": 9, 
-                    "output_name": "output1"
-                }
-            }, 
-            "inputs": [
-                {
-                    "description": "runtime parameter for tool Snip Finder", 
-                    "name": "sam_type"
-                }, 
-                {
-                    "description": "runtime parameter for tool Snip Finder", 
-                    "name": "input1"
-                }
-            ], 
-            "label": null, 
-            "name": "Snip Finder", 
-            "outputs": [
-                {
-                    "name": "output1", 
-                    "type": "tabular"
-                }
-            ], 
-            "position": {
-                "left": 1368, 
-                "top": 551
-            }, 
-            "post_job_actions": {}, 
-            "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/chrisd/snipfinder/snp_caller/0.1.0", 
-            "tool_shed_repository": {
-                "changeset_revision": "d9be5a7e70f5", 
-                "name": "snipfinder", 
-                "owner": "chrisd", 
-                "tool_shed": "toolshed.g2.bx.psu.edu"
-            }, 
-            "tool_state": "{\"sam_type\": \"{\\\"best\\\": \\\"false\\\", \\\"mode\\\": \\\"paired_end\\\", \\\"__current_case__\\\": 1, \\\"sampe_input2\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", 
-            "tool_version": "0.1.0", 
-            "type": "tool", 
-            "uuid": "3c0b1793-8625-4529-a406-6ffa822b38ab", 
-            "workflow_outputs": [
-                {
-                    "label": null, 
-                    "output_name": "output1", 
-                    "uuid": "b58e3331-4b37-49d9-b311-1120ca9606e6"
-                }
-            ]
-        }, 
         "11": {
             "annotation": "", 
             "content_id": "toolshed.g2.bx.psu.edu/repos/chrisd/coverage_sampler/gene_fraction/0.1.0", 
             "id": 11, 
             "input_connections": {
-                "input1": {
+                "reference": {
                     "id": 3, 
                     "output_name": "output"
                 }, 
-                "input2": {
-                    "id": 9, 
+                "sam": {
+                    "id": 10, 
                     "output_name": "output1"
                 }
             }, 
             "inputs": [
                 {
                     "description": "runtime parameter for tool Coverage Sampler", 
-                    "name": "input2"
+                    "name": "reference"
                 }, 
                 {
                     "description": "runtime parameter for tool Coverage Sampler", 
-                    "name": "input1"
+                    "name": "sam"
                 }
             ], 
             "label": null, 
             "name": "Coverage Sampler", 
             "outputs": [
                 {
-                    "name": "output1", 
+                    "name": "output", 
                     "type": "tabular"
                 }
             ], 
             "position": {
-                "left": 1618.5, 
-                "top": 553
+                "left": 1631.5, 
+                "top": 545
             }, 
-            "post_job_actions": {
-                "HideDatasetActionoutput1": {
-                    "action_arguments": {}, 
-                    "action_type": "HideDatasetAction", 
-                    "output_name": "output1"
-                }
-            }, 
+            "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/chrisd/coverage_sampler/gene_fraction/0.1.0", 
             "tool_shed_repository": {
-                "changeset_revision": "72901052a829", 
+                "changeset_revision": "ec439b0e7512", 
                 "name": "coverage_sampler", 
                 "owner": "chrisd", 
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             }, 
-            "tool_state": "{\"input2\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": 0, \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"min\": \"\\\"5\\\"\", \"max\": \"\\\"100\\\"\", \"__rerun_remap_job_id__\": null, \"samples\": \"\\\"1\\\"\", \"skip\": \"\\\"5\\\"\", \"threshold\": \"\\\"80\\\"\"}", 
+            "tool_state": "{\"__page__\": 0, \"reference\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"sam\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"min\": \"\\\"5\\\"\", \"max\": \"\\\"100\\\"\", \"__rerun_remap_job_id__\": null, \"samples\": \"\\\"1\\\"\", \"skip\": \"\\\"5\\\"\", \"threshold\": \"\\\"80\\\"\"}", 
             "tool_version": "0.1.0", 
             "type": "tool", 
-            "uuid": "0907193f-3458-40a1-b0ba-beac3998da62", 
-            "workflow_outputs": []
+            "uuid": "a74c17eb-f115-40b3-847d-03b89c251bc7", 
+            "workflow_outputs": [
+                {
+                    "label": null, 
+                    "output_name": "output", 
+                    "uuid": "57902fb4-a733-4429-8dfd-905ad0dd2f03"
+                }
+            ]
         }
     }, 
-    "uuid": "5f790d55-b08b-45e8-8471-005678ec4eef"
+    "uuid": "9ed4d064-e299-406d-a56f-e7eec8120829"
 }
\ No newline at end of file
--- a/repository_dependencies.xml	Sat Jun 25 17:17:42 2016 -0400
+++ b/repository_dependencies.xml	Thu Jul 14 19:04:32 2016 -0400
@@ -1,4 +1,4 @@
 <?xml version="1.0"?>
 <repositories description="A meta-package of tools needed to run the amrPlusPlus workflow">
-    <repository changeset_revision="29818e0c3fb5" name="amrplusplus_suite" owner="chrisd" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="284f6d4422a6" name="suite_amrplusplus" owner="chrisd" toolshed="https://toolshed.g2.bx.psu.edu" />
 </repositories>