changeset 9:1fbe965e22e2 draft default tip

Uploaded
author urgi-team
date Fri, 08 Apr 2016 12:17:38 -0400
parents 3ca0f78f1102
children
files Galaxy-Workflow-workflow_gandalf_1_set.ga Galaxy-Workflow-workflow_gandalf_2_sets.ga gandalfworkflow/Galaxy-Workflow-workflow_gandalf_1_set.ga gandalfworkflow/Galaxy-Workflow-workflow_gandalf_2_sets.ga gandalfworkflow/repository_dependencies.xml repository_dependencies.xml
diffstat 6 files changed, 1327 insertions(+), 1327 deletions(-) [+]
line wrap: on
line diff
--- a/Galaxy-Workflow-workflow_gandalf_1_set.ga	Tue Dec 15 05:38:37 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,384 +0,0 @@
-{
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-    "annotation": "", 
-    "format-version": "0.1", 
-    "name": "workflow gandalf 1 set", 
-    "steps": {
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-            "annotation": "", 
-            "id": 0, 
-            "input_connections": {}, 
-            "inputs": [
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-                    "description": "", 
-                    "name": "Reference genome"
-                }
-            ], 
-            "name": "Input dataset", 
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-                "top": 198
-            }, 
-            "tool_errors": null, 
-            "tool_id": null, 
-            "tool_state": "{\"name\": \"Reference genome\"}", 
-            "tool_version": null, 
-            "type": "data_input", 
-            "user_outputs": []
-        }, 
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-            "annotation": "", 
-            "id": 1, 
-            "input_connections": {}, 
-            "inputs": [
-                {
-                    "description": "", 
-                    "name": "Genome reads forward "
-                }
-            ], 
-            "name": "Input dataset", 
-            "outputs": [], 
-            "position": {
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-                "top": 295
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-            "tool_id": null, 
-            "tool_state": "{\"name\": \"Genome reads forward \"}", 
-            "tool_version": null, 
-            "type": "data_input", 
-            "user_outputs": []
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-        "2": {
-            "annotation": "", 
-            "id": 2, 
-            "input_connections": {}, 
-            "inputs": [
-                {
-                    "description": "", 
-                    "name": "Genome read Reverse"
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-                {
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-            "inputs": [], 
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\ No newline at end of file
--- a/Galaxy-Workflow-workflow_gandalf_2_sets.ga	Tue Dec 15 05:38:37 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,933 +0,0 @@
-{
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-    "annotation": "", 
-    "format-version": "0.1", 
-    "name": "workflow gandalf 2 sets", 
-    "steps": {
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-                    "name": "Reference genome"
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-            "tool_id": null, 
-            "tool_state": "{\"name\": \"Reference genome\"}", 
-            "tool_version": null, 
-            "type": "data_input", 
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-            "annotation": "", 
-            "id": 1, 
-            "input_connections": {}, 
-            "inputs": [
-                {
-                    "description": "", 
-                    "name": "genome 1 reads forward"
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-            "name": "Input dataset", 
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-            "id": 2, 
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-            "name": "Input dataset", 
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+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 2298, 
+                "top": 593
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionoutputVCFStorage": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "outputVCFStorage"
+                }, 
+                "RenameDatasetActionoutputVCFStorage": {
+                    "action_arguments": {
+                        "newname": "#{inputFasta | basename}.matrix"
+                    }, 
+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "outputVCFStorage"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/vcfgandalftools/VCFStorage/0.01", 
+            "tool_state": "{\"__page__\": 0, \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"VCFFile\": \"[{\\\"strainName\\\": \\\"strain1\\\", \\\"__index__\\\": 0, \\\"inputStrainVCF\\\": null}, {\\\"strainName\\\": \\\"strain2\\\", \\\"__index__\\\": 1, \\\"inputStrainVCF\\\": null}]\", \"inputFasta\": \"null\"}", 
+            "tool_version": "0.01", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "19": {
+            "annotation": "", 
+            "id": 19, 
+            "input_connections": {
+                "inputTabular": {
+                    "id": 18, 
+                    "output_name": "outputVCFStorage"
+                }
+            }, 
+            "inputs": [], 
+            "name": "VCFCarto", 
+            "outputs": [
+                {
+                    "name": "outputVCFCarto", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "output_html", 
+                    "type": "html"
+                }, 
+                {
+                    "name": "output_bed", 
+                    "type": "bed"
+                }
+            ], 
+            "position": {
+                "left": 2618, 
+                "top": 593
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionoutput_bed": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_bed"
+                }, 
+                "HideDatasetActionoutput_html": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_html"
+                }, 
+                "RenameDatasetActionoutputVCFCarto": {
+                    "action_arguments": {
+                        "newname": "#{inputTabular | basename}.red"
+                    }, 
+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "outputVCFCarto"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/vcfgandalftools/VCFCarto/0.01", 
+            "tool_state": "{\"__page__\": 0, \"parentA\": \"\\\"strain1\\\"\", \"__rerun_remap_job_id__\": null, \"outputType\": \"\\\"raw\\\"\", \"parentH\": \"\\\"strain2\\\"\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"inputTabular\": \"null\"}", 
+            "tool_version": "0.01", 
+            "type": "tool", 
+            "user_outputs": []
+        }
+    }, 
+    "uuid": "f217cc60-5c89-442b-80ee-3d055e407367"
+}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gandalfworkflow/repository_dependencies.xml	Fri Apr 08 12:17:38 2016 -0400
@@ -0,0 +1,10 @@
+<?xml version="1.0"?>
+<repositories description="Gandalf worflow needed repository">
+    <repository changeset_revision="d8c9597bfb09" name="bwa" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="74980f9f1ccc" name="mapqfilter" owner="urgi-team" toolshed="http://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="379fdf4c41ac" name="picard" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="874dd6c0fcde" name="freebayes4workflow" owner="urgi-team" toolshed="http://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="1fd1f727c330" name="vcfgandalftools" owner="urgi-team" toolshed="http://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="af65bfb54977" name="suite_samtools_0_1_19" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="79feb4eb7832" name="mdust" owner="urgi-team" toolshed="http://toolshed.g2.bx.psu.edu" />
+</repositories>
--- a/repository_dependencies.xml	Tue Dec 15 05:38:37 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,10 +0,0 @@
-<?xml version="1.0"?>
-<repositories description="Gandalf worflow needed repository">
-    <repository changeset_revision="d8c9597bfb09" name="bwa" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
-    <repository changeset_revision="74980f9f1ccc" name="mapqfilter" owner="urgi-team" toolshed="http://toolshed.g2.bx.psu.edu" />
-    <repository changeset_revision="379fdf4c41ac" name="picard" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
-    <repository changeset_revision="874dd6c0fcde" name="freebayes4workflow" owner="urgi-team" toolshed="http://toolshed.g2.bx.psu.edu" />
-    <repository changeset_revision="cfd4eaadad42" name="vcfgandalftools" owner="urgi-team" toolshed="http://toolshed.g2.bx.psu.edu" />
-    <repository changeset_revision="af65bfb54977" name="suite_samtools_0_1_19" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
-    <repository changeset_revision="79feb4eb7832" name="mdust" owner="urgi-team" toolshed="http://toolshed.g2.bx.psu.edu" />
-</repositories>