changeset 3:ba15c770fd40 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
author drosofff
date Thu, 17 Nov 2016 07:27:04 -0500
parents 48b020a0d2f7
children 46614c7dd247
files Galaxy-Workflow-Metavisitor__Spades_test_in_Use_Case_2-2.ga Galaxy-Workflow-Metavisitor__Trinity_test_in_Use_Case_2-2.ga Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_1-1.ga Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_1-2.ga Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_1-3.ga Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_1-4.ga Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_2-1.ga Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_2-2.ga Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_3-1.ga Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_3-2.ga Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_3-3.ga Galaxy-Workflow-Metavisitor__Workflow_for_remapping_in_Use_Cases_1-1,2,3.ga Galaxy-Workflow-Metavisitor__Workflow_for_remapping_in_Use_Cases_2-1,2.ga Galaxy-Workflow-Metavisitor__Workflow_for_small_RNA_profiling_of_contigs.ga repository_dependencies.xml
diffstat 15 files changed, 1833 insertions(+), 172 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Galaxy-Workflow-Metavisitor__Spades_test_in_Use_Case_2-2.ga	Thu Nov 17 07:27:04 2016 -0500
@@ -0,0 +1,508 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Galaxy-Workflow-Metavisitor__Trinity_test_in_Use_Case_2-2.ga	Thu Nov 17 07:27:04 2016 -0500
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--- a/Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_1-1.ga	Fri May 13 05:46:40 2016 -0400
+++ b/Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_1-1.ga	Thu Nov 17 07:27:04 2016 -0500
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--- a/Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_1-2.ga	Fri May 13 05:46:40 2016 -0400
+++ b/Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_1-2.ga	Thu Nov 17 07:27:04 2016 -0500
@@ -107,7 +107,7 @@
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@@ -778,4 +778,4 @@
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+}
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+++ b/Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_1-3.ga	Thu Nov 17 07:27:04 2016 -0500
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             "tool_shed_repository": {
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--- a/Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_1-4.ga	Fri May 13 05:46:40 2016 -0400
+++ b/Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_1-4.ga	Thu Nov 17 07:27:04 2016 -0500
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             "tool_shed_repository": {
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             "tool_shed_repository": {
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+++ b/Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_2-2.ga	Thu Nov 17 07:27:04 2016 -0500
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+++ b/Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_3-3.ga	Thu Nov 17 07:27:04 2016 -0500
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+++ b/Galaxy-Workflow-Metavisitor__Workflow_for_remapping_in_Use_Cases_1-1,2,3.ga	Thu Nov 17 07:27:04 2016 -0500
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+++ b/Galaxy-Workflow-Metavisitor__Workflow_for_remapping_in_Use_Cases_2-1,2.ga	Thu Nov 17 07:27:04 2016 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Galaxy-Workflow-Metavisitor__Workflow_for_small_RNA_profiling_of_contigs.ga	Thu Nov 17 07:27:04 2016 -0500
@@ -0,0 +1,471 @@
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+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [
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+                    "name": "gff"
+                }, 
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+                    "name": "refGenomeSource"
+                }
+            ], 
+            "label": null, 
+            "name": "Generate readmap and histograms from alignment files", 
+            "outputs": [
+                {
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+                    "type": "tabular"
+                }, 
+                {
+                    "name": "size_distribution_dataframe", 
+                    "type": "tabular"
+                }, 
+                {
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+                    "type": "pdf"
+                }, 
+                {
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+                    "type": "pdf"
+                }, 
+                {
+                    "name": "combi_PDF", 
+                    "type": "pdf"
+                }
+            ], 
+            "position": {
+                "left": 1243.5, 
+                "top": 273
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionreadmap_dataframe": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "readmap_dataframe"
+                }, 
+                "HideDatasetActionsize_distribution_dataframe": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "size_distribution_dataframe"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_readmap_and_size_histograms/Readmap/1.2.0", 
+            "tool_shed_repository": {
+                "changeset_revision": "92898cc3ea19", 
+                "name": "msp_sr_readmap_and_size_histograms", 
+                "owner": "drosofff", 
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+            }, 
+            "tool_state": "{\"minquery\": \"\\\"18\\\"\", \"__page__\": 0, \"rows_per_page\": \"\\\"8\\\"\", \"yrange\": \"\\\"0\\\"\", \"title\": \"\\\"Readmaps and size distributions\\\"\", \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"history\\\", \\\"series\\\": [{\\\"__index__\\\": 0, \\\"norm\\\": \\\"1.0\\\", \\\"input\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}], \\\"ownFile\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"maxquery\": \"\\\"30\\\"\", \"xlabel\": \"\\\"Coordinates/read size\\\"\", \"ylabel\": \"\\\"Number of reads\\\"\", \"gff\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", 
+            "tool_version": "1.2.0", 
+            "type": "tool", 
+            "uuid": "87f9f9b5-5c71-465b-9422-c0696a3048a5", 
+            "workflow_outputs": [
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+                    "output_name": "size_PDF", 
+                    "uuid": "91fa9c78-72dd-41e8-9937-c4b44682f79b"
+                }, 
+                {
+                    "label": null, 
+                    "output_name": "combi_PDF", 
+                    "uuid": "68f021f3-087b-4f77-813f-74fa61877a0e"
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+                {
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+                    "output_name": "readmap_PDF", 
+                    "uuid": "70966192-62e8-4dff-99b1-3f5dc8de8c28"
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+            ]
+        }
+    }, 
+    "uuid": "c3853e65-8d66-47fc-aad9-6a40f5517622"
+}
\ No newline at end of file
--- a/repository_dependencies.xml	Fri May 13 05:46:40 2016 -0400
+++ b/repository_dependencies.xml	Thu Nov 17 07:27:04 2016 -0500
@@ -1,4 +1,4 @@
 <?xml version="1.0"?>
 <repositories description="These workflows require the repository suite_metavisitor_1_2">
-    <repository changeset_revision="0f33d75ae19b" name="suite_metavisitor_1_2" owner="drosofff" toolshed="http://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="9f66ff54d573" name="suite_metavisitor_1_2" owner="drosofff" toolshed="http://toolshed.g2.bx.psu.edu" />
 </repositories>