# HG changeset patch
# User scottx611x
# Date 1536083612 14400
# Node ID 064dbe5f3b2f96e7d21841ae2c37455f3c4cc24d

planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8

diff -r 000000000000 -r 064dbe5f3b2f Qualimap_BAM_QC.ga
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Qualimap_BAM_QC.ga	Tue Sep 04 13:53:32 2018 -0400
@@ -0,0 +1,109 @@
+{
+    "a_galaxy_workflow": "true", 
+    "annotation": "{ \n    \"description\": \"Quality control of mapped reads\", \n    \"file_relationship\": { \n        \"file_relationship\": {}, \n        \"value_type\": \"LIST\", \n        \"name\": \"List of BAM Files\", \n        \"input_files\": [ \n            { \n                \"allowed_filetypes\": [{\"name\": \"BAM\"}], \n                \"name\": \"Input File\", \n                \"description\": \"File to run Qualimap BAM QC on\" \n            } \n        ] \n    } \n}", 
+    "format-version": "0.1", 
+    "name": "Qualimap Bam QC", 
+    "steps": {
+        "0": {
+            "annotation": "", 
+            "content_id": null, 
+            "errors": null, 
+            "id": 0, 
+            "input_connections": {}, 
+            "inputs": [], 
+            "label": null, 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 494, 
+                "top": 304.5
+            }, 
+            "tool_id": null, 
+            "tool_state": "{}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "uuid": "354d9a2d-aadd-4c58-886f-5cf9659df944", 
+            "workflow_outputs": [
+                {
+                    "label": null, 
+                    "output_name": "output", 
+                    "uuid": "6e6fd3a9-4d85-4095-9e25-e868020b97f7"
+                }
+            ]
+        }, 
+        "1": {
+            "annotation": "", 
+            "content_id": "toolshed.g2.bx.psu.edu/repos/refinery-platform/qualimap2_bamqc/qualimap_bamqc/2.2", 
+            "errors": null, 
+            "id": 1, 
+            "input_connections": {
+                "input_realigned_bam_file": {
+                    "id": 0, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool QualiMap BamQC", 
+                    "name": "input_realigned_bam_file"
+                }
+            ], 
+            "label": null, 
+            "name": "QualiMap BamQC", 
+            "outputs": [
+                {
+                    "name": "genome_results", 
+                    "type": "txt"
+                }, 
+                {
+                    "name": "raw_data_qualimapReport", 
+                    "type": "zip"
+                }
+            ], 
+            "position": {
+                "left": 872, 
+                "top": 359.5
+            }, 
+            "post_job_actions": {
+                "RenameDatasetActiongenome_results": {
+                    "action_arguments": {
+                        "newname": "genome_results"
+                    }, 
+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "genome_results"
+                }, 
+                "RenameDatasetActionraw_data_qualimapReport": {
+                    "action_arguments": {
+                        "newname": "raw_data_qualimapReport"
+                    }, 
+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "raw_data_qualimapReport"
+                }
+            }, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/refinery-platform/qualimap2_bamqc/qualimap_bamqc/2.2", 
+            "tool_shed_repository": {
+                "changeset_revision": "a2438e0f1bbf", 
+                "name": "qualimap2_bamqc", 
+                "owner": "refinery-platform", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "tool_state": "{\"mem_size\": \"\\\"8G\\\"\", \"__rerun_remap_job_id__\": null, \"input_realigned_bam_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": null}", 
+            "tool_version": "2.2", 
+            "type": "tool", 
+            "uuid": "8e63fbd9-22df-4b7b-a0d1-88e8be17bf16", 
+            "workflow_outputs": [
+                {
+                    "label": null, 
+                    "output_name": "raw_data_qualimapReport", 
+                    "uuid": "71d23433-f0ef-452d-9c4b-b4376e2665de"
+                }, 
+                {
+                    "label": null, 
+                    "output_name": "genome_results", 
+                    "uuid": "d5f56231-b611-425a-b2e1-d2a9072111f9"
+                }
+            ]
+        }
+    }, 
+    "uuid": "27bccc25-073c-4061-b573-9cfe9ed47324"
+}
\ No newline at end of file
diff -r 000000000000 -r 064dbe5f3b2f repository_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml	Tue Sep 04 13:53:32 2018 -0400
@@ -0,0 +1,4 @@
+<?xml version="1.0"?>
+<repositories description="Stem Cell Commons Qualimap BAM QC requires qualimap2_bamqc tool.">
+  <repository toolshed="https://toolshed.g2.bx.psu.edu" name="qualimap2_bamqc" owner="refinery-platform" changeset_revision="a2438e0f1bbf" />
+</repositories>