# HG changeset patch
# User chrisd
# Date 1466569634 14400
# Node ID 04f9c20fecf8a126e93a4cb3e68e1058cb2f316b
# Parent  d1896971200b2a67acb8628b4805aad27d9f3023
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty

diff -r d1896971200b -r 04f9c20fecf8 README.rst
--- a/README.rst	Sun Mar 27 02:42:55 2016 -0400
+++ b/README.rst	Wed Jun 22 00:27:14 2016 -0400
@@ -1,7 +1,9 @@
 What is this?
 =============
 
-This is a suite that contains a collection of tools which can be used to analyze metagenomic sequence data.
+A suite that contains a collection of tools and workflows which can be used to identify and characterize resistance and virulence genes.
+
+.. image:: https://raw.githubusercontent.com/cdeanj/galaxytools/master/workflows/amrplusplus/workflow.jpeg
 
 Availability
 ============
diff -r d1896971200b -r 04f9c20fecf8 amrplusplus_pe.ga
--- a/amrplusplus_pe.ga	Sun Mar 27 02:42:55 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,547 +0,0 @@
-{
-    "a_galaxy_workflow": "true", 
-    "annotation": "", 
-    "format-version": "0.1", 
-    "name": "amrplusplus_wf_pe", 
-    "steps": {
-        "0": {
-            "annotation": "", 
-            "content_id": null, 
-            "id": 0, 
-            "input_connections": {}, 
-            "inputs": [
-                {
-                    "description": "", 
-                    "name": "Input Dataset"
-                }
-            ], 
-            "label": "AMR Database", 
-            "name": "Input dataset", 
-            "outputs": [], 
-            "position": {
-                "left": 200, 
-                "top": 200
-            }, 
-            "tool_errors": null, 
-            "tool_id": null, 
-            "tool_state": "{\"name\": \"Input Dataset\"}", 
-            "tool_version": null, 
-            "type": "data_input", 
-            "uuid": "c33b3302-86dd-4020-920b-e91904994b0b", 
-            "workflow_outputs": []
-        }, 
-        "1": {
-            "annotation": "", 
-            "content_id": null, 
-            "id": 1, 
-            "input_connections": {}, 
-            "inputs": [
-                {
-                    "description": "", 
-                    "name": "Input Dataset"
-                }
-            ], 
-            "label": "Host Genome", 
-            "name": "Input dataset", 
-            "outputs": [], 
-            "position": {
-                "left": 200, 
-                "top": 285
-            }, 
-            "tool_errors": null, 
-            "tool_id": null, 
-            "tool_state": "{\"name\": \"Input Dataset\"}", 
-            "tool_version": null, 
-            "type": "data_input", 
-            "uuid": "828c1738-4db6-4548-89b8-85e68a00491a", 
-            "workflow_outputs": []
-        }, 
-        "2": {
-            "annotation": "", 
-            "content_id": null, 
-            "id": 2, 
-            "input_connections": {}, 
-            "inputs": [
-                {
-                    "description": "", 
-                    "name": "Input Dataset"
-                }
-            ], 
-            "label": "FastQ Forward", 
-            "name": "Input dataset", 
-            "outputs": [], 
-            "position": {
-                "left": 200, 
-                "top": 370
-            }, 
-            "tool_errors": null, 
-            "tool_id": null, 
-            "tool_state": "{\"name\": \"Input Dataset\"}", 
-            "tool_version": null, 
-            "type": "data_input", 
-            "uuid": "1956acf3-af87-497d-bced-1dc18003b4ee", 
-            "workflow_outputs": []
-        }, 
-        "3": {
-            "annotation": "", 
-            "content_id": null, 
-            "id": 3, 
-            "input_connections": {}, 
-            "inputs": [
-                {
-                    "description": "", 
-                    "name": "Input Dataset"
-                }
-            ], 
-            "label": "FastQ Reverse", 
-            "name": "Input dataset", 
-            "outputs": [], 
-            "position": {
-                "left": 200, 
-                "top": 455
-            }, 
-            "tool_errors": null, 
-            "tool_id": null, 
-            "tool_state": "{\"name\": \"Input Dataset\"}", 
-            "tool_version": null, 
-            "type": "data_input", 
-            "uuid": "0e020fbd-697d-4ebc-bd3d-0b45d5104b44", 
-            "workflow_outputs": []
-        }, 
-        "4": {
-            "annotation": "", 
-            "content_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.32.3", 
-            "id": 4, 
-            "input_connections": {
-                "paired_end|paired_input_type_conditional|fastq_r1_in": {
-                    "id": 2, 
-                    "output_name": "output"
-                }, 
-                "paired_end|paired_input_type_conditional|fastq_r2_in": {
-                    "id": 3, 
-                    "output_name": "output"
-                }
-            }, 
-            "inputs": [], 
-            "label": null, 
-            "name": "Trimmomatic", 
-            "outputs": [
-                {
-                    "name": "fastq_out_paired", 
-                    "type": "input"
-                }, 
-                {
-                    "name": "fastq_out_unpaired", 
-                    "type": "input"
-                }, 
-                {
-                    "name": "fastq_out_r1_paired", 
-                    "type": "fastqsanger"
-                }, 
-                {
-                    "name": "fastq_out_r2_paired", 
-                    "type": "fastqsanger"
-                }, 
-                {
-                    "name": "fastq_out_r1_unpaired", 
-                    "type": "fastqsanger"
-                }, 
-                {
-                    "name": "fastq_out_r2_unpaired", 
-                    "type": "fastqsanger"
-                }, 
-                {
-                    "name": "fastq_out", 
-                    "type": "fastqsanger"
-                }
-            ], 
-            "position": {
-                "left": 435, 
-                "top": 200
-            }, 
-            "post_job_actions": {
-                "DeleteIntermediatesActionfastq_out_paired": {
-                    "action_arguments": {}, 
-                    "action_type": "DeleteIntermediatesAction", 
-                    "output_name": "fastq_out_paired"
-                }, 
-                "HideDatasetActionfastq_out": {
-                    "action_arguments": {}, 
-                    "action_type": "HideDatasetAction", 
-                    "output_name": "fastq_out"
-                }, 
-                "HideDatasetActionfastq_out_paired": {
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-                    "action_type": "HideDatasetAction", 
-                    "output_name": "fastq_out_paired"
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-                "HideDatasetActionfastq_out_r1_unpaired": {
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-                    "action_type": "HideDatasetAction", 
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-                }, 
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-                    "action_type": "HideDatasetAction", 
-                    "output_name": "fastq_out_r2_unpaired"
-                }, 
-                "HideDatasetActionfastq_out_unpaired": {
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-                    "action_type": "HideDatasetAction", 
-                    "output_name": "fastq_out_unpaired"
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-            "type": "tool", 
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-                    "output_name": "fastq_out_r1_paired"
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-                "input_type|fastq_input2": {
-                    "id": 4, 
-                    "output_name": "fastq_out_r2_paired"
-                }, 
-                "reference_source|ref_file": {
-                    "id": 1, 
-                    "output_name": "output"
-                }
-            }, 
-            "inputs": [], 
-            "label": null, 
-            "name": "Map with BWA", 
-            "outputs": [
-                {
-                    "name": "bam_output", 
-                    "type": "bam"
-                }
-            ], 
-            "position": {
-                "left": 763, 
-                "top": 200
-            }, 
-            "post_job_actions": {
-                "DeleteIntermediatesActionbam_output": {
-                    "action_arguments": {}, 
-                    "action_type": "DeleteIntermediatesAction", 
-                    "output_name": "bam_output"
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-            "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.12.1", 
-            "tool_state": "{\"__page__\": 0, \"input_type\": \"{\\\"adv_pe_options\\\": {\\\"__current_case__\\\": 1, \\\"adv_pe_options_selector\\\": \\\"do_not_set\\\"}, \\\"fastq_input2\\\": null, \\\"input_type_selector\\\": \\\"paired\\\", \\\"__current_case__\\\": 0, \\\"fastq_input1\\\": null}\", \"__rerun_remap_job_id__\": null, \"rg\": \"{\\\"rg_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 3}\", \"analysis_type\": \"{\\\"analysis_type_selector\\\": \\\"illumina\\\", \\\"__current_case__\\\": 0}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"__current_case__\\\": 1, \\\"index_a\\\": \\\"auto\\\"}\"}", 
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-            "inputs": [], 
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-            "name": "Coverage Sampler", 
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-            "inputs": [], 
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-            "tool_version": "0.1.0", 
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-    "uuid": "6c6ee2ed-be38-4787-9a8e-5ab9a872a00e"
-}
\ No newline at end of file
diff -r d1896971200b -r 04f9c20fecf8 amrplusplus_workflow.ga
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/amrplusplus_workflow.ga	Wed Jun 22 00:27:14 2016 -0400
@@ -0,0 +1,595 @@
+{
+    "a_galaxy_workflow": "true", 
+    "annotation": "", 
+    "format-version": "0.1", 
+    "name": "aa", 
+    "steps": {
+        "0": {
+            "annotation": "", 
+            "content_id": null, 
+            "id": 0, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "FASTQ Forward"
+                }
+            ], 
+            "label": "FASTQ Forward", 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 252, 
+                "top": 323
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"FASTQ Forward\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "uuid": "9c1f5852-9697-40e2-bc6f-7ac65ad647ce", 
+            "workflow_outputs": []
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diff -r d1896971200b -r 04f9c20fecf8 repository_dependencies.xml
--- a/repository_dependencies.xml	Sun Mar 27 02:42:55 2016 -0400
+++ b/repository_dependencies.xml	Wed Jun 22 00:27:14 2016 -0400
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diff -r d1896971200b -r 04f9c20fecf8 workflow.jpeg
Binary file workflow.jpeg has changed