# HG changeset patch
# User drosofff
# Date 1479385624 18000
# Node ID ba15c770fd40b95ac6e59923f75879d0e98f3d00
# Parent  48b020a0d2f72b41b0dc140ffbda6e2b2f55d0a9
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4

diff -r 48b020a0d2f7 -r ba15c770fd40 Galaxy-Workflow-Metavisitor__Spades_test_in_Use_Case_2-2.ga
--- /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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diff -r 48b020a0d2f7 -r ba15c770fd40 Galaxy-Workflow-Metavisitor__Trinity_test_in_Use_Case_2-2.ga
--- /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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+}
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diff -r 48b020a0d2f7 -r ba15c770fd40 Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_1-1.ga
--- 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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diff -r 48b020a0d2f7 -r ba15c770fd40 Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_1-2.ga
--- 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
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             "tool_shed_repository": {
-                "changeset_revision": "befdb392fece", 
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             "tool_shed_repository": {
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@@ -778,4 +778,4 @@
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diff -r 48b020a0d2f7 -r ba15c770fd40 Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_1-3.ga
--- a/Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_1-3.ga	Fri May 13 05:46:40 2016 -0400
+++ 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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+                "changeset_revision": "a9d8f69d59fb", 
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+                "changeset_revision": "ee081dc6c578", 
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diff -r 48b020a0d2f7 -r ba15c770fd40 Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_1-4.ga
--- 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": {
-                "changeset_revision": "330dd8a8c31a", 
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diff -r 48b020a0d2f7 -r ba15c770fd40 Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_3-3.ga
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diff -r 48b020a0d2f7 -r ba15c770fd40 Galaxy-Workflow-Metavisitor__Workflow_for_remapping_in_Use_Cases_1-1,2,3.ga
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diff -r 48b020a0d2f7 -r ba15c770fd40 Galaxy-Workflow-Metavisitor__Workflow_for_remapping_in_Use_Cases_2-1,2.ga
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             "tool_state": "{\"__page__\": 0, \"output_format\": \"\\\"tabular\\\"\", \"additional_fasta\": \"\\\"No\\\"\", \"v_mismatches\": \"\\\"0\\\"\", \"__rerun_remap_job_id__\": null, \"input\": \"null\", \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"history\\\", \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\", \"method\": \"\\\"multiple\\\"\"}", 
-            "tool_version": "1.1.2", 
+            "tool_version": "1.1.2.1", 
             "type": "tool", 
             "uuid": "7c3b7910-0490-4b69-ad32-c4ab81d01046", 
             "workflow_outputs": []
@@ -284,7 +284,7 @@
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         "6": {
             "annotation": "", 
-            "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_readmap_and_size_histograms/Readmap/1.1.5", 
+            "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_readmap_and_size_histograms/Readmap/1.2.0", 
             "id": 6, 
             "input_connections": {
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@@ -338,15 +338,15 @@
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             "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_readmap_and_size_histograms/Readmap/1.1.5", 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_readmap_and_size_histograms/Readmap/1.2.0", 
             "tool_shed_repository": {
-                "changeset_revision": "68f58363f1c6", 
+                "changeset_revision": "92898cc3ea19", 
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                 "owner": "drosofff", 
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             }, 
             "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\\\": null}], \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"maxquery\": \"\\\"30\\\"\", \"xlabel\": \"\\\"Coordinates/read size\\\"\", \"ylabel\": \"\\\"Number of reads\\\"\", \"gff\": \"null\"}", 
-            "tool_version": "1.1.5", 
+            "tool_version": "1.2.0", 
             "type": "tool", 
             "uuid": "ebaf90ab-b8ea-428f-876c-8f9fabd1fbf9", 
             "workflow_outputs": [
diff -r 48b020a0d2f7 -r ba15c770fd40 Galaxy-Workflow-Metavisitor__Workflow_for_small_RNA_profiling_of_contigs.ga
--- /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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+    "name": "Metavisitor: Workflow for small RNA profiling of contigs", 
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+                "top": 213
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+            "tool_errors": null, 
+            "tool_id": null, 
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+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"de novo assembled Oases contigs\"}", 
+            "tool_version": null, 
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+                    "output_name": "output"
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+                    "name": "input"
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+            "label": null, 
+            "name": "Clip adapter", 
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+                {
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+            "name": "Concatenate multiple datasets", 
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+                    "name": "input"
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+            "outputs": [
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+                    "type": "input"
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+                }
+            ], 
+            "label": null, 
+            "name": "sRbowtie", 
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+                    "type": "tabular"
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+                {
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+                    "type": "fasta"
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+                "top": 287
+            }, 
+            "post_job_actions": {
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+                    "action_type": "HideDatasetAction", 
+                    "output_name": "aligned"
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+                "HideDatasetActionunaligned": {
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+                    "action_type": "HideDatasetAction", 
+                    "output_name": "unaligned"
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+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.2.1", 
+            "tool_shed_repository": {
+                "changeset_revision": "615d2550977f", 
+                "name": "msp_sr_bowtie", 
+                "owner": "drosofff", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
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+            "tool_state": "{\"__page__\": 0, \"output_format\": \"\\\"tabular\\\"\", \"additional_fasta\": \"\\\"No\\\"\", \"v_mismatches\": \"\\\"0\\\"\", \"__rerun_remap_job_id__\": null, \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"history\\\", \\\"ownFile\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 1}\", \"method\": \"\\\"a_option\\\"\"}", 
+            "tool_version": "1.1.2.1", 
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+        "7": {
+            "annotation": "", 
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+            "input_connections": {
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+                    "output_name": "out_file1"
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+                "refGenomeSource|series_0|input": {
+                    "id": 6, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Generate readmap and histograms from alignment files", 
+                    "name": "gff"
+                }, 
+                {
+                    "description": "runtime parameter for tool Generate readmap and histograms from alignment files", 
+                    "name": "refGenomeSource"
+                }
+            ], 
+            "label": null, 
+            "name": "Generate readmap and histograms from alignment files", 
+            "outputs": [
+                {
+                    "name": "readmap_dataframe", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "size_distribution_dataframe", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "readmap_PDF", 
+                    "type": "pdf"
+                }, 
+                {
+                    "name": "size_PDF", 
+                    "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", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "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": [
+                {
+                    "label": null, 
+                    "output_name": "size_PDF", 
+                    "uuid": "91fa9c78-72dd-41e8-9937-c4b44682f79b"
+                }, 
+                {
+                    "label": null, 
+                    "output_name": "combi_PDF", 
+                    "uuid": "68f021f3-087b-4f77-813f-74fa61877a0e"
+                }, 
+                {
+                    "label": null, 
+                    "output_name": "readmap_PDF", 
+                    "uuid": "70966192-62e8-4dff-99b1-3f5dc8de8c28"
+                }
+            ]
+        }
+    }, 
+    "uuid": "c3853e65-8d66-47fc-aad9-6a40f5517622"
+}
\ No newline at end of file
diff -r 48b020a0d2f7 -r ba15c770fd40 repository_dependencies.xml
--- 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>