changeset 0:1b2ba1496c6a draft

Initial version
author stemcellcommons
date Mon, 14 Jan 2019 14:31:36 -0500
parents
children dbf43bc73806
files ATAC-seq_-_Human.ga ATAC-seq_-_Mouse.ga ATAC-seq_-_Mouse_(mm9).ga ATAC-seq_-_Zebrafish.ga repository_dependencies.xml
diffstat 5 files changed, 1748 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ATAC-seq_-_Human.ga	Mon Jan 14 14:31:36 2019 -0500
@@ -0,0 +1,435 @@
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\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ATAC-seq_-_Mouse.ga	Mon Jan 14 14:31:36 2019 -0500
@@ -0,0 +1,435 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ATAC-seq_-_Mouse_(mm9).ga	Mon Jan 14 14:31:36 2019 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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+                "HideDatasetActionoutput_broadpeaks": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_broadpeaks"
+                }, 
+                "HideDatasetActionoutput_control_lambda": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_control_lambda"
+                }, 
+                "HideDatasetActionoutput_extra_files": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_extra_files"
+                }, 
+                "HideDatasetActionoutput_gappedpeaks": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_gappedpeaks"
+                }, 
+                "HideDatasetActionoutput_plot": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_plot"
+                }, 
+                "HideDatasetActionoutput_treat_pileup": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_treat_pileup"
+                }
+            }, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.0.20151222.0", 
+            "tool_shed_repository": {
+                "changeset_revision": "56e104999978", 
+                "name": "macs2", 
+                "owner": "iuc", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "tool_state": "{\"__page__\": null, \"effective_genome_size_options\": \"{\\\"gsize\\\": \\\"1400000000\\\", \\\"effective_genome_size_options_selector\\\": \\\"user_defined\\\", \\\"__current_case__\\\": 4}\", \"bampe\": \"\\\"true\\\"\", \"input_control_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"band_width\": \"\\\"300\\\"\", \"cutoff_options\": \"{\\\"cutoff_options_selector\\\": \\\"qvalue\\\", \\\"qvalue\\\": \\\"0.05\\\", \\\"__current_case__\\\": 1}\", \"advanced_options\": \"{\\\"advanced_options_selector\\\": \\\"on\\\", \\\"ratio\\\": \\\"1.0\\\", \\\"to_large\\\": \\\"false\\\", \\\"slocal\\\": \\\"1000\\\", \\\"broad_options\\\": {\\\"broad_options_selector\\\": \\\"nobroad\\\", \\\"call_summits\\\": \\\"false\\\", \\\"__current_case__\\\": 1}, \\\"nolambda\\\": \\\"false\\\", \\\"llocal\\\": \\\"10000\\\", \\\"keep_dup_options\\\": {\\\"__current_case__\\\": 2, \\\"keep_dup_options_selector\\\": \\\"all\\\"}, \\\"__current_case__\\\": 0}\", \"input_treatment_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"nomodel_type\": \"{\\\"nomodel_type_selector\\\": \\\"create_model\\\", \\\"__current_case__\\\": 0}\", \"outputs\": \"[\\\"peaks_tabular\\\", \\\"summits\\\", \\\"bdg\\\"]\"}", 
+            "tool_version": "2.1.0.20151222.0", 
+            "type": "tool", 
+            "uuid": "f58a8811-f8e3-4e91-a8b9-4c635e7d00c5", 
+            "workflow_outputs": [
+                {
+                    "label": null, 
+                    "output_name": "output_tabular", 
+                    "uuid": "29b6c2d4-6f1a-48d2-82a3-b0d45c186bda"
+                }, 
+                {
+                    "label": null, 
+                    "output_name": "output_summits", 
+                    "uuid": "26d6760f-5f82-4d24-a4fa-0294c37290ef"
+                }, 
+                {
+                    "label": null, 
+                    "output_name": "output_narrowpeaks", 
+                    "uuid": "b6445346-e10b-4deb-a7e8-b8df81c73796"
+                }
+            ]
+        }
+    }, 
+    "uuid": "0497d800-74b0-4a7a-8915-215a6b142d08"
+}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml	Mon Jan 14 14:31:36 2019 -0500
@@ -0,0 +1,8 @@
+<?xml version="1.0"?>
+<repositories description="Stem Cell Commons ATAC-seq workflows">
+  <repository toolshed="toolshed.g2.bx.psu.edu" name="picard" owner="devteam" changeset_revision="6f9c0884a3e7" />
+  <repository toolshed="toolshed.g2.bx.psu.edu" name="bowtie_wrappers" owner="devteam" changeset_revision="df86f29bedee" />
+  <repository toolshed="toolshed.g2.bx.psu.edu" name="sam_to_bam" owner="devteam" changeset_revision="d04d9f1c6791" />
+  <repository toolshed="toolshed.g2.bx.psu.edu" name="macs2" owner="iuc" changeset_revision="6d4babad010f" />
+  <repository toolshed="toolshed.g2.bx.psu.edu" name="split_paired_collection" owner="refinery-platform" changeset_revision="3a60513b51a2" />
+</repositories>