Mercurial > repos > rnateam > blockclust_workflow

changeset 2:e9b2400cc569 draft

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Uploaded
author bgruening
date Tue, 22 Oct 2013 17:35:13 -0400
parents d0ae001db6d7
children d6553277b759
files blockclust_workflow.ga repository_dependencies.xml
diffstat 2 files changed, 285 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/blockclust_workflow.ga	Tue Oct 22 17:35:13 2013 -0400
@@ -0,0 +1,283 @@
+{
+    "a_galaxy_workflow": "true", 
+    "annotation": "", 
+    "format-version": "0.1", 
+    "name": "BlockClustWorkflow", 
+    "steps": {
+        "0": {
+            "annotation": "", 
+            "id": 0, 
+            "input_connections": {}, 
+            "inputs": [], 
+            "name": "BlockClust", 
+            "outputs": [
+                {
+                    "name": "tags_bed", 
+                    "type": "bed"
+                }, 
+                {
+                    "name": "hclust_plot", 
+                    "type": "pdf"
+                }, 
+                {
+                    "name": "clusters", 
+                    "type": "bed"
+                }, 
+                {
+                    "name": "sim_tab_out", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "analysis", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "cluster_dist", 
+                    "type": "pdf"
+                }
+            ], 
+            "position": {
+                "left": 200, 
+                "top": 308
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "testtoolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/0.1", 
+            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"mode\": \"{\\\"operation\\\": \\\"pre\\\", \\\"reads_bam\\\": null, \\\"__current_case__\\\": 0}\"}", 
+            "tool_version": "0.1", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "1": {
+            "annotation": "", 
+            "id": 1, 
+            "input_connections": {
+                "input": {
+                    "id": 0, 
+                    "output_name": "tags_bed"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Sort", 
+            "outputs": [
+                {
+                    "name": "out_file1", 
+                    "type": "input"
+                }
+            ], 
+            "position": {
+                "left": 466, 
+                "top": 308
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "sort1", 
+            "tool_state": "{\"__page__\": 0, \"style\": \"\\\"alpha\\\"\", \"column\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"1\\\"}\", \"__rerun_remap_job_id__\": null, \"order\": \"\\\"ASC\\\"\", \"input\": \"null\", \"column_set\": \"[{\\\"other_order\\\": \\\"ASC\\\", \\\"__index__\\\": 0, \\\"other_column\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"6\\\"}, \\\"other_style\\\": \\\"alpha\\\"}, {\\\"other_order\\\": \\\"ASC\\\", \\\"__index__\\\": 1, \\\"other_column\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"2\\\"}, \\\"other_style\\\": \\\"num\\\"}, {\\\"other_order\\\": \\\"ASC\\\", \\\"__index__\\\": 2, \\\"other_column\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"3\\\"}, \\\"other_style\\\": \\\"num\\\"}]\"}", 
+            "tool_version": "1.0.3", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "2": {
+            "annotation": "", 
+            "id": 2, 
+            "input_connections": {
+                "input": {
+                    "id": 1, 
+                    "output_name": "out_file1"
+                }
+            }, 
+            "inputs": [], 
+            "name": "blockbuster", 
+            "outputs": [
+                {
+                    "name": "output", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 694, 
+                "top": 308
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "testtoolshed.g2.bx.psu.edu/repos/rnateam/blockbuster/blockbuster/0.1", 
+            "tool_state": "{\"distance\": \"\\\"30\\\"\", \"scale\": \"\\\"0.4\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"print\": \"\\\"1\\\"\", \"tagFilter\": \"\\\"0\\\"\", \"merge\": \"\\\"0\\\"\", \"minBlockHeight\": \"\\\"2.0\\\"\", \"input\": \"null\", \"minClusterHeight\": \"\\\"10.0\\\"\"}", 
+            "tool_version": "0.1", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "3": {
+            "annotation": "", 
+            "id": 3, 
+            "input_connections": {
+                "mode|input_bbo": {
+                    "id": 2, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool BlockClust", 
+                    "name": "mode"
+                }
+            ], 
+            "name": "BlockClust", 
+            "outputs": [
+                {
+                    "name": "tags_bed", 
+                    "type": "bed"
+                }, 
+                {
+                    "name": "hclust_plot", 
+                    "type": "pdf"
+                }, 
+                {
+                    "name": "clusters", 
+                    "type": "bed"
+                }, 
+                {
+                    "name": "sim_tab_out", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "analysis", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "cluster_dist", 
+                    "type": "pdf"
+                }
+            ], 
+            "position": {
+                "left": 922, 
+                "top": 308
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "testtoolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/0.1", 
+            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"mode\": \"{\\\"operation\\\": \\\"clust\\\", \\\"reference\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 1, \\\"input_bbo\\\": null}\"}", 
+            "tool_version": "0.1", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "4": {
+            "annotation": "", 
+            "id": 4, 
+            "input_connections": {
+                "input": {
+                    "id": 3, 
+                    "output_name": "clusters"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Extract Genomic DNA", 
+            "outputs": [
+                {
+                    "name": "out_file1", 
+                    "type": "input"
+                }
+            ], 
+            "position": {
+                "left": 1164, 
+                "top": 201
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "Extract genomic DNA 1", 
+            "tool_state": "{\"out_format\": \"\\\"fasta\\\"\", \"__page__\": 0, \"interpret_features\": \"\\\"yes\\\"\", \"__rerun_remap_job_id__\": null, \"seq_source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"__current_case__\\\": 0}\", \"input\": \"null\"}", 
+            "tool_version": "2.2.2", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "5": {
+            "annotation": "", 
+            "id": 5, 
+            "input_connections": {
+                "seqdb": {
+                    "id": 4, 
+                    "output_name": "out_file1"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Search covariance model(s)", 
+            "outputs": [
+                {
+                    "name": "outfile", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "multiple_alignment_output", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 1422, 
+                "top": 200
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "testtoolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmsearch/1.1.0.1", 
+            "tool_state": "{\"A\": \"\\\"False\\\"\", \"nohmm\": \"\\\"False\\\"\", \"--acyk\": \"\\\"False\\\"\", \"bottomonly\": \"\\\"False\\\"\", \"g\": \"\\\"False\\\"\", \"inclusion_thresholds_opts\": \"{\\\"inclusion_thresholds_selector\\\": \\\"\\\", \\\"__current_case__\\\": 3}\", \"__page__\": 0, \"max\": \"\\\"False\\\"\", \"notrunc\": \"\\\"False\\\"\", \"mid\": \"\\\"False\\\"\", \"seqdb\": \"null\", \"toponly\": \"\\\"False\\\"\", \"cm_opts\": \"{\\\"database\\\": null, \\\"__current_case__\\\": 0, \\\"cm_opts_selector\\\": \\\"db\\\"}\", \"reporting_thresholds_opts\": \"{\\\"reporting_thresholds_selector\\\": \\\"\\\", \\\"__current_case__\\\": 3}\", \"cyk\": \"\\\"False\\\"\", \"__rerun_remap_job_id__\": null}", 
+            "tool_version": "1.1.0.1", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "6": {
+            "annotation": "", 
+            "id": 6, 
+            "input_connections": {
+                "mode|clusters_bed": {
+                    "id": 3, 
+                    "output_name": "clusters"
+                }, 
+                "mode|cmsearch_out": {
+                    "id": 5, 
+                    "output_name": "outfile"
+                }, 
+                "mode|sim_tab_in": {
+                    "id": 3, 
+                    "output_name": "sim_tab_out"
+                }
+            }, 
+            "inputs": [], 
+            "name": "BlockClust", 
+            "outputs": [
+                {
+                    "name": "tags_bed", 
+                    "type": "bed"
+                }, 
+                {
+                    "name": "hclust_plot", 
+                    "type": "pdf"
+                }, 
+                {
+                    "name": "clusters", 
+                    "type": "bed"
+                }, 
+                {
+                    "name": "sim_tab_out", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "analysis", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "cluster_dist", 
+                    "type": "pdf"
+                }
+            ], 
+            "position": {
+                "left": 1738, 
+                "top": 308
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "testtoolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/0.1", 
+            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"mode\": \"{\\\"cmsearch_out\\\": null, \\\"operation\\\": \\\"post\\\", \\\"clusters_bed\\\": null, \\\"__current_case__\\\": 2, \\\"sim_tab_in\\\": null}\"}", 
+            "tool_version": "0.1", 
+            "type": "tool", 
+            "user_outputs": []
+        }
+    }
+}
\ No newline at end of file
--- a/repository_dependencies.xml	Mon Oct 21 12:34:31 2013 -0400
+++ b/repository_dependencies.xml	Tue Oct 22 17:35:13 2013 -0400
@@ -1,10 +1,10 @@
 <?xml version="1.0"?>
 <repositories description="This workflow requires a number of different repositories.">
-    <repository changeset_revision="4882bc140680" name="blockclust" owner="rnateam" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="762937a63301" name="blockclust" owner="rnateam" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     <repository changeset_revision="94926c35b6f3" name="segemehl" owner="rnateam" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     <repository changeset_revision="2f9d4b518b03" name="blockbuster" owner="rnateam" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     <!--<repository name="graphclust" owner="rnateam" />-->
     <repository changeset_revision="5c6344f67ad0" name="infernal" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu" />
-    <repository changeset_revision="e86bc4b0ddb5" name="package_eden_1_1" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="72cb793d5fbb" name="package_eden_1_1" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     <repository changeset_revision="7003196be1b1" name="package_mcl_12_135" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
 </repositories>