Mercurial > repos > urgi-team > workflow_teiso

changeset 0:a4d1ca76edb8 draft

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Uploaded
author urgi-team
date Tue, 24 May 2016 09:57:57 -0400
parents
children e98d41dd261e
files TEiso/Galaxy-Workflow-TEiso_workflow.ga TEiso/repository_dependencies.xml
diffstat 2 files changed, 445 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/TEiso/Galaxy-Workflow-TEiso_workflow.ga	Tue May 24 09:57:57 2016 -0400
@@ -0,0 +1,439 @@
+{
+    "a_galaxy_workflow": "true", 
+    "annotation": "", 
+    "format-version": "0.1", 
+    "name": "TEiso_workflow", 
+    "steps": {
+        "0": {
+            "annotation": "", 
+            "id": 0, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "Input Dataset"
+                }
+            ], 
+            "label": null, 
+            "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", 
+            "user_outputs": [], 
+            "uuid": "a910dd6c-d6e5-4d3a-b3cd-3624c8c509b6"
+        }, 
+        "1": {
+            "annotation": "", 
+            "id": 1, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "Input Dataset"
+                }
+            ], 
+            "label": null, 
+            "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", 
+            "user_outputs": [], 
+            "uuid": "98cee5d8-d791-4f91-8f29-ccc98003e392"
+        }, 
+        "2": {
+            "annotation": "", 
+            "id": 2, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "Input Dataset"
+                }
+            ], 
+            "label": null, 
+            "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", 
+            "user_outputs": [], 
+            "uuid": "1fc62c7e-fbb8-48b4-89da-18c629838b7c"
+        }, 
+        "3": {
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+            "id": 3, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "Input Dataset"
+                }
+            ], 
+            "label": null, 
+            "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", 
+            "user_outputs": [], 
+            "uuid": "49264998-41ff-4776-81f2-06e3fbaac133"
+        }, 
+        "4": {
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+            "id": 4, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "Input Dataset"
+                }
+            ], 
+            "label": null, 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 200, 
+                "top": 540
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"Input Dataset\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": [], 
+            "uuid": "869588d6-af39-40d2-afaa-86a3c9935aa9"
+        }, 
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+            "input_connections": {
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+                    "output_name": "output"
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+                "singlePaired|input2": {
+                    "id": 1, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "label": null, 
+            "name": "TopHat", 
+            "outputs": [
+                {
+                    "name": "align_summary", 
+                    "type": "txt"
+                }, 
+                {
+                    "name": "fusions", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "insertions", 
+                    "type": "bed"
+                }, 
+                {
+                    "name": "deletions", 
+                    "type": "bed"
+                }, 
+                {
+                    "name": "junctions", 
+                    "type": "bed"
+                }, 
+                {
+                    "name": "accepted_hits", 
+                    "type": "bam"
+                }, 
+                {
+                    "name": "unmapped", 
+                    "type": "bam"
+                }
+            ], 
+            "position": {
+                "left": 428, 
+                "top": 200
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/0.9", 
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+            "tool_version": "0.9", 
+            "type": "tool", 
+            "user_outputs": [], 
+            "uuid": "3b5324aa-7209-4de0-9135-a267ae3d6266"
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+        "6": {
+            "annotation": "", 
+            "id": 6, 
+            "input_connections": {
+                "inputFile": {
+                    "id": 4, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "label": null, 
+            "name": "GFFToBed", 
+            "outputs": [
+                {
+                    "name": "outputFile", 
+                    "type": "bed"
+                }
+            ], 
+            "position": {
+                "left": 1071, 
+                "top": 535
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/teiso/GFFToBed/1.0", 
+            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/repet_cloud/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"inputFile\": \"null\"}", 
+            "tool_version": "1.0", 
+            "type": "tool", 
+            "user_outputs": [], 
+            "uuid": "ac60365f-0928-44d8-9829-5a616ab7ab23"
+        }, 
+        "7": {
+            "annotation": "", 
+            "id": 7, 
+            "input_connections": {
+                "input": {
+                    "id": 5, 
+                    "output_name": "accepted_hits"
+                }
+            }, 
+            "inputs": [], 
+            "label": null, 
+            "name": "Cufflinks", 
+            "outputs": [
+                {
+                    "name": "genes_expression", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "transcripts_expression", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "assembled_isoforms", 
+                    "type": "gtf"
+                }, 
+                {
+                    "name": "total_map_mass", 
+                    "type": "txt"
+                }, 
+                {
+                    "name": "skipped", 
+                    "type": "gtf"
+                }
+            ], 
+            "position": {
+                "left": 740, 
+                "top": 200
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.0", 
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+            "tool_version": "2.2.1.0", 
+            "type": "tool", 
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+            "uuid": "3a0017dc-8664-49a9-8963-5323cf575ef3"
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+            "id": 8, 
+            "input_connections": {
+                "inputFile": {
+                    "id": 7, 
+                    "output_name": "assembled_isoforms"
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+            }, 
+            "inputs": [], 
+            "label": null, 
+            "name": "CufflinksGTFToBed", 
+            "outputs": [
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+                    "name": "outputFile", 
+                    "type": "bed"
+                }
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+            "position": {
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+                "top": 200
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/teiso/CufflinksGTFToBed/1.0", 
+            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/repet_cloud/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"inputFile\": \"null\"}", 
+            "tool_version": "1.0", 
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+            "user_outputs": [], 
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+            "input_connections": {
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+                    "output_name": "output"
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+                "inputs": {
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+                    "output_name": "skipped"
+                }, 
+                "seq_data|seq_source|ref_file": {
+                    "id": 3, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "label": null, 
+            "name": "Cuffcompare", 
+            "outputs": [
+                {
+                    "name": "transcripts_accuracy", 
+                    "type": "txt"
+                }, 
+                {
+                    "name": "input1_tmap", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "input1_refmap", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "input2_tmap", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "input2_refmap", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "transcripts_tracking", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "transcripts_combined", 
+                    "type": "gtf"
+                }
+            ], 
+            "position": {
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+                "top": 716
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/cuffcompare/cuffcompare/2.2.1.0", 
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+                    "output_name": "outputFile"
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+                    "output_name": "outputFile"
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+            "label": null, 
+            "name": "ClosestBed", 
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+                }
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+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.24.0", 
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+            "uuid": "9313c43f-34a3-4f5d-bb44-544bfe63de1f"
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+        "11": {
+            "annotation": "", 
+            "id": 11, 
+            "input_connections": {
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+                    "id": 9, 
+                    "output_name": "input1_tmap"
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+                "inputFile": {
+                    "id": 10, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "label": null, 
+            "name": "ClosestToStartSite", 
+            "outputs": [
+                {
+                    "name": "outputFile", 
+                    "type": "bed"
+                }
+            ], 
+            "position": {
+                "left": 1823.5, 
+                "top": 461
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/teiso/ClosestToStartSite/1.0", 
+            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"ClassCode\": \"{\\\"cuffcom_tmap\\\": null, \\\"get_class_code\\\": \\\"True\\\", \\\"__current_case__\\\": 1}\", \"inputFile\": \"null\"}", 
+            "tool_version": "1.0", 
+            "type": "tool", 
+            "user_outputs": [], 
+            "uuid": "760d9506-a1a6-4a84-81fa-db67ea91ef53"
+        }
+    }, 
+    "uuid": "ad643964-b679-41d0-a74f-e712a8550c7f"
+}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/TEiso/repository_dependencies.xml	Tue May 24 09:57:57 2016 -0400
@@ -0,0 +1,6 @@
+<repositories description="TEiso worflow1 needed repository">
+	<repository changeset_revision="4eb3c3beb9c7" name="tophat2" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu"/>
+	<repository changeset_revision="a1ea9af8d5f4" name="cufflinks" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu"/>
+	<repository changeset_revision="15d6811e6bf5" name="teiso" owner="urgi-team" toolshed="http://toolshed.g2.bx.psu.edu"/>
+	<repository changeset_revision="f8b7dc21b4ee" name="bedtools" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu"/>
+</repositories>