| Previous changeset 2:bfd4dc7f50c5 (2016-05-25) |
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Commit message:
Uploaded |
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added:
Teiso-workflow-final/Galaxy-Workflow-TEiso_workflow.ga Teiso-workflow-final/repository_dependencies.xml |
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removed:
TEiso/Galaxy-Workflow-TEiso_workflow.ga TEiso/repository_dependencies.xml |
| b |
| diff -r bfd4dc7f50c5 -r f8221945b946 TEiso/Galaxy-Workflow-TEiso_workflow.ga --- a/TEiso/Galaxy-Workflow-TEiso_workflow.ga Wed May 25 10:28:25 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,439 +0,0 @@\n-{\n- "a_galaxy_workflow": "true", \n- "annotation": "", \n- "format-version": "0.1", \n- "name": "TEiso_workflow", \n- "steps": {\n- "0": {\n- "annotation": "", \n- "id": 0, \n- "input_connections": {}, \n- "inputs": [\n- {\n- "description": "", \n- "name": "Input Dataset"\n- }\n- ], \n- "label": null, \n- "name": "Input dataset", \n- "outputs": [], \n- "position": {\n- "left": 200, \n- "top": 200\n- }, \n- "tool_errors": null, \n- "tool_id": null, \n- "tool_state": "{\\"name\\": \\"Input Dataset\\"}", \n- "tool_version": null, \n- "type": "data_input", \n- "user_outputs": [], \n- "uuid": "a910dd6c-d6e5-4d3a-b3cd-3624c8c509b6"\n- }, \n- "1": {\n- "annotation": "", \n- "id": 1, \n- "input_connections": {}, \n- "inputs": [\n- {\n- "description": "", \n- "name": "Input Dataset"\n- }\n- ], \n- "label": null, \n- "name": "Input dataset", \n- "outputs": [], \n- "position": {\n- "left": 200, \n- "top": 285\n- }, \n- "tool_errors": null, \n- "tool_id": null, \n- "tool_state": "{\\"name\\": \\"Input Dataset\\"}", \n- "tool_version": null, \n- "type": "data_input", \n- "user_outputs": [], \n- "uuid": "98cee5d8-d791-4f91-8f29-ccc98003e392"\n- }, \n- "2": {\n- "annotation": "", \n- "id": 2, \n- "input_connections": {}, \n- "inputs": [\n- {\n- "description": "", \n- "name": "Input Dataset"\n- }\n- ], \n- "label": null, \n- "name": "Input dataset", \n- "outputs": [], \n- "position": {\n- "left": 200, \n- "top": 370\n- }, \n- "tool_errors": null, \n- "tool_id": null, \n- "tool_state": "{\\"name\\": \\"Input Dataset\\"}", \n- "tool_version": null, \n- "type": "data_input", \n- "user_outputs": [], \n- "uuid": "1fc62c7e-fbb8-48b4-89da-18c629838b7c"\n- }, \n- "3": {\n- "annotation": "", \n- "id": 3, \n- "input_connections": {}, \n- "inputs": [\n- {\n- "description": "", \n- "name": "Input Dataset"\n- }\n- ], \n- "label": null, \n- "name": "Input dataset", \n- "outputs": [], \n- "position": {\n- "left": 200, \n- "top": 455\n- }, \n- "tool_errors": null, \n- "tool_id": null, \n- "tool_state": "{\\"name\\": \\"Input Dataset\\"}", \n- "tool_version": null, \n- "type": "data_input", \n- "user_outputs": [], \n- "uuid": "49264998-41ff-4776-81f2-06e3fbaac133"\n- }, \n- "4": {\n- "annotation": "", \n- "id": 4, \n- "input_connections": {}, \n- "inputs": [\n- {\n- "description": "", \n- "name": "Input Dataset"\n- }\n- ], \n- "label": null, \n- "name": "Input dataset", \n- "outputs": [], \n- "position": {\n- "left": 200, \n- "top": 540\n- }, \n- "tool_errors": null, \n- "tool_id": null, \n- "tool_state": "{\\"name\\": \\"Input Dataset\\"}", \n- "tool_version": null, \n- "type": "data_input", \n- "user_outputs": [], \n- '..b'rce\\\\\\": {\\\\\\"index_source\\\\\\": \\\\\\"history\\\\\\", \\\\\\"ref_file\\\\\\": null, \\\\\\"__current_case__\\\\\\": 1}, \\\\\\"__current_case__\\\\\\": 1}\\", \\"inputs\\": \\"null\\", \\"max_dist_group\\": \\"\\\\\\"100\\\\\\"\\", \\"__page__\\": 0, \\"discard_intron_redundant_transfrags\\": \\"\\\\\\"False\\\\\\"\\", \\"max_dist_exon\\": \\"\\\\\\"100\\\\\\"\\", \\"__rerun_remap_job_id__\\": null, \\"additional_inputs\\": \\"[]\\", \\"discard_single_exon\\": \\"\\\\\\"\\\\\\"\\", \\"chromInfo\\": \\"\\\\\\"/home/repet_cloud/galaxy/tool-data/shared/ucsc/chrom/?.len\\\\\\"\\", \\"annotation\\": \\"{\\\\\\"reference_annotation\\\\\\": null, \\\\\\"use_ref_annotation\\\\\\": \\\\\\"Yes\\\\\\", \\\\\\"ignore_nonoverlapping_reference\\\\\\": \\\\\\"False\\\\\\", \\\\\\"__current_case__\\\\\\": 0, \\\\\\"ignore_nonoverlapping_transfrags\\\\\\": \\\\\\"False\\\\\\"}\\"}", \n- "tool_version": "2.2.1.0", \n- "type": "tool", \n- "user_outputs": [], \n- "uuid": "4e1afb8e-9c8b-431f-b25f-75e19e3e95f2"\n- }, \n- "10": {\n- "annotation": "", \n- "id": 10, \n- "input_connections": {\n- "inputA": {\n- "id": 8, \n- "output_name": "outputFile"\n- }, \n- "inputB": {\n- "id": 6, \n- "output_name": "outputFile"\n- }\n- }, \n- "inputs": [], \n- "label": null, \n- "name": "ClosestBed", \n- "outputs": [\n- {\n- "name": "output", \n- "type": "bed"\n- }\n- ], \n- "position": {\n- "left": 1436, \n- "top": 303\n- }, \n- "post_job_actions": {}, \n- "tool_errors": null, \n- "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.24.0", \n- "tool_state": "{\\"__page__\\": 0, \\"addition\\": \\"\\\\\\"True\\\\\\"\\", \\"k\\": \\"\\\\\\"1\\\\\\"\\", \\"inputB\\": \\"null\\", \\"mdb\\": \\"\\\\\\"each\\\\\\"\\", \\"inputA\\": \\"null\\", \\"io\\": \\"\\\\\\"False\\\\\\"\\", \\"ties\\": \\"\\\\\\"all\\\\\\"\\", \\"addition2\\": \\"{\\\\\\"fu\\\\\\": \\\\\\"False\\\\\\", \\\\\\"iu\\\\\\": \\\\\\"False\\\\\\", \\\\\\"fd\\\\\\": \\\\\\"False\\\\\\", \\\\\\"__current_case__\\\\\\": 2, \\\\\\"addition2_select\\\\\\": \\\\\\"a\\\\\\", \\\\\\"id\\\\\\": \\\\\\"False\\\\\\"}\\", \\"chromInfo\\": \\"\\\\\\"/home/repet_cloud/galaxy/tool-data/shared/ucsc/chrom/?.len\\\\\\"\\", \\"__rerun_remap_job_id__\\": null, \\"strand\\": \\"\\\\\\"\\\\\\"\\"}", \n- "tool_version": "2.24.0", \n- "type": "tool", \n- "user_outputs": [], \n- "uuid": "9313c43f-34a3-4f5d-bb44-544bfe63de1f"\n- }, \n- "11": {\n- "annotation": "", \n- "id": 11, \n- "input_connections": {\n- "ClassCode|cuffcom_tmap": {\n- "id": 9, \n- "output_name": "input1_tmap"\n- }, \n- "inputFile": {\n- "id": 10, \n- "output_name": "output"\n- }\n- }, \n- "inputs": [], \n- "label": null, \n- "name": "ClosestToStartSite", \n- "outputs": [\n- {\n- "name": "outputFile", \n- "type": "bed"\n- }\n- ], \n- "position": {\n- "left": 1823.5, \n- "top": 461\n- }, \n- "post_job_actions": {}, \n- "tool_errors": null, \n- "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/teiso/ClosestToStartSite/1.0", \n- "tool_state": "{\\"__page__\\": 0, \\"__rerun_remap_job_id__\\": null, \\"ClassCode\\": \\"{\\\\\\"cuffcom_tmap\\\\\\": null, \\\\\\"get_class_code\\\\\\": \\\\\\"True\\\\\\", \\\\\\"__current_case__\\\\\\": 1}\\", \\"inputFile\\": \\"null\\"}", \n- "tool_version": "1.0", \n- "type": "tool", \n- "user_outputs": [], \n- "uuid": "760d9506-a1a6-4a84-81fa-db67ea91ef53"\n- }\n- }, \n- "uuid": "ad643964-b679-41d0-a74f-e712a8550c7f"\n-}\n\\ No newline at end of file\n' |
| b |
| diff -r bfd4dc7f50c5 -r f8221945b946 TEiso/repository_dependencies.xml --- a/TEiso/repository_dependencies.xml Wed May 25 10:28:25 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,7 +0,0 @@ -<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="b77178f66fc3" name="cuffcompare" 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> |
| b |
| diff -r bfd4dc7f50c5 -r f8221945b946 Teiso-workflow-final/Galaxy-Workflow-TEiso_workflow.ga --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Teiso-workflow-final/Galaxy-Workflow-TEiso_workflow.ga Thu May 26 09:27:07 2016 -0400 |
| [ |
| b'@@ -0,0 +1,439 @@\n+{\n+ "a_galaxy_workflow": "true", \n+ "annotation": "", \n+ "format-version": "0.1", \n+ "name": "TEiso_workflow", \n+ "steps": {\n+ "0": {\n+ "annotation": "", \n+ "id": 0, \n+ "input_connections": {}, \n+ "inputs": [\n+ {\n+ "description": "", \n+ "name": "Input Dataset"\n+ }\n+ ], \n+ "label": null, \n+ "name": "Input dataset", \n+ "outputs": [], \n+ "position": {\n+ "left": 200, \n+ "top": 200\n+ }, \n+ "tool_errors": null, \n+ "tool_id": null, \n+ "tool_state": "{\\"name\\": \\"Input Dataset\\"}", \n+ "tool_version": null, \n+ "type": "data_input", \n+ "user_outputs": [], \n+ "uuid": "a910dd6c-d6e5-4d3a-b3cd-3624c8c509b6"\n+ }, \n+ "1": {\n+ "annotation": "", \n+ "id": 1, \n+ "input_connections": {}, \n+ "inputs": [\n+ {\n+ "description": "", \n+ "name": "Input Dataset"\n+ }\n+ ], \n+ "label": null, \n+ "name": "Input dataset", \n+ "outputs": [], \n+ "position": {\n+ "left": 200, \n+ "top": 285\n+ }, \n+ "tool_errors": null, \n+ "tool_id": null, \n+ 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\n+ "tool_id": null, \n+ "tool_state": "{\\"name\\": \\"Input Dataset\\"}", \n+ "tool_version": null, \n+ "type": "data_input", \n+ "user_outputs": [], \n+ "uuid": "49264998-41ff-4776-81f2-06e3fbaac133"\n+ }, \n+ "4": {\n+ "annotation": "", \n+ "id": 4, \n+ "input_connections": {}, \n+ "inputs": [\n+ {\n+ "description": "", \n+ "name": "Input Dataset"\n+ }\n+ ], \n+ "label": null, \n+ "name": "Input dataset", \n+ "outputs": [], \n+ "position": {\n+ "left": 200, \n+ "top": 540\n+ }, \n+ "tool_errors": null, \n+ "tool_id": null, \n+ "tool_state": "{\\"name\\": \\"Input Dataset\\"}", \n+ "tool_version": null, \n+ "type": "data_input", \n+ "user_outputs": [], \n+ '..b'rce\\\\\\": {\\\\\\"index_source\\\\\\": \\\\\\"history\\\\\\", \\\\\\"ref_file\\\\\\": null, \\\\\\"__current_case__\\\\\\": 1}, \\\\\\"__current_case__\\\\\\": 1}\\", \\"inputs\\": \\"null\\", \\"max_dist_group\\": \\"\\\\\\"100\\\\\\"\\", \\"__page__\\": 0, \\"discard_intron_redundant_transfrags\\": 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"2.24.0", \n+ "type": "tool", \n+ "user_outputs": [], \n+ "uuid": "9313c43f-34a3-4f5d-bb44-544bfe63de1f"\n+ }, \n+ "11": {\n+ "annotation": "", \n+ "id": 11, \n+ "input_connections": {\n+ "ClassCode|cuffcom_tmap": {\n+ "id": 9, \n+ "output_name": "input1_tmap"\n+ }, \n+ "inputFile": {\n+ "id": 10, \n+ "output_name": "output"\n+ }\n+ }, \n+ "inputs": [], \n+ "label": null, \n+ "name": "ClosestToStartSite", \n+ "outputs": [\n+ {\n+ "name": "outputFile", \n+ "type": "bed"\n+ }\n+ ], \n+ "position": {\n+ "left": 1823.5, \n+ "top": 461\n+ }, \n+ "post_job_actions": {}, \n+ "tool_errors": null, \n+ "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/teiso/ClosestToStartSite/1.0", \n+ "tool_state": "{\\"__page__\\": 0, \\"__rerun_remap_job_id__\\": null, \\"ClassCode\\": \\"{\\\\\\"cuffcom_tmap\\\\\\": null, \\\\\\"get_class_code\\\\\\": \\\\\\"True\\\\\\", \\\\\\"__current_case__\\\\\\": 1}\\", \\"inputFile\\": \\"null\\"}", \n+ "tool_version": "1.0", \n+ "type": "tool", \n+ "user_outputs": [], \n+ "uuid": "760d9506-a1a6-4a84-81fa-db67ea91ef53"\n+ }\n+ }, \n+ "uuid": "ad643964-b679-41d0-a74f-e712a8550c7f"\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r bfd4dc7f50c5 -r f8221945b946 Teiso-workflow-final/repository_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Teiso-workflow-final/repository_dependencies.xml Thu May 26 09:27:07 2016 -0400 |
| b |
| @@ -0,0 +1,7 @@ +<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="b77178f66fc3" name="cuffcompare" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu"/> + <repository changeset_revision="775f119b9ac2" 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> |