| Next changeset 1:11cda6ec58b0 (2013-09-18) |
|
Commit message:
Uploaded |
|
added:
chemicaltoolbox_merging_chemical_databases_workflow.ga readme.rst repository_dependencies.xml |
| b |
| diff -r 000000000000 -r e1bc8415f875 chemicaltoolbox_merging_chemical_databases_workflow.ga --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/chemicaltoolbox_merging_chemical_databases_workflow.ga Mon Aug 26 07:37:31 2013 -0400 |
| [ |
| b'@@ -0,0 +1,1190 @@\n+{\n+ "a_galaxy_workflow": "true",\n+ "annotation": "Runs the chemicaltoolbox to merge chemical libraries.<br />\\n<br />\\nThis workflow is <a href=\\"https://github.com/bgruening/galaxytools/tree/master/workflows/chemicaltoolbox\\" target=\\"_blank\\">available on the Galaxy Tool Shed</a> with a README file giving more information, and full citation details (Gruening et al. 2013).",\n+ "format-version": "0.1", \n+ "name": "Preparation of a large compound library by merging of chemical databases.",\n+ "steps": {\n+ "0": {\n+ "annotation": "", \n+ "id": 0, \n+ "input_connections": {}, \n+ "inputs": [], \n+ "name": "Online data", \n+ "outputs": [\n+ {\n+ "name": "output", \n+ "type": "txt"\n+ }\n+ ], \n+ "position": {\n+ "left": 291, \n+ "top": 391\n+ }, \n+ "post_job_actions": {\n+ "ChangeDatatypeActionoutput": {\n+ "action_arguments": {\n+ "newtype": "sdf"\n+ }, \n+ "action_type": "ChangeDatatypeAction", \n+ "output_name": "output"\n+ }, \n+ "HideDatasetActionoutput": {\n+ "action_arguments": {}, \n+ "action_type": "HideDatasetAction", \n+ "output_name": "output"\n+ }\n+ }, \n+ "tool_errors": null, \n+ "tool_id": "ctb_online_data_fetch", \n+ "tool_state": "{\\"__page__\\": 0, \\"whitelist\\": \\"\\\\\\"\\\\\\"\\", \\"url_paste\\": \\"\\\\\\"http://www.drugbank.ca/system/downloads/current/structures/all.sdf.zip\\\\\\"\\"}", \n+ "tool_version": "0.2", \n+ "type": "tool", \n+ "user_outputs": []\n+ }, \n+ "1": {\n+ "annotation": "", \n+ "id": 1, \n+ "input_connections": {}, \n+ "inputs": [], \n+ "name": "Online data", \n+ "outputs": [\n+ {\n+ "name": "output", \n+ "type": "txt"\n+ }\n+ ], \n+ "position": {\n+ "left": 304, \n+ "top": 733\n+ }, \n+ "post_job_actions": {\n+ "ChangeDatatypeActionoutput": {\n+ "action_arguments": {\n+ "newtype": "tabular"\n+ }, \n+ "action_type": "ChangeDatatypeAction", \n+ "output_name": "output"\n+ }, \n+ "HideDatasetActionoutput": {\n+ "action_arguments": {}, \n+ "action_type": "HideDatasetAction", \n+ "output_name": "output"\n+ }\n+ }, \n+ "tool_errors": null, \n+ "tool_id": "ctb_online_data_fetch", \n+ "tool_state": "{\\"__page__\\": 0, \\"whitelist\\": \\"\\\\\\"\\\\\\"\\", \\"url_paste\\": \\"\\\\\\"http://zinc.docking.org/db/bysubset/6/6_p0.smi.gz\\\\\\\\nhttp://zinc.docking.org/db/bysubset/46/46_p0.smi.gz\\\\\\"\\"}", \n+ "tool_version": "0.2", \n+ "type": "tool", \n+ "user_outputs": []\n+ }, \n+ "2": {\n+ "annotation": "", \n+ "id": 2, \n+ "input_connections": {}, \n+ "inputs": [], \n+ "name": "Online data", \n+ "outputs": [\n+ {\n+ "name": "output", \n+ "type": "txt"\n+ }\n+ ], \n+ "position": {\n+ "left": 305, \n+ "top": 1048\n+ }, \n+ "post_job_actions": {\n+ "ChangeDatatypeActionoutput": {\n+ "action_arguments": {\n+ "newtype": "sdf"\n+ }, \n+ "action_type": "ChangeDatatypeAction", \n+ '..b' {\n+ "action_arguments": {}, \n+ "action_type": "HideDatasetAction", \n+ "output_name": "out_file1"\n+ }\n+ }, \n+ "tool_errors": null, \n+ "tool_id": "Grep1", \n+ "tool_state": "{\\"__page__\\": 0, \\"input\\": \\"null\\", \\"invert\\": \\"\\\\\\"true\\\\\\"\\", \\"pattern\\": \\"\\\\\\"\\\\\\\\\\\\\\\\*\\\\\\"\\"}", \n+ "tool_version": "1.0.1", \n+ "type": "tool", \n+ "user_outputs": []\n+ }, \n+ "28": {\n+ "annotation": "", \n+ "id": 28, \n+ "input_connections": {\n+ "input": {\n+ "id": 27, \n+ "output_name": "out_file1"\n+ }\n+ }, \n+ "inputs": [], \n+ "name": "Unique", \n+ "outputs": [\n+ {\n+ "name": "outfile", \n+ "type": "input"\n+ }\n+ ], \n+ "position": {\n+ "left": 2444, \n+ "top": 678\n+ }, \n+ "post_job_actions": {\n+ "ChangeDatatypeActionoutfile": {\n+ "action_arguments": {\n+ "newtype": "tabular"\n+ }, \n+ "action_type": "ChangeDatatypeAction", \n+ "output_name": "outfile"\n+ }, \n+ "RenameDatasetActionoutfile": {\n+ "action_arguments": {\n+ "newname": "Filtered merged libraries"\n+ }, \n+ "action_type": "RenameDatasetAction", \n+ "output_name": "outfile"\n+ }\n+ }, \n+ "tool_errors": null, \n+ "tool_id": "bg_uniq", \n+ "tool_state": "{\\"adv_opts\\": \\"{\\\\\\"adv_opts_selector\\\\\\": \\\\\\"basic\\\\\\", \\\\\\"__current_case__\\\\\\": 0}\\", \\"input\\": \\"null\\", \\"ignore_case\\": \\"\\\\\\"False\\\\\\"\\", \\"is_numeric\\": \\"\\\\\\"False\\\\\\"\\", \\"__page__\\": 0}", \n+ "tool_version": "0.3", \n+ "type": "tool", \n+ "user_outputs": []\n+ }, \n+ "29": {\n+ "annotation": "", \n+ "id": 29, \n+ "input_connections": {\n+ "input": {\n+ "id": 28, \n+ "output_name": "outfile"\n+ }\n+ }, \n+ "inputs": [], \n+ "name": "Unique", \n+ "outputs": [\n+ {\n+ "name": "outfile", \n+ "type": "input"\n+ }\n+ ], \n+ "position": {\n+ "left": 2444, \n+ "top": 562\n+ }, \n+ "post_job_actions": {\n+ "ChangeDatatypeActionoutfile": {\n+ "action_arguments": {\n+ "newtype": "smi"\n+ }, \n+ "action_type": "ChangeDatatypeAction", \n+ "output_name": "outfile"\n+ }, \n+ "RenameDatasetActionoutfile": {\n+ "action_arguments": {\n+ "newname": "Non-redundant filtered merged libraries"\n+ }, \n+ "action_type": "RenameDatasetAction", \n+ "output_name": "outfile"\n+ }\n+ }, \n+ "tool_errors": null, \n+ "tool_id": "bg_uniq", \n+ "tool_state": "{\\"adv_opts\\": \\"{\\\\\\"column_end\\\\\\": {\\\\\\"__class__\\\\\\": \\\\\\"UnvalidatedValue\\\\\\", \\\\\\"value\\\\\\": \\\\\\"1\\\\\\"}, \\\\\\"column_start\\\\\\": {\\\\\\"__class__\\\\\\": \\\\\\"UnvalidatedValue\\\\\\", \\\\\\"value\\\\\\": \\\\\\"1\\\\\\"}, \\\\\\"adv_opts_selector\\\\\\": \\\\\\"advanced\\\\\\", \\\\\\"__current_case__\\\\\\": 1}\\", \\"input\\": \\"null\\", \\"ignore_case\\": \\"\\\\\\"False\\\\\\"\\", \\"is_numeric\\": \\"\\\\\\"False\\\\\\"\\", \\"__page__\\": 0}", \n+ "tool_version": "0.3", \n+ "type": "tool", \n+ "user_outputs": []\n+ }\n+ }\n+}\n' |
| b |
| diff -r 000000000000 -r e1bc8415f875 readme.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readme.rst Mon Aug 26 07:37:31 2013 -0400 |
| b |
| @@ -0,0 +1,44 @@ +This package is a Galaxy workflow for merging of chemical libraries using the chemicaltoolbox. + +To learn more about the chemicaltoolbox and all the integrated tools, +please have a look at https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox. + + +Sample Data +=========== + +The workflow will fetch the sample data from online resources, like PubChem, DrugBank. + + +Citation +======== + +If you use this workflow directly, or a derivative of it, or the associated +chemicaltoolbox wrappers for Galaxy, in work leading to a scientific publication, +please cite: + +Grüning, B. et al. (2013) +ChemicalToolBoX, a new Galaxy for cheminformatics (Submitted). + + +Availability +============ + +This workflow is available on the main Galaxy Tool Shed: + + http://toolshed.g2.bx.psu.edu/view/bgruening/chemicaltoolbox_merging_chemical_databases_workflow + +Development is being done on github: + +https://github.com/bgruening/galaxytools/workflows/chemicaltoolbox + + +Dependencies +============ + +These dependencies should be resolved automatically via the Galaxy Tool Shed: + +* http://toolshed.g2.bx.psu.edu/view/bgruening/unique +* http://toolshed.g2.bx.psu.edu/view/bjoern-gruening/sed_wrapper +* http://toolshed.g2.bx.psu.edu/view/bgruening/chemicaltoolbox + |
| b |
| diff -r 000000000000 -r e1bc8415f875 repository_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Mon Aug 26 07:37:31 2013 -0400 |
| b |
| @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<repositories description="This requires the unique and sed wrapper, as well as the chemicaltoolbox suite."> + <repository changeset_revision="30ae0e5218b4" name="chemicaltoolbox" owner="bgruening" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="4382d742830f" name="unique" owner="bgruening" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="e850a63e5aed" name="sed_wrapper" owner="bjoern-gruening" toolshed="http://toolshed.g2.bx.psu.edu" /> +</repositories> |