# HG changeset patch # User bgruening # Date 1414577911 14400 # Node ID c326f1405473df7b8bc77dcfcf2cb8a19b572d34 Uploaded diff -r 000000000000 -r c326f1405473 chemicaltoolbox_library_hole_filling_workflow.ga --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/chemicaltoolbox_library_hole_filling_workflow.ga Wed Oct 29 06:18:31 2014 -0400 @@ -0,0 +1,457 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "", + "format-version": "0.1", + "name": "Library hole-filling", + "steps": { + "0": { + "annotation": "", + "id": 0, + "input_connections": {}, + "inputs": [], + "name": "Online data", + "outputs": [ + { + "name": "output", + "type": "txt" + } + ], + "position": { + "left": 251.5, + "top": 410.5 + }, + "post_job_actions": { + "ChangeDatatypeActionoutput": { + "action_arguments": { + "newtype": "sdf" + }, + "action_type": "ChangeDatatypeAction", + "output_name": "output" + }, + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/chemical_data_sources/ctb_online_data_fetch/0.2", + "tool_state": "{\"__page__\": 0, \"whitelist\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"url_paste\": \"\\\"http://www.drugbank.ca/system/downloads/current/structures/approved.sdf.zip\\\"\"}", + "tool_version": "0.2", + "type": "tool", + "user_outputs": [] + }, + "1": { + "annotation": "", + "id": 1, + "input_connections": {}, + "inputs": [], + "name": "Online data", + "outputs": [ + { + "name": "output", + "type": "txt" + } + ], + "position": { + "left": 250.5, + "top": 836.5 + }, + "post_job_actions": { + "ChangeDatatypeActionoutput": { + "action_arguments": { + "newtype": "sdf" + }, + "action_type": "ChangeDatatypeAction", + "output_name": "output" + }, + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/chemical_data_sources/ctb_online_data_fetch/0.2", + "tool_state": "{\"__page__\": 0, \"whitelist\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"url_paste\": \"\\\"http://www.drugbank.ca/system/downloads/current/structures/experimental.sdf.zip\\\"\"}", + "tool_version": "0.2", + "type": "tool", + "user_outputs": [] + }, + "2": { + "annotation": "", + "id": 2, + "input_connections": { + "infile": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "name": "Change Title", + "outputs": [ + { + "name": "outfile", + "type": "sdf" + } + ], + "position": { + "left": 515.5, + "top": 517.5 + }, + "post_job_actions": { + "HideDatasetActionoutfile": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "outfile" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_change_title/0.0.1", + "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"infile\": \"null\", \"key\": \"\\\"DATABASE_ID\\\"\"}", + "tool_version": "0.0.1", + "type": "tool", + "user_outputs": [] + }, + "3": { + "annotation": "", + "id": 3, + "input_connections": { + "infile": { + "id": 1, + "output_name": "output" + } + }, + "inputs": [], + "name": "Change Title", + "outputs": [ + { + "name": "outfile", + "type": "sdf" + } + ], + "position": { + "left": 517.5, + "top": 955.5 + }, + "post_job_actions": { + "HideDatasetActionoutfile": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "outfile" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_change_title/0.0.1", + "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"infile\": \"null\", \"key\": \"\\\"DATABASE_ID\\\"\"}", + "tool_version": "0.0.1", + "type": "tool", + "user_outputs": [] + }, + "4": { + "annotation": "", + "id": 4, + "input_connections": { + "infile": { + "id": 2, + "output_name": "outfile" + } + }, + "inputs": [], + "name": "Compound Convert", + "outputs": [ + { + "name": "outfile", + "type": "text" + } + ], + "position": { + "left": 761.5, + "top": 391.5 + }, + "post_job_actions": { + "RenameDatasetActionoutfile": { + "action_arguments": { + "newname": "Approved DrugBank set" + }, + "action_type": "RenameDatasetAction", + "output_name": "outfile" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_compound_convert/0.1", + "tool_state": "{\"__page__\": 0, \"dative_bonds\": \"\\\"True\\\"\", \"__rerun_remap_job_id__\": null, \"appendtotitle\": \"\\\"\\\"\", \"remove_h\": \"\\\"False\\\"\", \"oformat\": \"{\\\"can_iso_chi\\\": \\\"True\\\", \\\"can_atomclass_out\\\": \\\"False\\\", \\\"can_rad\\\": \\\"False\\\", \\\"can_exp_h\\\": \\\"False\\\", \\\"oformat_opts_selector\\\": \\\"can\\\", \\\"__current_case__\\\": 10}\", \"ph\": \"\\\"-1.0\\\"\", \"unique\": \"{\\\"unique_opts_selector\\\": \\\"cansmiNS\\\", \\\"__current_case__\\\": 2}\", \"infile\": \"null\"}", + "tool_version": "0.1", + "type": "tool", + "user_outputs": [] + }, + "5": { + "annotation": "", + "id": 5, + "input_connections": { + "infile": { + "id": 3, + "output_name": "outfile" + } + }, + "inputs": [], + "name": "Compound Convert", + "outputs": [ + { + "name": "outfile", + "type": "text" + } + ], + "position": { + "left": 766.5, + "top": 841.5 + }, + "post_job_actions": { + "RenameDatasetActionoutfile": { + "action_arguments": { + "newname": "Experimental DrugBank set" + }, + "action_type": "RenameDatasetAction", + "output_name": "outfile" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_compound_convert/0.1", + "tool_state": "{\"__page__\": 0, \"dative_bonds\": \"\\\"True\\\"\", \"__rerun_remap_job_id__\": null, \"appendtotitle\": \"\\\"\\\"\", \"remove_h\": \"\\\"False\\\"\", \"oformat\": \"{\\\"can_iso_chi\\\": \\\"True\\\", \\\"can_atomclass_out\\\": \\\"False\\\", \\\"can_rad\\\": \\\"False\\\", \\\"can_exp_h\\\": \\\"False\\\", \\\"oformat_opts_selector\\\": \\\"can\\\", \\\"__current_case__\\\": 10}\", \"ph\": \"\\\"-1.0\\\"\", \"unique\": \"{\\\"unique_opts_selector\\\": \\\"cansmiNS\\\", \\\"__current_case__\\\": 2}\", \"infile\": \"null\"}", + "tool_version": "0.1", + "type": "tool", + "user_outputs": [] + }, + "6": { + "annotation": "", + "id": 6, + "input_connections": { + "infile": { + "id": 4, + "output_name": "outfile" + } + }, + "inputs": [], + "name": "Molecules to Fingerprints", + "outputs": [ + { + "name": "outfile", + "type": "fps" + } + ], + "position": { + "left": 1127.5, + "top": 512.5 + }, + "post_job_actions": { + "HideDatasetActionoutfile": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "outfile" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_chemfp_mol2fps/0.2.0", + "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"fp_opts\": \"{\\\"fp_opts_selector\\\": \\\"--substruct\\\", \\\"__current_case__\\\": 9}\", \"infile\": \"null\"}", + "tool_version": "0.2.0", + "type": "tool", + "user_outputs": [] + }, + "7": { + "annotation": "", + "id": 7, + "input_connections": { + "infile": { + "id": 5, + "output_name": "outfile" + } + }, + "inputs": [], + "name": "Molecules to Fingerprints", + "outputs": [ + { + "name": "outfile", + "type": "fps" + } + ], + "position": { + "left": 1141.5, + "top": 796.5 + }, + "post_job_actions": { + "HideDatasetActionoutfile": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "outfile" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_chemfp_mol2fps/0.2.0", + "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"fp_opts\": \"{\\\"fp_opts_selector\\\": \\\"--substruct\\\", \\\"__current_case__\\\": 9}\", \"infile\": \"null\"}", + "tool_version": "0.2.0", + "type": "tool", + "user_outputs": [] + }, + "8": { + "annotation": "", + "id": 8, + "input_connections": { + "method_opts|query_opts|query": { + "id": 7, + "output_name": "outfile" + }, + "method_opts|query_opts|targets": { + "id": 6, + "output_name": "outfile" + } + }, + "inputs": [], + "name": "Similarity Search", + "outputs": [ + { + "name": "outfile", + "type": "tabular" + } + ], + "position": { + "left": 1434.5, + "top": 711.5 + }, + "post_job_actions": { + "HideDatasetActionoutfile": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "outfile" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/simsearch/ctb_simsearch/0.1.1", + "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"method_opts\": \"{\\\"knn\\\": \\\"1\\\", \\\"method_opts_selector\\\": \\\"chemfp\\\", \\\"__current_case__\\\": 0, \\\"query_opts\\\": {\\\"query\\\": null, \\\"query_opts_selector\\\": \\\"normal\\\", \\\"targets\\\": null, \\\"__current_case__\\\": 0}, \\\"threshold\\\": \\\"0.7\\\", \\\"counts\\\": \\\"False\\\"}\"}", + "tool_version": "0.1.1", + "type": "tool", + "user_outputs": [] + }, + "9": { + "annotation": "", + "id": 9, + "input_connections": { + "input": { + "id": 8, + "output_name": "outfile" + } + }, + "inputs": [], + "name": "Filter", + "outputs": [ + { + "name": "out_file1", + "type": "input" + } + ], + "position": { + "left": 1672.5, + "top": 986.5 + }, + "post_job_actions": { + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + } + }, + "tool_errors": null, + "tool_id": "Filter1", + "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"header_lines\": \"\\\"0\\\"\", \"cond\": \"\\\"c1==0\\\"\", \"__page__\": 0}", + "tool_version": "1.1.0", + "type": "tool", + "user_outputs": [] + }, + "10": { + "annotation": "", + "id": 10, + "input_connections": { + "input1": { + "id": 5, + "output_name": "outfile" + }, + "input2": { + "id": 9, + "output_name": "out_file1" + } + }, + "inputs": [], + "name": "Compare two Datasets", + "outputs": [ + { + "name": "out_file1", + "type": "input" + } + ], + "position": { + "left": 1906, + "top": 1168.5 + }, + "post_job_actions": { + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + } + }, + "tool_errors": null, + "tool_id": "comp1", + "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"input1\": \"null\", \"field2\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"2\\\"}\", \"__rerun_remap_job_id__\": null, \"field1\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"2\\\"}\", \"mode\": \"\\\"N\\\"\"}", + "tool_version": "1.0.2", + "type": "tool", + "user_outputs": [] + }, + "11": { + "annotation": "", + "id": 11, + "input_connections": { + "input1": { + "id": 4, + "output_name": "outfile" + }, + "queries_0|input2": { + "id": 10, + "output_name": "out_file1" + } + }, + "inputs": [], + "name": "Concatenate datasets", + "outputs": [ + { + "name": "out_file1", + "type": "input" + } + ], + "position": { + "left": 2084.5, + "top": 492.5 + }, + "post_job_actions": { + "ChangeDatatypeActionout_file1": { + "action_arguments": { + "newtype": "smi" + }, + "action_type": "ChangeDatatypeAction", + "output_name": "out_file1" + }, + "RenameDatasetActionout_file1": { + "action_arguments": { + "newname": "Hole-filled set" + }, + "action_type": "RenameDatasetAction", + "output_name": "out_file1" + } + }, + "tool_errors": null, + "tool_id": "cat1", + "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"queries\": \"[{\\\"input2\\\": null, \\\"__index__\\\": 0}]\"}", + "tool_version": "1.0.0", + "type": "tool", + "user_outputs": [] + } + } +} \ No newline at end of file diff -r 000000000000 -r c326f1405473 readme.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readme.rst Wed Oct 29 06:18:31 2014 -0400 @@ -0,0 +1,42 @@ +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. + + +What it does +============ + +Given one library, it extends all molecules by similar molecules of an other library and thus fill gaps in an automatic manner. + + +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: + +GrĂ¼ning, B. et al. (2014) +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/chemicaltoolbox + diff -r 000000000000 -r c326f1405473 repository_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Wed Oct 29 06:18:31 2014 -0400 @@ -0,0 +1,4 @@ + + + +