Mercurial > repos > bgruening > chemicaltoolbox_merging_chemical_databases_workflow

changeset 4:87bf73b6578e draft

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Uploaded
author bgruening
date Sun, 27 Oct 2013 12:57:21 -0400
parents 3376374ca458
children fdabd3833502
files chemicaltoolbox_merging_chemical_databases_workflow.ga
diffstat 1 files changed, 117 insertions(+), 117 deletions(-) [+]
line wrap: on
line diff
--- a/chemicaltoolbox_merging_chemical_databases_workflow.ga	Mon Oct 07 12:24:53 2013 -0400
+++ b/chemicaltoolbox_merging_chemical_databases_workflow.ga	Sun Oct 27 12:57:21 2013 -0400
@@ -1,8 +1,8 @@
 {
-    "a_galaxy_workflow": "true",
-    "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).",
+    "a_galaxy_workflow": "true", 
+    "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).", 
     "format-version": "0.1", 
-    "name": "Preparation of a large compound library by merging of chemical databases.",
+    "name": "Preparation of a large compound library by merging of chemical databases.", 
     "steps": {
         "0": {
             "annotation": "", 
@@ -17,8 +17,8 @@
                 }
             ], 
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@@ -35,8 +35,8 @@
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+            "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/all.sdf.zip\\\"\"}", 
             "tool_version": "0.2", 
             "type": "tool", 
             "user_outputs": []
@@ -54,8 +54,8 @@
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@@ -72,8 +72,8 @@
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-            "tool_id": "ctb_online_data_fetch", 
-            "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\\\"\"}", 
+            "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://zinc.docking.org/db/bysubset/6/6_p0.smi.gz\\\\nhttp://zinc.docking.org/db/bysubset/46/46_p0.smi.gz\\\"\"}", 
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             "type": "tool", 
             "user_outputs": []
@@ -91,8 +91,8 @@
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@@ -109,8 +109,8 @@
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-            "tool_id": "ctb_online_data_fetch", 
-            "tool_state": "{\"__page__\": 0, \"whitelist\": \"\\\"\\\"\", \"url_paste\": \"\\\"ftp://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_17/chembl_17.sdf.gz\\\"\"}", 
+            "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\": \"\\\"ftp://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_16/chembl_16.sdf.gz\\\"\"}", 
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@@ -128,8 +128,8 @@
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@@ -146,8 +146,8 @@
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-            "tool_state": "{\"__page__\": 0, \"infile\": \"null\"}", 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/chemical_data_sources/ctb_pubchem_download_as_smiles/1.0.0", 
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@@ -170,8 +170,8 @@
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@@ -181,8 +181,8 @@
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-            "tool_state": "{\"__page__\": 0, \"infile\": \"null\", \"key\": \"\\\"DRUGBANK_ID\\\"\"}", 
+            "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\": \"\\\"DRUGBANK_ID\\\"\"}", 
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@@ -205,8 +205,8 @@
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@@ -224,7 +224,7 @@
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@@ -247,8 +247,8 @@
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@@ -258,14 +258,14 @@
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-            "tool_state": "{\"__page__\": 0, \"infile\": \"null\", \"key\": \"\\\"chembl_id\\\"\"}", 
+            "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\": \"\\\"chembl_id\\\"\"}", 
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         "7": {
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+            "annotation": "The \"c1.find('N=[N+]=NC1=')\" filter step can be omitted as soon as the openbabel bug #900 (https://sourceforge.net/p/openbabel/bugs/900/) is fixed.", 
             "id": 7, 
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@@ -282,8 +282,8 @@
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@@ -324,8 +324,8 @@
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