{"action":"created","comment":{"url":"https://api.github.com/repos/bgruening/galaxytools/pulls/comments/65578573","id":65578573,"diff_hunk":"@@ -0,0 +1,92 @@\n+<tool id=\"prepare_receptor\" name=\"Prepare receptor\" version=\"0.1.0\">\n+    <description>- Tool to prepare receptor for Autodock Vina</description>\n+    <requirements>\n+        <requirement type=\"package\" version=\"1.5.6\">mgltools</requirement>\n+    </requirements>\n+    <stdio>\n+        <exit_code range=\"1\" />\n+    </stdio>\n+    <command><![CDATA[\n+        prepare_receptor4.py -r \"$receptor\" -o \"$file_output\" -v -U nphs_lps -A hydrogens\n+    ]]></command>\n+    <inputs>\n+        <param type=\"data\" name=\"receptor\" format=\"pdb\" label=\"Receptor: \" help=\"Select a pdb file.\" />\n+    </inputs>\n+    <outputs>\n+        <data name=\"file_output\" format=\"pdbqt\" label=\"#echo os.path.splitext (str($receptor.name))[0]#.pdbqt\" />","path":"chemicaltoolbox/autodock_vina/prepare_receptor/prepare_receptor.xml","position":16,"original_position":16,"commit_id":"008f0c56d7655c038564d43783a5e144720761c8","original_commit_id":"008f0c56d7655c038564d43783a5e144720761c8","user":{"login":"bgruening","id":469983,"avatar_url":"https://avatars.githubusercontent.com/u/469983?v=3","gravatar_id":"","url":"https://api.github.com/users/bgruening","html_url":"https://github.com/bgruening","followers_url":"https://api.github.com/users/bgruening/followers","following_url":"https://api.github.com/users/bgruening/following{/other_user}","gists_url":"https://api.github.com/users/bgruening/gists{/gist_id}","starred_url":"https://api.github.com/users/bgruening/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bgruening/subscriptions","organizations_url":"https://api.github.com/users/bgruening/orgs","repos_url":"https://api.github.com/users/bgruening/repos","events_url":"https://api.github.com/users/bgruening/events{/privacy}","received_events_url":"https://api.github.com/users/bgruening/received_events","type":"User","site_admin":false},"body":"This somehow assumes that you input is labeld ****.pdb isn't it?\r\nI don't think this will be often the case. I would take the standard Galaxy label.","created_at":"2016-06-02T17:01:36Z","updated_at":"2016-06-02T17:01:36Z","html_url":"https://github.com/bgruening/galaxytools/pull/310#discussion_r65578573","pull_request_url":"https://api.github.com/repos/bgruening/galaxytools/pulls/310","_links":{"self":{"href":"https://api.github.com/repos/bgruening/galaxytools/pulls/comments/65578573"},"html":{"href":"https://github.com/bgruening/galaxytools/pull/310#discussion_r65578573"},"pull_request":{"href":"https://api.github.com/repos/bgruening/galaxytools/pulls/310"}}},"pull_request":{"url":"https://api.github.com/repos/bgruening/galaxytools/pulls/310","id":62864252,"html_url":"https://github.com/bgruening/galaxytools/pull/310","diff_url":"https://github.com/bgruening/galaxytools/pull/310.diff","patch_url":"https://github.com/bgruening/galaxytools/pull/310.patch","issue_url":"https://api.github.com/repos/bgruening/galaxytools/issues/310","number":310,"state":"open","locked":false,"title":"Autodock vina tools","user":{"login":"leobiscassi","id":1977418,"avatar_url":"https://avatars.githubusercontent.com/u/1977418?v=3","gravatar_id":"","url":"https://api.github.com/users/leobiscassi","html_url":"https://github.com/leobiscassi","followers_url":"https://api.github.com/users/leobiscassi/followers","following_url":"https://api.github.com/users/leobiscassi/following{/other_user}","gists_url":"https://api.github.com/users/leobiscassi/gists{/gist_id}","starred_url":"https://api.github.com/users/leobiscassi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/leobiscassi/subscriptions","organizations_url":"https://api.github.com/users/leobiscassi/orgs","repos_url":"https://api.github.com/users/leobiscassi/repos","events_url":"https://api.github.com/users/leobiscassi/events{/privacy}","received_events_url":"https://api.github.com/users/leobiscassi/received_events","type":"User","site_admin":false},"body":"Hi @bgruening, I added my tools for docking protein-compounds according this thread [1] and this trello card [2].\r\nIt was told in [1], the docking tool not pass in planemo functional tests because the content of example output file isn't the same that output file, I need help with this. I tried install tool dependencies in test tool shed, but this was not totally validated.\r\nI will be grateful if you can assist me with the functional tests on the docking tool and the final validation of the tool dependencies.\r\n\r\n[1] [http://dev.list.galaxyproject.org/Galaxy-tools-for-docking-protein-compounds-td4668604.html](url)\r\n[2] [https://trello.com/c/2eIu6SBa](url)\r\n\r\nBest regards,\r\nLeo 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