{"action":"created","issue":{"url":"https://api.github.com/repos/bgruening/galaxytools/issues/747","repository_url":"https://api.github.com/repos/bgruening/galaxytools","labels_url":"https://api.github.com/repos/bgruening/galaxytools/issues/747/labels{/name}","comments_url":"https://api.github.com/repos/bgruening/galaxytools/issues/747/comments","events_url":"https://api.github.com/repos/bgruening/galaxytools/issues/747/events","html_url":"https://github.com/bgruening/galaxytools/pull/747","id":330330700,"node_id":"MDExOlB1bGxSZXF1ZXN0MTkzMzY2NzE4","number":747,"title":"Diamond update","user":{"login":"bernt-matthias","id":25689525,"node_id":"MDQ6VXNlcjI1Njg5NTI1","avatar_url":"https://avatars1.githubusercontent.com/u/25689525?v=4","gravatar_id":"","url":"https://api.github.com/users/bernt-matthias","html_url":"https://github.com/bernt-matthias","followers_url":"https://api.github.com/users/bernt-matthias/followers","following_url":"https://api.github.com/users/bernt-matthias/following{/other_user}","gists_url":"https://api.github.com/users/bernt-matthias/gists{/gist_id}","starred_url":"https://api.github.com/users/bernt-matthias/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bernt-matthias/subscriptions","organizations_url":"https://api.github.com/users/bernt-matthias/orgs","repos_url":"https://api.github.com/users/bernt-matthias/repos","events_url":"https://api.github.com/users/bernt-matthias/events{/privacy}","received_events_url":"https://api.github.com/users/bernt-matthias/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":9,"created_at":"2018-06-07T15:43:25Z","updated_at":"2018-07-04T23:53:31Z","closed_at":null,"author_association":"CONTRIBUTOR","pull_request":{"url":"https://api.github.com/repos/bgruening/galaxytools/pulls/747","html_url":"https://github.com/bgruening/galaxytools/pull/747","diff_url":"https://github.com/bgruening/galaxytools/pull/747.diff","patch_url":"https://github.com/bgruening/galaxytools/pull/747.patch"},"body":"- [x] update to 0.9.21\r\n- [x] added new parameters (eg taxonomic filtering)\r\n- [x] Should we remove the `--sall*` parameters? According to the pdf manual the -sall... parameters apply for the DAA output only which is not (yet) supported by the wrapper. \r\n  - moved them to the output options where they seem to work\r\n- [x] The different defaults of the gap parameters could be solved by a conditional for the matrix.\r\n  - solution: gap parameters optional (defaults are chosen via substitution matrix)\r\n- [x] more tests?\r\n\r\nNote, appart from the `--min-orf` parameter the tool still ignores all advanced parameters.\r\n\r\nThe modes getseq (Retrieve sequences from a DIAMOND database file) and dbinfo (Print information about a DIAMOND database file) are also not included in the wrapper. \r\n\r\nAny comments? Happy to finish this soon. Will start testing on real data on our instance soon.\r\n\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/bgruening/galaxytools/issues/comments/402573237","html_url":"https://github.com/bgruening/galaxytools/pull/747#issuecomment-402573237","issue_url":"https://api.github.com/repos/bgruening/galaxytools/issues/747","id":402573237,"node_id":"MDEyOklzc3VlQ29tbWVudDQwMjU3MzIzNw==","user":{"login":"bgruening","id":469983,"node_id":"MDQ6VXNlcjQ2OTk4Mw==","avatar_url":"https://avatars2.githubusercontent.com/u/469983?v=4","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},"created_at":"2018-07-04T23:53:31Z","updated_at":"2018-07-04T23:53:31Z","author_association":"OWNER","body":"This one `bg_diamond_view[0]: failed` is failing for me locally. Seems like no output is produced."}}
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