{"action":"created","issue":{"url":"https://api.github.com/repos/galaxyproteomics/tools-galaxyp/issues/312","repository_url":"https://api.github.com/repos/galaxyproteomics/tools-galaxyp","labels_url":"https://api.github.com/repos/galaxyproteomics/tools-galaxyp/issues/312/labels{/name}","comments_url":"https://api.github.com/repos/galaxyproteomics/tools-galaxyp/issues/312/comments","events_url":"https://api.github.com/repos/galaxyproteomics/tools-galaxyp/issues/312/events","html_url":"https://github.com/galaxyproteomics/tools-galaxyp/pull/312","id":358671099,"node_id":"MDExOlB1bGxSZXF1ZXN0MjE0MzUwOTEw","number":312,"title":"searchgui home fix and enzyme list 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":3,"created_at":"2018-09-10T15:17:51Z","updated_at":"2018-09-15T11:48:49Z","closed_at":null,"author_association":"CONTRIBUTOR","pull_request":{"url":"https://api.github.com/repos/galaxyproteomics/tools-galaxyp/pulls/312","html_url":"https://github.com/galaxyproteomics/tools-galaxyp/pull/312","diff_url":"https://github.com/galaxyproteomics/tools-galaxyp/pull/312.diff","patch_url":"https://github.com/galaxyproteomics/tools-galaxyp/pull/312.patch"},"body":"- fixes https://github.com/galaxyproteomics/tools-galaxyp/issues/293\r\n- removes enzymes that are not supported anymore. \r\n- adds OOM regex checks to stdio\r\n- removed unnecessary default enzyme (since there was a typo in the command block the option never worked anyway, so we can savely remove it)\r\n\r\nPing @CarlosHorro, @hbarsnes. Thanks for your help .. could you have a look?\r\n\r\nThe second part of the PR solves the problem described below: \r\n\r\nI noticed that many of the parameters to -enzyme parameter of IdentificationParametersCLI do not work at the moment, e.g. \"Trypsin, no P rule\". I guess the options are wrong in some cases, \"Trypsin (no P rule)\" seems to work. \r\n\r\nThe command line help mentions:\r\n- EnzymesCLI, but I could not find it. \r\n- the possibility give a comma separated list of enzymes which does not work if there are commas in the enzyme names\r\n- also the example \"Trypsin, Glu-C\" does not work .. actually gives an exception\r\n\r\nA fixed the one enzyme that our users interested in at the moment. "},"comment":{"url":"https://api.github.com/repos/galaxyproteomics/tools-galaxyp/issues/comments/421556899","html_url":"https://github.com/galaxyproteomics/tools-galaxyp/pull/312#issuecomment-421556899","issue_url":"https://api.github.com/repos/galaxyproteomics/tools-galaxyp/issues/312","id":421556899,"node_id":"MDEyOklzc3VlQ29tbWVudDQyMTU1Njg5OQ==","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},"created_at":"2018-09-15T11:48:49Z","updated_at":"2018-09-15T11:48:49Z","author_association":"CONTRIBUTOR","body":"wondering why the wrong output name did work... I tested and noticed that any name con be used. Is this because it's a single output? "}}
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