{"action":"created","issue":{"url":"https://api.github.com/repos/smith-chem-wisc/MetaMorpheus/issues/1277","repository_url":"https://api.github.com/repos/smith-chem-wisc/MetaMorpheus","labels_url":"https://api.github.com/repos/smith-chem-wisc/MetaMorpheus/issues/1277/labels{/name}","comments_url":"https://api.github.com/repos/smith-chem-wisc/MetaMorpheus/issues/1277/comments","events_url":"https://api.github.com/repos/smith-chem-wisc/MetaMorpheus/issues/1277/events","html_url":"https://github.com/smith-chem-wisc/MetaMorpheus/issues/1277","id":339834274,"node_id":"MDU6SXNzdWUzMzk4MzQyNzQ=","number":1277,"title":"File names in command line","user":{"login":"ncarrut","id":7575597,"node_id":"MDQ6VXNlcjc1NzU1OTc=","avatar_url":"https://avatars2.githubusercontent.com/u/7575597?v=4","gravatar_id":"","url":"https://api.github.com/users/ncarrut","html_url":"https://github.com/ncarrut","followers_url":"https://api.github.com/users/ncarrut/followers","following_url":"https://api.github.com/users/ncarrut/following{/other_user}","gists_url":"https://api.github.com/users/ncarrut/gists{/gist_id}","starred_url":"https://api.github.com/users/ncarrut/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ncarrut/subscriptions","organizations_url":"https://api.github.com/users/ncarrut/orgs","repos_url":"https://api.github.com/users/ncarrut/repos","events_url":"https://api.github.com/users/ncarrut/events{/privacy}","received_events_url":"https://api.github.com/users/ncarrut/received_events","type":"User","site_admin":false},"labels":[{"id":659953902,"node_id":"MDU6TGFiZWw2NTk5NTM5MDI=","url":"https://api.github.com/repos/smith-chem-wisc/MetaMorpheus/labels/Question%20(support)","name":"Question (support)","color":"ec5afc","default":false}],"state":"open","locked":false,"assignee":{"login":"ianhirsch","id":39777768,"node_id":"MDQ6VXNlcjM5Nzc3NzY4","avatar_url":"https://avatars2.githubusercontent.com/u/39777768?v=4","gravatar_id":"","url":"https://api.github.com/users/ianhirsch","html_url":"https://github.com/ianhirsch","followers_url":"https://api.github.com/users/ianhirsch/followers","following_url":"https://api.github.com/users/ianhirsch/following{/other_user}","gists_url":"https://api.github.com/users/ianhirsch/gists{/gist_id}","starred_url":"https://api.github.com/users/ianhirsch/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ianhirsch/subscriptions","organizations_url":"https://api.github.com/users/ianhirsch/orgs","repos_url":"https://api.github.com/users/ianhirsch/repos","events_url":"https://api.github.com/users/ianhirsch/events{/privacy}","received_events_url":"https://api.github.com/users/ianhirsch/received_events","type":"User","site_admin":false},"assignees":[{"login":"ianhirsch","id":39777768,"node_id":"MDQ6VXNlcjM5Nzc3NzY4","avatar_url":"https://avatars2.githubusercontent.com/u/39777768?v=4","gravatar_id":"","url":"https://api.github.com/users/ianhirsch","html_url":"https://github.com/ianhirsch","followers_url":"https://api.github.com/users/ianhirsch/followers","following_url":"https://api.github.com/users/ianhirsch/following{/other_user}","gists_url":"https://api.github.com/users/ianhirsch/gists{/gist_id}","starred_url":"https://api.github.com/users/ianhirsch/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ianhirsch/subscriptions","organizations_url":"https://api.github.com/users/ianhirsch/orgs","repos_url":"https://api.github.com/users/ianhirsch/repos","events_url":"https://api.github.com/users/ianhirsch/events{/privacy}","received_events_url":"https://api.github.com/users/ianhirsch/received_events","type":"User","site_admin":false}],"milestone":null,"comments":4,"created_at":"2018-07-10T13:07:37Z","updated_at":"2018-07-30T20:09:34Z","closed_at":null,"author_association":"NONE","body":"Hi,\r\nI'm using MetaMorpheus in command line mode and then parsing the results.  Can I set file names from the command line?  For example make the result folder \"myResult\" instead of the date stamp.  Also set the base result file name to get \"nyName_Peptides.psmtsv\" instead of the current result which is either aggregate_Peptides.psmtsv or the raw-file name _Peptides.psmtsv depending on how many files were searched.  \r\nNick"},"comment":{"url":"https://api.github.com/repos/smith-chem-wisc/MetaMorpheus/issues/comments/408993617","html_url":"https://github.com/smith-chem-wisc/MetaMorpheus/issues/1277#issuecomment-408993617","issue_url":"https://api.github.com/repos/smith-chem-wisc/MetaMorpheus/issues/1277","id":408993617,"node_id":"MDEyOklzc3VlQ29tbWVudDQwODk5MzYxNw==","user":{"login":"rmillikin","id":24705713,"node_id":"MDQ6VXNlcjI0NzA1NzEz","avatar_url":"https://avatars3.githubusercontent.com/u/24705713?v=4","gravatar_id":"","url":"https://api.github.com/users/rmillikin","html_url":"https://github.com/rmillikin","followers_url":"https://api.github.com/users/rmillikin/followers","following_url":"https://api.github.com/users/rmillikin/following{/other_user}","gists_url":"https://api.github.com/users/rmillikin/gists{/gist_id}","starred_url":"https://api.github.com/users/rmillikin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rmillikin/subscriptions","organizations_url":"https://api.github.com/users/rmillikin/orgs","repos_url":"https://api.github.com/users/rmillikin/repos","events_url":"https://api.github.com/users/rmillikin/events{/privacy}","received_events_url":"https://api.github.com/users/rmillikin/received_events","type":"User","site_admin":false},"created_at":"2018-07-30T20:09:34Z","updated_at":"2018-07-30T20:09:34Z","author_association":"CONTRIBUTOR","body":"This is pretty much done and will be included in the next release. We've just made the aggregate file always be output. We've also revised the names of the files and put the individual files in a subdirectory to clean things up a bit. Attached is an example.\r\n\r\nSo it'll break your current program (sorry) but the end result is much cleaner/simpler.\r\n\r\n![capture](https://user-images.githubusercontent.com/24705713/43420772-6ef93be2-940a-11e8-9d04-904c802a9427.PNG)\r\n"}}
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