{"action":"created","issue":{"url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/197","labels_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/197/labels{/name}","comments_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/197/comments","events_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/197/events","html_url":"https://github.com/galaxyproject/tools-iuc/pull/197","id":90929073,"number":197,"title":"Various fixes to the vsearch dereplication tool","user":{"login":"pjbriggs","id":840204,"avatar_url":"https://avatars.githubusercontent.com/u/840204?v=3","gravatar_id":"","url":"https://api.github.com/users/pjbriggs","html_url":"https://github.com/pjbriggs","followers_url":"https://api.github.com/users/pjbriggs/followers","following_url":"https://api.github.com/users/pjbriggs/following{/other_user}","gists_url":"https://api.github.com/users/pjbriggs/gists{/gist_id}","starred_url":"https://api.github.com/users/pjbriggs/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pjbriggs/subscriptions","organizations_url":"https://api.github.com/users/pjbriggs/orgs","repos_url":"https://api.github.com/users/pjbriggs/repos","events_url":"https://api.github.com/users/pjbriggs/events{/privacy}","received_events_url":"https://api.github.com/users/pjbriggs/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-06-25T10:57:29Z","updated_at":"2015-06-25T10:59:00Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/197","html_url":"https://github.com/galaxyproject/tools-iuc/pull/197","diff_url":"https://github.com/galaxyproject/tools-iuc/pull/197.diff","patch_url":"https://github.com/galaxyproject/tools-iuc/pull/197.patch"},"body":"This PR attempts to address a number of issues with the dereplication tool in the vsearch tool suite, and adds two new test cases.\r\n\r\nSpecifically the issues are:\r\n\r\n1. The existing test case was broken: the test specified --sizeout but the reference output wasn't generated using this option. Fixed by removing --sizeout from the test case.\r\n\r\n2. Tool fails if no value is supplied for the number of top sequences to output (--topn).\r\nAdded a test case for this, and fixed by omitting --topn option if no value was supplied.\r\n\r\n3. There is an ambiguity when UCLUST-like output is requested (--uc), as both the 'uclust_like_output' macro and the tool define params called 'uc'. Added a test case for this and fixed by renaming the second 'uc' parameter to 'uc_outfile'.\r\n\r\n4. The generation of the --sizein and --sizeout options in the <command> section was incorrect (it resulted in e.g. '--sizein --sizein' rather than '--sizein'), although vsearch still appears to operate correctly. However this has been fixed."},"comment":{"url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/comments/115210428","html_url":"https://github.com/galaxyproject/tools-iuc/pull/197#issuecomment-115210428","issue_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/197","id":115210428,"user":{"login":"erasche","id":458683,"avatar_url":"https://avatars.githubusercontent.com/u/458683?v=3","gravatar_id":"","url":"https://api.github.com/users/erasche","html_url":"https://github.com/erasche","followers_url":"https://api.github.com/users/erasche/followers","following_url":"https://api.github.com/users/erasche/following{/other_user}","gists_url":"https://api.github.com/users/erasche/gists{/gist_id}","starred_url":"https://api.github.com/users/erasche/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/erasche/subscriptions","organizations_url":"https://api.github.com/users/erasche/orgs","repos_url":"https://api.github.com/users/erasche/repos","events_url":"https://api.github.com/users/erasche/events{/privacy}","received_events_url":"https://api.github.com/users/erasche/received_events","type":"User","site_admin":false},"created_at":"2015-06-25T10:59:00Z","updated_at":"2015-06-25T10:59:00Z","body":"[Jenkins Bot] Can one of the admins sign off on testing this PR? (Security reasons, simply comment \"ok to test\")"}}