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Quoting again shouldn't be necessary, no? If I look at the generated commandline this is quoted ...","created_at":"2016-12-18T18:40:26Z","updated_at":"2016-12-18T18:40:26Z","html_url":"https://github.com/galaxyproject/tools-iuc/pull/1082#discussion_r92947805","pull_request_url":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/1082","_links":{"self":{"href":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/comments/92947805"},"html":{"href":"https://github.com/galaxyproject/tools-iuc/pull/1082#discussion_r92947805"},"pull_request":{"href":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/1082"}}},"pull_request":{"url":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/1082","id":98481771,"html_url":"https://github.com/galaxyproject/tools-iuc/pull/1082","diff_url":"https://github.com/galaxyproject/tools-iuc/pull/1082.diff","patch_url":"https://github.com/galaxyproject/tools-iuc/pull/1082.patch","issue_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/1082","number":1082,"state":"open","locked":false,"title":"Samblaster","user":{"login":"mvdbeek","id":6804901,"avatar_url":"https://avatars.githubusercontent.com/u/6804901?v=3","gravatar_id":"","url":"https://api.github.com/users/mvdbeek","html_url":"https://github.com/mvdbeek","followers_url":"https://api.github.com/users/mvdbeek/followers","following_url":"https://api.github.com/users/mvdbeek/following{/other_user}","gists_url":"https://api.github.com/users/mvdbeek/gists{/gist_id}","starred_url":"https://api.github.com/users/mvdbeek/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mvdbeek/subscriptions","organizations_url":"https://api.github.com/users/mvdbeek/orgs","repos_url":"https://api.github.com/users/mvdbeek/repos","events_url":"https://api.github.com/users/mvdbeek/events{/privacy}","received_events_url":"https://api.github.com/users/mvdbeek/received_events","type":"User","site_admin":false},"body":"This is a nice tool that can mark duplicate reads, output discordant read pairs, and most importantly, clipped reads according to various criteria. 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