{"action":"created","issue":{"url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/910","repository_url":"https://api.github.com/repos/galaxyproject/tools-iuc","labels_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/910/labels{/name}","comments_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/910/comments","events_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/910/events","html_url":"https://github.com/galaxyproject/tools-iuc/issues/910","id":170900625,"number":910,"title":"shuffleBed - failure preparing job when selecting an additional BED file ","user":{"login":"pajanne","id":214738,"avatar_url":"https://avatars.githubusercontent.com/u/214738?v=3","gravatar_id":"","url":"https://api.github.com/users/pajanne","html_url":"https://github.com/pajanne","followers_url":"https://api.github.com/users/pajanne/followers","following_url":"https://api.github.com/users/pajanne/following{/other_user}","gists_url":"https://api.github.com/users/pajanne/gists{/gist_id}","starred_url":"https://api.github.com/users/pajanne/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pajanne/subscriptions","organizations_url":"https://api.github.com/users/pajanne/orgs","repos_url":"https://api.github.com/users/pajanne/repos","events_url":"https://api.github.com/users/pajanne/events{/privacy}","received_events_url":"https://api.github.com/users/pajanne/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":5,"created_at":"2016-08-12T15:44:08Z","updated_at":"2016-08-12T16:17:04Z","closed_at":null,"body":"https://github.com/galaxyproject/tools-iuc/blob/master/tools/bedtools/shuffleBed.xml returns this error message when selecting an additional BED file\r\n\r\n```\r\nTraceback (most recent call last):\r\n  File \"/data/galaxy/galaxy-dist/lib/galaxy/jobs/runners/__init__.py\", line 163, in prepare_job\r\n    job_wrapper.prepare()\r\n  File \"/data/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py\", line 859, in prepare\r\n    self.command_line, self.extra_filenames, self.environment_variables = tool_evaluator.build()\r\n  File \"/data/galaxy/galaxy-dist/lib/galaxy/tools/evaluation.py\", line 422, in build\r\n    raise e\r\nNotFound: cannot find 'add_bed_select'\r\n```\r\nOnly works when no additional BED file is selected.\r\nGalaxy Tool ID:\ttoolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.24.0\r\n\r\nThere may be a problem in the xml wrapper file with the conditional parameter `add_bed`.\r\nAny help would be great, many thanks."},"comment":{"url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/comments/239490597","html_url":"https://github.com/galaxyproject/tools-iuc/issues/910#issuecomment-239490597","issue_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/910","id":239490597,"user":{"login":"pajanne","id":214738,"avatar_url":"https://avatars.githubusercontent.com/u/214738?v=3","gravatar_id":"","url":"https://api.github.com/users/pajanne","html_url":"https://github.com/pajanne","followers_url":"https://api.github.com/users/pajanne/followers","following_url":"https://api.github.com/users/pajanne/following{/other_user}","gists_url":"https://api.github.com/users/pajanne/gists{/gist_id}","starred_url":"https://api.github.com/users/pajanne/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pajanne/subscriptions","organizations_url":"https://api.github.com/users/pajanne/orgs","repos_url":"https://api.github.com/users/pajanne/repos","events_url":"https://api.github.com/users/pajanne/events{/privacy}","received_events_url":"https://api.github.com/users/pajanne/received_events","type":"User","site_admin":false},"created_at":"2016-08-12T16:17:04Z","updated_at":"2016-08-12T16:17:04Z","body":"Thanks @nsoranzo for your answers. I was just trying to replicate my issue on usegalaxy.org to show you the issue I'm having. \r\nI do think I have the latest version installed, thanks for pointing out at the #634 fix."}}
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