{"action":"opened","issue":{"url":"https://api.github.com/repos/bgruening/galaxytools/issues/434","repository_url":"https://api.github.com/repos/bgruening/galaxytools","labels_url":"https://api.github.com/repos/bgruening/galaxytools/issues/434/labels{/name}","comments_url":"https://api.github.com/repos/bgruening/galaxytools/issues/434/comments","events_url":"https://api.github.com/repos/bgruening/galaxytools/issues/434/events","html_url":"https://github.com/bgruening/galaxytools/issues/434","id":190330092,"number":434,"title":"bowtie index wrong path in xml","user":{"login":"bimbam23","id":2727580,"avatar_url":"https://avatars.githubusercontent.com/u/2727580?v=3","gravatar_id":"","url":"https://api.github.com/users/bimbam23","html_url":"https://github.com/bimbam23","followers_url":"https://api.github.com/users/bimbam23/followers","following_url":"https://api.github.com/users/bimbam23/following{/other_user}","gists_url":"https://api.github.com/users/bimbam23/gists{/gist_id}","starred_url":"https://api.github.com/users/bimbam23/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bimbam23/subscriptions","organizations_url":"https://api.github.com/users/bimbam23/orgs","repos_url":"https://api.github.com/users/bimbam23/repos","events_url":"https://api.github.com/users/bimbam23/events{/privacy}","received_events_url":"https://api.github.com/users/bimbam23/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2016-11-18T14:20:57Z","updated_at":"2016-11-18T14:20:57Z","closed_at":null,"body":" galaxytools/tools/rna_tools/miRDeep2/miRDeep2_mapper/mapper.xml \r\n\r\n`       \r\n#if $operation.collapse_map == \"collapse_and_map\" or $operation.collapse_map == \"only_map\"\r\n            -p \r\n            \r\n            #if $operation.refGenomeSource.genomeSource == \"history\"\r\n                custom_bowtie_indices\r\n            #else\r\n                $operation.refGenomeSource.index\r\n            #end if\r\n            $operation.map_mismatch\r\n            -r $operation.map_threshold\r\n            \r\n            -t $output_mapping\r\n        #end if\r\n`\r\n\r\nneeds to be changed to:\r\n\r\n`        \r\n#if $operation.collapse_map == \"collapse_and_map\" or $operation.collapse_map == \"only_map\"\r\n            -p \r\n            \r\n            #if $operation.refGenomeSource.genomeSource == \"history\"\r\n                custom_bowtie_indices\r\n            #else\r\n                '$operation.refGenomeSource.index.fields.path'\r\n            #end if\r\n            $operation.map_mismatch\r\n            -r $operation.map_threshold\r\n            \r\n            -t $output_mapping\r\n        #end if\r\n`\r\n"}}
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