{"action":"created","comment":{"url":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/comments/27023156","id":27023156,"diff_hunk":"@@ -0,0 +1,59 @@\n+<tool\tid=\"gedlab-khmer-count-median\"\n+\tname=\"Count Median\"\n+\tversion=\"1.1-1\"\n+\tforce_history_refresh=\"true\">\n+\n+\t<description>\n+\t\tCount the median/avg k-mer abundance for each sequence in the\n+\t\tinput file, based on the k-mer counts in the given k-mer\n+\t\tcounting table. Can be used to estimate expression levels\n+\t\t(mRNAseq) or coverage (genomic/metagenomic).\n+\t</description>\n+        <macros>\n+\t\t<token name=\"@BINARY@\">count-median.py</token>\n+\t\t<import>macros.xml</import>\n+        </macros>\n+\t<expand macro=\"requirements\" />\n+\t<expand macro=\"stdio\" />\n+\t<expand macro=\"version\" />\n+\t<command>\n+@BINARY@\n+$input_counting_table_filename\n+$input_sequence_filename\n+$output_summary_filename\n+\t</command>\n+\n+\t<inputs>\n+\t\t<expand macro=\"input_sequence_filename\" />\n+\t\t<expand macro=\"input_counting_table_filename\" />\n+\t</inputs>\n+\t<outputs>\n+\t\t<data name=\"output_summary_filename\" format=\"text\"\n+\t\t\tlabel=\"${input_sequence_filename} sequence id, median, average, stddev, and seq length\" />\n+\t</outputs>\n+\t<tests>\n+\t\t<test interactor=\"api\">","path":"tools/khmer/count-median.xml","position":35,"original_position":35,"commit_id":"0e9ff4adfc7ab70f04352194137281fc7fcc3470","original_commit_id":"0e9ff4adfc7ab70f04352194137281fc7fcc3470","user":{"login":"bgruening","id":469983,"avatar_url":"https://avatars.githubusercontent.com/u/469983?v=3","gravatar_id":"","url":"https://api.github.com/users/bgruening","html_url":"https://github.com/bgruening","followers_url":"https://api.github.com/users/bgruening/followers","following_url":"https://api.github.com/users/bgruening/following{/other_user}","gists_url":"https://api.github.com/users/bgruening/gists{/gist_id}","starred_url":"https://api.github.com/users/bgruening/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bgruening/subscriptions","organizations_url":"https://api.github.com/users/bgruening/orgs","repos_url":"https://api.github.com/users/bgruening/repos","events_url":"https://api.github.com/users/bgruening/events{/privacy}","received_events_url":"https://api.github.com/users/bgruening/received_events","type":"User","site_admin":false},"body":"This should not be part of the wrapper I think.","created_at":"2015-03-24T12:40:44Z","updated_at":"2015-03-24T12:40:44Z","html_url":"https://github.com/galaxyproject/tools-iuc/pull/80#discussion_r27023156","pull_request_url":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/80","_links":{"self":{"href":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/comments/27023156"},"html":{"href":"https://github.com/galaxyproject/tools-iuc/pull/80#discussion_r27023156"},"pull_request":{"href":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/80"}}},"pull_request":{"url":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/80","id":31804879,"html_url":"https://github.com/galaxyproject/tools-iuc/pull/80","diff_url":"https://github.com/galaxyproject/tools-iuc/pull/80.diff","patch_url":"https://github.com/galaxyproject/tools-iuc/pull/80.patch","issue_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/80","number":80,"state":"open","locked":false,"title":"initial import of khmer wrappers","user":{"login":"mr-c","id":1330696,"avatar_url":"https://avatars.githubusercontent.com/u/1330696?v=3","gravatar_id":"","url":"https://api.github.com/users/mr-c","html_url":"https://github.com/mr-c","followers_url":"https://api.github.com/users/mr-c/followers","following_url":"https://api.github.com/users/mr-c/following{/other_user}","gists_url":"https://api.github.com/users/mr-c/gists{/gist_id}","starred_url":"https://api.github.com/users/mr-c/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mr-c/subscriptions","organizations_url":"https://api.github.com/users/mr-c/orgs","repos_url":"https://api.github.com/users/mr-c/repos","events_url":"https://api.github.com/users/mr-c/events{/privacy}","received_events_url":"https://api.github.com/users/mr-c/received_events","type":"User","site_admin":false},"body":"\r\nTodo\r\n\r\n- [ ] help section for abundance-dist-single.xml\r\n- [ ] help section for abundance-dist.xml\r\n- [ ] help section for count-median.xml\r\n- [ ] help section for do-partition.xml\r\n- [ ] help section for extract-partitions.xml\r\n- [ ] help section for filter-abund.xml\r\n- [ ] help section for filter-below-abund.py\r\n- [ ] help section for filter-below-abund.xml\r\n- [ ] help section for normalize-by-median.xml\r\n\r\n- [ ] add tests for `do-partition.xml`\r\n\r\n- [ ] update citations in macros.xml & audit citations against khmer v1.3 generally\r\n\r\n- [ ] get tests running with `planemo test --install_galaxy ...`","created_at":"2015-03-24T08:19:13Z","updated_at":"2015-03-24T12:40:44Z","closed_at":null,"merged_at":null,"merge_commit_sha":"29891da1351337e02f87ead8fee0202e6fcaf504","assignee":null,"milestone":null,"commits_url":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/80/commits","review_comments_url":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/80/comments","review_comment_url":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/comments{/number}","comments_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/80/comments","statuses_url":"https://api.github.com/repos/galaxyproject/tools-iuc/statuses/0e9ff4adfc7ab70f04352194137281fc7fcc3470","head":{"label":"mr-c:khmer-wrappers","ref":"khmer-wrappers","sha":"0e9ff4adfc7ab70f04352194137281fc7fcc3470","user":{"login":"mr-c","id":1330696,"avatar_url":"https://avatars.githubusercontent.com/u/1330696?v=3","gravatar_id":"","url":"https://api.github.com/users/mr-c","html_url":"https://github.com/mr-c","followers_url":"https://api.github.com/users/mr-c/followers","following_url":"https://api.github.com/users/mr-c/following{/other_user}","gists_url":"https://api.github.com/users/mr-c/gists{/gist_id}","starred_url":"https://api.github.com/users/mr-c/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mr-c/subscriptions","organizations_url":"https://api.github.com/users/mr-c/orgs","repos_url":"https://api.github.com/users/mr-c/repos","events_url":"https://api.github.com/users/mr-c/events{/privacy}","received_events_url":"https://api.github.com/users/mr-c/received_events","type":"User","site_admin":false},"repo":{"id":26415825,"name":"tools-iuc","full_name":"mr-c/tools-iuc","owner":{"login":"mr-c","id":1330696,"avatar_url":"https://avatars.githubusercontent.com/u/1330696?v=3","gravatar_id":"","url":"https://api.github.com/users/mr-c","html_url":"https://github.com/mr-c","followers_url":"https://api.github.com/users/mr-c/followers","following_url":"https://api.github.com/users/mr-c/following{/other_user}","gists_url":"https://api.github.com/users/mr-c/gists{/gist_id}","starred_url":"https://api.github.com/users/mr-c/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mr-c/subscriptions","organizations_url":"https://api.github.com/users/mr-c/orgs","repos_url":"https://api.github.com/users/mr-c/repos","events_url":"https://api.github.com/users/mr-c/events{/privacy}","received_events_url":"https://api.github.com/users/mr-c/received_events","type":"User","site_admin":false},"private":false,"html_url":"https://github.com/mr-c/tools-iuc","description":"Tool 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