{"action":"created","comment":{"url":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/comments/49848779","id":49848779,"diff_hunk":"@@ -0,0 +1,201 @@\n+<tool id=\"Extract genomic DNA 1\" name=\"Extract Genomic DNA\" version=\"3.0.0\">\n+    <description>using coordinates from assembled/unassembled genomes</description>\n+    <requirements>\n+        <requirement type=\"package\" version=\"35x1\">faToTwoBit</requirement>\n+    </requirements>\n+    <command>\n+        <![CDATA[\n+            #set genome = $input.metadata.dbkey\n+            #set datatype = $input.datatype\n+            mkdir -p output_dir &&\n+            python $__tool_directory__/extract_genomic_dna.py\n+            --input \"$input\"\n+            --genome \"$genome\"\n+            #if isinstance($datatype, $__app__.datatypes_registry.get_datatype_by_extension('gff').__class__):","path":"tools/extract_genomic_dna/extract_genomic_dna.xml","position":14,"original_position":14,"commit_id":"b6f614568d402c6bafaa6187115dd165cd4f54e5","original_commit_id":"b6f614568d402c6bafaa6187115dd165cd4f54e5","user":{"login":"gregvonkuster","id":6947053,"avatar_url":"https://avatars.githubusercontent.com/u/6947053?v=3","gravatar_id":"","url":"https://api.github.com/users/gregvonkuster","html_url":"https://github.com/gregvonkuster","followers_url":"https://api.github.com/users/gregvonkuster/followers","following_url":"https://api.github.com/users/gregvonkuster/following{/other_user}","gists_url":"https://api.github.com/users/gregvonkuster/gists{/gist_id}","starred_url":"https://api.github.com/users/gregvonkuster/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gregvonkuster/subscriptions","organizations_url":"https://api.github.com/users/gregvonkuster/orgs","repos_url":"https://api.github.com/users/gregvonkuster/repos","events_url":"https://api.github.com/users/gregvonkuster/events{/privacy}","received_events_url":"https://api.github.com/users/gregvonkuster/received_events","type":"User","site_admin":false},"body":"I think there is also gtf - something that comes out of cufflinks?. Are there other derivatives?  Will there be other derivatives in the future?","created_at":"2016-01-15T12:33:55Z","updated_at":"2016-01-15T12:33:55Z","html_url":"https://github.com/galaxyproject/tools-iuc/pull/543#discussion_r49848779","pull_request_url":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/543","_links":{"self":{"href":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/comments/49848779"},"html":{"href":"https://github.com/galaxyproject/tools-iuc/pull/543#discussion_r49848779"},"pull_request":{"href":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/543"}}},"pull_request":{"url":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/543","id":56059443,"html_url":"https://github.com/galaxyproject/tools-iuc/pull/543","diff_url":"https://github.com/galaxyproject/tools-iuc/pull/543.diff","patch_url":"https://github.com/galaxyproject/tools-iuc/pull/543.patch","issue_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/543","number":543,"state":"open","locked":false,"title":"Add the modern version of the legacy Extract Genomic DNA tool ","user":{"login":"gregvonkuster","id":6947053,"avatar_url":"https://avatars.githubusercontent.com/u/6947053?v=3","gravatar_id":"","url":"https://api.github.com/users/gregvonkuster","html_url":"https://github.com/gregvonkuster","followers_url":"https://api.github.com/users/gregvonkuster/followers","following_url":"https://api.github.com/users/gregvonkuster/following{/other_user}","gists_url":"https://api.github.com/users/gregvonkuster/gists{/gist_id}","starred_url":"https://api.github.com/users/gregvonkuster/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gregvonkuster/subscriptions","organizations_url":"https://api.github.com/users/gregvonkuster/orgs","repos_url":"https://api.github.com/users/gregvonkuster/repos","events_url":"https://api.github.com/users/gregvonkuster/events{/privacy}","received_events_url":"https://api.github.com/users/gregvonkuster/received_events","type":"User","site_admin":false},"body":"(which is still contained within the Galaxy code base).  This version makes use of tool dependency definitions, Galaxy Data Managers, validators, and other features that were not available when the original tool was written.  All original functional test data is included (but has been made smaller in some cases, especially outputs), and functional tests were manually tested for correctness.","created_at":"2016-01-14T16:36:35Z","updated_at":"2016-01-15T12:33:55Z","closed_at":null,"merged_at":null,"merge_commit_sha":"03a945aac0950d7fbee42ca67b146613da558f65","assignee":null,"milestone":null,"commits_url":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/543/commits","review_comments_url":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/543/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/543/comments","statuses_url":"https://api.github.com/repos/galaxyproject/tools-iuc/statuses/b6f614568d402c6bafaa6187115dd165cd4f54e5","head":{"label":"gregvonkuster:extract_genomic_dna","ref":"extract_genomic_dna","sha":"b6f614568d402c6bafaa6187115dd165cd4f54e5","user":{"login":"gregvonkuster","id":6947053,"avatar_url":"https://avatars.githubusercontent.com/u/6947053?v=3","gravatar_id":"","url":"https://api.github.com/users/gregvonkuster","html_url":"https://github.com/gregvonkuster","followers_url":"https://api.github.com/users/gregvonkuster/followers","following_url":"https://api.github.com/users/gregvonkuster/following{/other_user}","gists_url":"https://api.github.com/users/gregvonkuster/gists{/gist_id}","starred_url":"https://api.github.com/users/gregvonkuster/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gregvonkuster/subscriptions","organizations_url":"https://api.github.com/users/gregvonkuster/orgs","repos_url":"https://api.github.com/users/gregvonkuster/repos","events_url":"https://api.github.com/users/gregvonkuster/events{/privacy}","received_events_url":"https://api.github.com/users/gregvonkuster/received_events","type":"User","site_admin":false},"repo":{"id":33613378,"name":"tools-iuc","full_name":"gregvonkuster/tools-iuc","owner":{"login":"gregvonkuster","id":6947053,"avatar_url":"https://avatars.githubusercontent.com/u/6947053?v=3","gravatar_id":"","url":"https://api.github.com/users/gregvonkuster","html_url":"https://github.com/gregvonkuster","followers_url":"https://api.github.com/users/gregvonkuster/followers","following_url":"https://api.github.com/users/gregvonkuster/following{/other_user}","gists_url":"https://api.github.com/users/gregvonkuster/gists{/gist_id}","starred_url":"https://api.github.com/users/gregvonkuster/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gregvonkuster/subscriptions","organizations_url":"https://api.github.com/users/gregvonkuster/orgs","repos_url":"https://api.github.com/users/gregvonkuster/repos","events_url":"https://api.github.com/users/gregvonkuster/events{/privacy}","received_events_url":"https://api.github.com/users/gregvonkuster/received_events","type":"User","site_admin":false},"private":false,"html_url":"https://github.com/gregvonkuster/tools-iuc","description":"Tool Shed repositories maintained and developed by the Intergalactic Utilities Commission","fork":true,"url":"https://api.github.com/repos/gregvonkuster/tools-iuc","forks_url":"https://api.github.com/repos/gregvonkuster/tools-iuc/forks","keys_url":"https://api.github.com/repos/gregvonkuster/tools-iuc/keys{/key_id}","collaborators_url":"https://api.github.com/repos/gregvonkuster/tools-iuc/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/gregvonkuster/tools-iuc/teams","hooks_url":"https://api.github.com/repos/gregvonkuster/tools-iuc/hooks","issue_events_url":"https://api.github.com/repos/gregvonkuster/tools-iuc/issues/events{/number}","events_url":"https://api.github.com/repos/gregvonkuster/tools-iuc/events","assignees_url":"https://api.github.com/repos/gregvonkuster/tools-iuc/assignees{/user}","branches_url":"https://api.github.com/repos/gregvonkuster/tools-iuc/branches{/branch}","tags_url":"https://api.github.com/repos/gregvonkuster/tools-iuc/tags","blobs_url":"https://api.github.com/repos/gregvonkuster/tools-iuc/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/gregvonkuster/tools-iuc/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/gregvonkuster/tools-iuc/git/refs{/sha}","trees_url":"https://api.github.com/repos/gregvonkuster/tools-iuc/git/trees{/sha}","statuses_url":"https://api.github.com/repos/gregvonkuster/tools-iuc/statuses/{sha}","languages_url":"https://api.github.com/repos/gregvonkuster/tools-iuc/languages","stargazers_url":"https://api.github.com/repos/gregvonkuster/tools-iuc/stargazers","contributors_url":"https://api.github.com/repos/gregvonkuster/tools-iuc/contributors","subscribers_url":"https://api.github.com/repos/gregvonkuster/tools-iuc/subscribers","subscription_url":"https://api.github.com/repos/gregvonkuster/tools-iuc/subscription","commits_url":"https://api.github.com/repos/gregvonkuster/tools-iuc/commits{/sha}","git_commits_url":"https://api.github.com/repos/gregvonkuster/tools-iuc/git/commits{/sha}","comments_url":"https://api.github.com/repos/gregvonkuster/tools-iuc/comments{/number}","issue_comment_url":"https://api.github.com/repos/gregvonkuster/tools-iuc/issues/comments{/number}","contents_url":"https://api.github.com/repos/gregvonkuster/tools-iuc/contents/{+path}","compare_url":"https://api.github.com/repos/gregvonkuster/tools-iuc/compare/{base}...{head}","merges_url":"https://api.github.com/repos/gregvonkuster/tools-iuc/merges","archive_url":"https://api.github.com/repos/gregvonkuster/tools-iuc/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/gregvonkuster/tools-iuc/downloads","issues_url":"https://api.github.com/repos/gregvonkuster/tools-iuc/issues{/number}","pulls_url":"https://api.github.com/repos/gregvonkuster/tools-iuc/pulls{/number}","milestones_url":"https://api.github.com/repos/gregvonkuster/tools-iuc/milestones{/number}","notifications_url":"https://api.github.com/repos/gregvonkuster/tools-iuc/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/gregvonkuster/tools-iuc/labels{/name}","releases_url":"https://api.github.com/repos/gregvonkuster/tools-iuc/releases{/id}","created_at":"2015-04-08T14:53:04Z","updated_at":"2016-01-13T13:04:34Z","pushed_at":"2016-01-14T17:53:05Z","git_url":"git://github.com/gregvonkuster/tools-iuc.git","ssh_url":"git@github.com:gregvonkuster/tools-iuc.git","clone_url":"https://github.com/gregvonkuster/tools-iuc.git","svn_url":"https://github.com/gregvonkuster/tools-iuc","homepage":"https://wiki.galaxyproject.org/IUC","size":45334,"stargazers_count":0,"watchers_count":0,"language":"Python","has_issues":false,"has_downloads":true,"has_wiki":true,"has_pages":false,"forks_count":1,"mirror_url":null,"open_issues_count":0,"forks":1,"open_issues":0,"watchers":0,"default_branch":"master"}},"base":{"label":"galaxyproject:master","ref":"master","sha":"dd2bada7005c72c16cd3ea047cdc64896c1f8977","user":{"login":"galaxyproject","id":7937847,"avatar_url":"https://avatars.githubusercontent.com/u/7937847?v=3","gravatar_id":"","url":"https://api.github.com/users/galaxyproject","html_url":"https://github.com/galaxyproject","followers_url":"https://api.github.com/users/galaxyproject/followers","following_url":"https://api.github.com/users/galaxyproject/following{/other_user}","gists_url":"https://api.github.com/users/galaxyproject/gists{/gist_id}","starred_url":"https://api.github.com/users/galaxyproject/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/galaxyproject/subscriptions","organizations_url":"https://api.github.com/users/galaxyproject/orgs","repos_url":"https://api.github.com/users/galaxyproject/repos","events_url":"https://api.github.com/users/galaxyproject/events{/privacy}","received_events_url":"https://api.github.com/users/galaxyproject/received_events","type":"Organization","site_admin":false},"repo":{"id":23992530,"name":"tools-iuc","full_name":"galaxyproject/tools-iuc","owner":{"login":"galaxyproject","id":7937847,"avatar_url":"https://avatars.githubusercontent.com/u/7937847?v=3","gravatar_id":"","url":"https://api.github.com/users/galaxyproject","html_url":"https://github.com/galaxyproject","followers_url":"https://api.github.com/users/galaxyproject/followers","following_url":"https://api.github.com/users/galaxyproject/following{/other_user}","gists_url":"https://api.github.com/users/galaxyproject/gists{/gist_id}","starred_url":"https://api.github.com/users/galaxyproject/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/galaxyproject/subscriptions","organizations_url":"https://api.github.com/users/galaxyproject/orgs","repos_url":"https://api.github.com/users/galaxyproject/repos","events_url":"https://api.github.com/users/galaxyproject/events{/privacy}","received_events_url":"https://api.github.com/users/galaxyproject/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/galaxyproject/tools-iuc","description":"Tool Shed repositories maintained and developed by the Intergalactic Utilities Commission","fork":false,"url":"https://api.github.com/repos/galaxyproject/tools-iuc","forks_url":"https://api.github.com/repos/galaxyproject/tools-iuc/forks","keys_url":"https://api.github.com/repos/galaxyproject/tools-iuc/keys{/key_id}","collaborators_url":"https://api.github.com/repos/galaxyproject/tools-iuc/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/galaxyproject/tools-iuc/teams","hooks_url":"https://api.github.com/repos/galaxyproject/tools-iuc/hooks","issue_events_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/events{/number}","events_url":"https://api.github.com/repos/galaxyproject/tools-iuc/events","assignees_url":"https://api.github.com/repos/galaxyproject/tools-iuc/assignees{/user}","branches_url":"https://api.github.com/repos/galaxyproject/tools-iuc/branches{/branch}","tags_url":"https://api.github.com/repos/galaxyproject/tools-iuc/tags","blobs_url":"https://api.github.com/repos/galaxyproject/tools-iuc/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/galaxyproject/tools-iuc/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/galaxyproject/tools-iuc/git/refs{/sha}","trees_url":"https://api.github.com/repos/galaxyproject/tools-iuc/git/trees{/sha}","statuses_url":"https://api.github.com/repos/galaxyproject/tools-iuc/statuses/{sha}","languages_url":"https://api.github.com/repos/galaxyproject/tools-iuc/languages","stargazers_url":"https://api.github.com/repos/galaxyproject/tools-iuc/stargazers","contributors_url":"https://api.github.com/repos/galaxyproject/tools-iuc/contributors","subscribers_url":"https://api.github.com/repos/galaxyproject/tools-iuc/subscribers","subscription_url":"https://api.github.com/repos/galaxyproject/tools-iuc/subscription","commits_url":"https://api.github.com/repos/galaxyproject/tools-iuc/commits{/sha}","git_commits_url":"https://api.github.com/repos/galaxyproject/tools-iuc/git/commits{/sha}","comments_url":"https://api.github.com/repos/galaxyproject/tools-iuc/comments{/number}","issue_comment_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/comments{/number}","contents_url":"https://api.github.com/repos/galaxyproject/tools-iuc/contents/{+path}","compare_url":"https://api.github.com/repos/galaxyproject/tools-iuc/compare/{base}...{head}","merges_url":"https://api.github.com/repos/galaxyproject/tools-iuc/merges","archive_url":"https://api.github.com/repos/galaxyproject/tools-iuc/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/galaxyproject/tools-iuc/downloads","issues_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues{/number}","pulls_url":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls{/number}","milestones_url":"https://api.github.com/repos/galaxyproject/tools-iuc/milestones{/number}","notifications_url":"https://api.github.com/repos/galaxyproject/tools-iuc/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/galaxyproject/tools-iuc/labels{/name}","releases_url":"https://api.github.com/repos/galaxyproject/tools-iuc/releases{/id}","created_at":"2014-09-13T11:18:49Z","updated_at":"2016-01-12T09:46:44Z","pushed_at":"2016-01-15T08:35:53Z","git_url":"git://github.com/galaxyproject/tools-iuc.git","ssh_url":"git@github.com:galaxyproject/tools-iuc.git","clone_url":"https://github.com/galaxyproject/tools-iuc.git","svn_url":"https://github.com/galaxyproject/tools-iuc","homepage":"https://wiki.galaxyproject.org/IUC","size":120616,"stargazers_count":21,"watchers_count":21,"language":"Python","has_issues":true,"has_downloads":true,"has_wiki":true,"has_pages":false,"forks_count":58,"mirror_url":null,"open_issues_count":92,"forks":58,"open_issues":92,"watchers":21,"default_branch":"master"}},"_links":{"self":{"href":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/543"},"html":{"href":"https://github.com/galaxyproject/tools-iuc/pull/543"},"issue":{"href":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/543"},"comments":{"href":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/543/comments"},"review_comments":{"href":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/543/comments"},"review_comment":{"href":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/comments{/number}"},"commits":{"href":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/543/commits"},"statuses":{"href":"https://api.github.com/repos/galaxyproject/tools-iuc/statuses/b6f614568d402c6bafaa6187115dd165cd4f54e5"}}}}