{"action":"created","comment":{"url":"https://api.github.com/repos/galaxyproject/galaxy/pulls/comments/45608021","id":45608021,"diff_hunk":"@@ -0,0 +1,35 @@\n+<tool id=\"output_format_collection\" name=\"output_format_collection\" version=\"1.0.0\">\n+  <command>\n+    echo \"test\" > 1;\n+    echo \"test\" > 2;\n+  </command>\n+  <inputs>\n+    <param name=\"input_collection\" type=\"data_collection\" format=\"data\" />\n+  </inputs>\n+  <outputs>\n+    <!-- Access by element name (for paired data) -->\n+    <data format=\"txt\" from_work_dir=\"1\" name=\"format_source_1_output\" format_source=\"input_collection['forward']\" />","path":"test/functional/tools/output_format_collection.xml","position":11,"original_position":11,"commit_id":"312746d1698e99e13b9a60db881d0093da6cc4c0","original_commit_id":"312746d1698e99e13b9a60db881d0093da6cc4c0","user":{"login":"nsoranzo","id":4924623,"avatar_url":"https://avatars.githubusercontent.com/u/4924623?v=3","gravatar_id":"","url":"https://api.github.com/users/nsoranzo","html_url":"https://github.com/nsoranzo","followers_url":"https://api.github.com/users/nsoranzo/followers","following_url":"https://api.github.com/users/nsoranzo/following{/other_user}","gists_url":"https://api.github.com/users/nsoranzo/gists{/gist_id}","starred_url":"https://api.github.com/users/nsoranzo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nsoranzo/subscriptions","organizations_url":"https://api.github.com/users/nsoranzo/orgs","repos_url":"https://api.github.com/users/nsoranzo/repos","events_url":"https://api.github.com/users/nsoranzo/events{/privacy}","received_events_url":"https://api.github.com/users/nsoranzo/received_events","type":"User","site_admin":false},"body":"I think `format=\"txt\"` here and below is hiding the fact the new code doesn't work :cry:.\r\nIf I removed them, I got \"Dataset metadata verification for [file_ext] failed, expected [txt] but found [data].\"\r\nSimilarly with `fastqsanger` in sickle.","created_at":"2015-11-23T14:28:23Z","updated_at":"2015-11-23T14:28:23Z","html_url":"https://github.com/galaxyproject/galaxy/pull/1113#discussion_r45608021","pull_request_url":"https://api.github.com/repos/galaxyproject/galaxy/pulls/1113","_links":{"self":{"href":"https://api.github.com/repos/galaxyproject/galaxy/pulls/comments/45608021"},"html":{"href":"https://github.com/galaxyproject/galaxy/pull/1113#discussion_r45608021"},"pull_request":{"href":"https://api.github.com/repos/galaxyproject/galaxy/pulls/1113"}}},"pull_request":{"url":"https://api.github.com/repos/galaxyproject/galaxy/pulls/1113","id":50990065,"html_url":"https://github.com/galaxyproject/galaxy/pull/1113","diff_url":"https://github.com/galaxyproject/galaxy/pull/1113.diff","patch_url":"https://github.com/galaxyproject/galaxy/pull/1113.patch","issue_url":"https://api.github.com/repos/galaxyproject/galaxy/issues/1113","number":1113,"state":"closed","locked":false,"title":"Allow accessing collection elements in format_source.","user":{"login":"jmchilton","id":216771,"avatar_url":"https://avatars.githubusercontent.com/u/216771?v=3","gravatar_id":"","url":"https://api.github.com/users/jmchilton","html_url":"https://github.com/jmchilton","followers_url":"https://api.github.com/users/jmchilton/followers","following_url":"https://api.github.com/users/jmchilton/following{/other_user}","gists_url":"https://api.github.com/users/jmchilton/gists{/gist_id}","starred_url":"https://api.github.com/users/jmchilton/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jmchilton/subscriptions","organizations_url":"https://api.github.com/users/jmchilton/orgs","repos_url":"https://api.github.com/users/jmchilton/repos","events_url":"https://api.github.com/users/jmchilton/events{/privacy}","received_events_url":"https://api.github.com/users/jmchilton/received_events","type":"User","site_admin":false},"body":"Can do it by numeric index or element name, e.g. input[0] or input[\"forward\"]. Only works for 1-D collections.\r\n\r\nImplements #699.\r\n\r\nRun new and most relevant existing tests with the following commands:\r\n\r\n```\r\nnosetests test/unit/tools/test_actions.py\r\n./run_tests.sh -framework -id output_format_collection\r\n./run_tests.sh -framework -id output_format\r\n```","created_at":"2015-11-17T19:11:08Z","updated_at":"2015-11-23T14:28:24Z","closed_at":"2015-11-22T04:38:39Z","merged_at":"2015-11-22T04:38:39Z","merge_commit_sha":"4a153cd267bd01d5f964445d5a735b7dc3b1d8b6","assignee":null,"milestone":null,"commits_url":"https://api.github.com/repos/galaxyproject/galaxy/pulls/1113/commits","review_comments_url":"https://api.github.com/repos/galaxyproject/galaxy/pulls/1113/comments","review_comment_url":"https://api.github.com/repos/galaxyproject/galaxy/pulls/comments{/number}","comments_url":"https://api.github.com/repos/galaxyproject/galaxy/issues/1113/comments","statuses_url":"https://api.github.com/repos/galaxyproject/galaxy/statuses/312746d1698e99e13b9a60db881d0093da6cc4c0","head":{"label":"jmchilton:format_source_collection","ref":"format_source_collection","sha":"312746d1698e99e13b9a60db881d0093da6cc4c0","user":{"login":"jmchilton","id":216771,"avatar_url":"https://avatars.githubusercontent.com/u/216771?v=3","gravatar_id":"","url":"https://api.github.com/users/jmchilton","html_url":"https://github.com/jmchilton","followers_url":"https://api.github.com/users/jmchilton/followers","following_url":"https://api.github.com/users/jmchilton/following{/other_user}","gists_url":"https://api.github.com/users/jmchilton/gists{/gist_id}","starred_url":"https://api.github.com/users/jmchilton/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jmchilton/subscriptions","organizations_url":"https://api.github.com/users/jmchilton/orgs","repos_url":"https://api.github.com/users/jmchilton/repos","events_url":"https://api.github.com/users/jmchilton/events{/privacy}","received_events_url":"https://api.github.com/users/jmchilton/received_events","type":"User","site_admin":false},"repo":{"id":31215230,"name":"galaxy","full_name":"jmchilton/galaxy","owner":{"login":"jmchilton","id":216771,"avatar_url":"https://avatars.githubusercontent.com/u/216771?v=3","gravatar_id":"","url":"https://api.github.com/users/jmchilton","html_url":"https://github.com/jmchilton","followers_url":"https://api.github.com/users/jmchilton/followers","following_url":"https://api.github.com/users/jmchilton/following{/other_user}","gists_url":"https://api.github.com/users/jmchilton/gists{/gist_id}","starred_url":"https://api.github.com/users/jmchilton/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jmchilton/subscriptions","organizations_url":"https://api.github.com/users/jmchilton/orgs","repos_url":"https://api.github.com/users/jmchilton/repos","events_url":"https://api.github.com/users/jmchilton/events{/privacy}","received_events_url":"https://api.github.com/users/jmchilton/received_events","type":"User","site_admin":false},"private":false,"html_url":"https://github.com/jmchilton/galaxy","description":"Galaxy Github repository BETA 2. May be destroyed and recreated if additional post-conversion problems are found (but post-conversion commits on this repo will be reapplied to any recreations). Full details:","fork":true,"url":"https://api.github.com/repos/jmchilton/galaxy","forks_url":"https://api.github.com/repos/jmchilton/galaxy/forks","keys_url":"https://api.github.com/repos/jmchilton/galaxy/keys{/key_id}","collaborators_url":"https://api.github.com/repos/jmchilton/galaxy/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/jmchilton/galaxy/teams","hooks_url":"https://api.github.com/repos/jmchilton/galaxy/hooks","issue_events_url":"https://api.github.com/repos/jmchilton/galaxy/issues/events{/number}","events_url":"https://api.github.com/repos/jmchilton/galaxy/events","assignees_url":"https://api.github.com/repos/jmchilton/galaxy/assignees{/user}","branches_url":"https://api.github.com/repos/jmchilton/galaxy/branches{/branch}","tags_url":"https://api.github.com/repos/jmchilton/galaxy/tags","blobs_url":"https://api.github.com/repos/jmchilton/galaxy/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/jmchilton/galaxy/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/jmchilton/galaxy/git/refs{/sha}","trees_url":"https://api.github.com/repos/jmchilton/galaxy/git/trees{/sha}","statuses_url":"https://api.github.com/repos/jmchilton/galaxy/statuses/{sha}","languages_url":"https://api.github.com/repos/jmchilton/galaxy/languages","stargazers_url":"https://api.github.com/repos/jmchilton/galaxy/stargazers","contributors_url":"https://api.github.com/repos/jmchilton/galaxy/contributors","subscribers_url":"https://api.github.com/repos/jmchilton/galaxy/subscribers","subscription_url":"https://api.github.com/repos/jmchilton/galaxy/subscription","commits_url":"https://api.github.com/repos/jmchilton/galaxy/commits{/sha}","git_commits_url":"https://api.github.com/repos/jmchilton/galaxy/git/commits{/sha}","comments_url":"https://api.github.com/repos/jmchilton/galaxy/comments{/number}","issue_comment_url":"https://api.github.com/repos/jmchilton/galaxy/issues/comments{/number}","contents_url":"https://api.github.com/repos/jmchilton/galaxy/contents/{+path}","compare_url":"https://api.github.com/repos/jmchilton/galaxy/compare/{base}...{head}","merges_url":"https://api.github.com/repos/jmchilton/galaxy/merges","archive_url":"https://api.github.com/repos/jmchilton/galaxy/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/jmchilton/galaxy/downloads","issues_url":"https://api.github.com/repos/jmchilton/galaxy/issues{/number}","pulls_url":"https://api.github.com/repos/jmchilton/galaxy/pulls{/number}","milestones_url":"https://api.github.com/repos/jmchilton/galaxy/milestones{/number}","notifications_url":"https://api.github.com/repos/jmchilton/galaxy/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/jmchilton/galaxy/labels{/name}","releases_url":"https://api.github.com/repos/jmchilton/galaxy/releases{/id}","created_at":"2015-02-23T15:54:52Z","updated_at":"2015-07-23T02:20:22Z","pushed_at":"2015-11-23T01:24:14Z","git_url":"git://github.com/jmchilton/galaxy.git","ssh_url":"git@github.com:jmchilton/galaxy.git","clone_url":"https://github.com/jmchilton/galaxy.git","svn_url":"https://github.com/jmchilton/galaxy","homepage":"https://trello.com/c/iiSBweRQ","size":72490,"stargazers_count":3,"watchers_count":3,"language":"Python","has_issues":false,"has_downloads":true,"has_wiki":true,"has_pages":false,"forks_count":0,"mirror_url":null,"open_issues_count":1,"forks":0,"open_issues":1,"watchers":3,"default_branch":"dev"}},"base":{"label":"galaxyproject:dev","ref":"dev","sha":"2374c55f7233a9b2ff4a72ff3c2535ce9dc732e3","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":31211061,"name":"galaxy","full_name":"galaxyproject/galaxy","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/galaxy","description":"Data intensive biology for everyone.","fork":false,"url":"https://api.github.com/repos/galaxyproject/galaxy","forks_url":"https://api.github.com/repos/galaxyproject/galaxy/forks","keys_url":"https://api.github.com/repos/galaxyproject/galaxy/keys{/key_id}","collaborators_url":"https://api.github.com/repos/galaxyproject/galaxy/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/galaxyproject/galaxy/teams","hooks_url":"https://api.github.com/repos/galaxyproject/galaxy/hooks","issue_events_url":"https://api.github.com/repos/galaxyproject/galaxy/issues/events{/number}","events_url":"https://api.github.com/repos/galaxyproject/galaxy/events","assignees_url":"https://api.github.com/repos/galaxyproject/galaxy/assignees{/user}","branches_url":"https://api.github.com/repos/galaxyproject/galaxy/branches{/branch}","tags_url":"https://api.github.com/repos/galaxyproject/galaxy/tags","blobs_url":"https://api.github.com/repos/galaxyproject/galaxy/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/galaxyproject/galaxy/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/galaxyproject/galaxy/git/refs{/sha}","trees_url":"https://api.github.com/repos/galaxyproject/galaxy/git/trees{/sha}","statuses_url":"https://api.github.com/repos/galaxyproject/galaxy/statuses/{sha}","languages_url":"https://api.github.com/repos/galaxyproject/galaxy/languages","stargazers_url":"https://api.github.com/repos/galaxyproject/galaxy/stargazers","contributors_url":"https://api.github.com/repos/galaxyproject/galaxy/contributors","subscribers_url":"https://api.github.com/repos/galaxyproject/galaxy/subscribers","subscription_url":"https://api.github.com/repos/galaxyproject/galaxy/subscription","commits_url":"https://api.github.com/repos/galaxyproject/galaxy/commits{/sha}","git_commits_url":"https://api.github.com/repos/galaxyproject/galaxy/git/commits{/sha}","comments_url":"https://api.github.com/repos/galaxyproject/galaxy/comments{/number}","issue_comment_url":"https://api.github.com/repos/galaxyproject/galaxy/issues/comments{/number}","contents_url":"https://api.github.com/repos/galaxyproject/galaxy/contents/{+path}","compare_url":"https://api.github.com/repos/galaxyproject/galaxy/compare/{base}...{head}","merges_url":"https://api.github.com/repos/galaxyproject/galaxy/merges","archive_url":"https://api.github.com/repos/galaxyproject/galaxy/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/galaxyproject/galaxy/downloads","issues_url":"https://api.github.com/repos/galaxyproject/galaxy/issues{/number}","pulls_url":"https://api.github.com/repos/galaxyproject/galaxy/pulls{/number}","milestones_url":"https://api.github.com/repos/galaxyproject/galaxy/milestones{/number}","notifications_url":"https://api.github.com/repos/galaxyproject/galaxy/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/galaxyproject/galaxy/labels{/name}","releases_url":"https://api.github.com/repos/galaxyproject/galaxy/releases{/id}","created_at":"2015-02-23T14:18:06Z","updated_at":"2015-11-15T13:48:39Z","pushed_at":"2015-11-23T01:12:01Z","git_url":"git://github.com/galaxyproject/galaxy.git","ssh_url":"git@github.com:galaxyproject/galaxy.git","clone_url":"https://github.com/galaxyproject/galaxy.git","svn_url":"https://github.com/galaxyproject/galaxy","homepage":"https://galaxyproject.org/","size":90830,"stargazers_count":87,"watchers_count":87,"language":"Python","has_issues":true,"has_downloads":true,"has_wiki":false,"has_pages":false,"forks_count":140,"mirror_url":null,"open_issues_count":179,"forks":140,"open_issues":179,"watchers":87,"default_branch":"dev"}},"_links":{"self":{"href":"https://api.github.com/repos/galaxyproject/galaxy/pulls/1113"},"html":{"href":"https://github.com/galaxyproject/galaxy/pull/1113"},"issue":{"href":"https://api.github.com/repos/galaxyproject/galaxy/issues/1113"},"comments":{"href":"https://api.github.com/repos/galaxyproject/galaxy/issues/1113/comments"},"review_comments":{"href":"https://api.github.com/repos/galaxyproject/galaxy/pulls/1113/comments"},"review_comment":{"href":"https://api.github.com/repos/galaxyproject/galaxy/pulls/comments{/number}"},"commits":{"href":"https://api.github.com/repos/galaxyproject/galaxy/pulls/1113/commits"},"statuses":{"href":"https://api.github.com/repos/galaxyproject/galaxy/statuses/312746d1698e99e13b9a60db881d0093da6cc4c0"}}}}