{"action":"created","comment":{"url":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/comments/153498504","pull_request_review_id":79511520,"id":153498504,"diff_hunk":"@@ -0,0 +1,59 @@\n+<tool id=\"glimmer_acgt_content\" name=\"ACGT Content\" version=\"@WRAPPER_VERSION@\">\n+    <description>of windows in each sequence</description>\n+    <macros>\n+\t       <import>macros.xml</import>\n+    </macros>\n+    <expand macro=\"requirements\"/>\n+    <command><![CDATA[\n+        window-acgt\n+            $percentage\n+            $input_win_len\n+            $input_win_skip\n+            < '$infile' > '$output'\n+\n+            ##TODO prettify the output\n+    ]]></command>\n+    <inputs>\n+        <param name=\"infile\" type=\"data\" format=\"fasta\" label=\"Genome Sequence\"/>\n+        <param name=\"input_win_len\" type=\"integer\" value=\"10\" label=\"The width of the sliding window\"/>\n+        <param name=\"input_win_skip\" type=\"integer\" value=\"10\" label=\"The number of positions between windows to report\"/>\n+        <param name=\"percentage\" type=\"boolean\" truevalue=\"-p\" falsevalue=\"\" checked=\"true\" label=\"Report percentages instead of counts\"/>\n+    </inputs>\n+    <outputs>\n+        <data name=\"output\" format=\"tabular\"/>\n+    </outputs>\n+    <tests>\n+        <test>\n+            <param name=\"infile\" value=\"streptomyces_Tu6071_genomic.fasta\" />\n+            <output name=\"output\" file=\"streptomyces_Tu6071_genomic.acgt\" />\n+        </test>\n+    </tests>\n+    <help>\n+<![CDATA[\n+\n+**What it does**\n+\n+This tool calculates the ACGT-Content from a given Sequence, given a sliding window.\n+\n+-------\n+\n+**Output**\n+\n+Output is in the format:\n+\n+\twindow-start\twindow-len\tA's\tC's\tG's\tT's\t#other\t%GC\n+\n+Note the last window in the sequence can be shorter than *window-len* if the sequence ends prematurely\n+\n+\n+\n+\n+**References**\n+\n+A.L. Delcher, K.A. Bratke, E.C. Powers, and S.L. Salzberg. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics (Advance online version) (2007).","path":"tools/glimmer/glimmer_acgt_content.xml","position":53,"original_position":53,"commit_id":"ac1fc739bf053d6c1e63eaac70e56a5638024b0b","original_commit_id":"ac1fc739bf053d6c1e63eaac70e56a5638024b0b","user":{"login":"bgruening","id":469983,"avatar_url":"https://avatars2.githubusercontent.com/u/469983?v=4","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":"can this now be removed if we have a citation?","created_at":"2017-11-28T13:59:27Z","updated_at":"2017-11-28T14:02:43Z","html_url":"https://github.com/galaxyproject/tools-iuc/pull/1593#discussion_r153498504","pull_request_url":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/1593","author_association":"MEMBER","_links":{"self":{"href":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/comments/153498504"},"html":{"href":"https://github.com/galaxyproject/tools-iuc/pull/1593#discussion_r153498504"},"pull_request":{"href":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/1593"}}},"pull_request":{"url":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/1593","id":153651419,"html_url":"https://github.com/galaxyproject/tools-iuc/pull/1593","diff_url":"https://github.com/galaxyproject/tools-iuc/pull/1593.diff","patch_url":"https://github.com/galaxyproject/tools-iuc/pull/1593.patch","issue_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/1593","number":1593,"state":"open","locked":false,"title":"Migrate Glimmer tools","user":{"login":"abretaud","id":238755,"avatar_url":"https://avatars3.githubusercontent.com/u/238755?v=4","gravatar_id":"","url":"https://api.github.com/users/abretaud","html_url":"https://github.com/abretaud","followers_url":"https://api.github.com/users/abretaud/followers","following_url":"https://api.github.com/users/abretaud/following{/other_user}","gists_url":"https://api.github.com/users/abretaud/gists{/gist_id}","starred_url":"https://api.github.com/users/abretaud/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/abretaud/subscriptions","organizations_url":"https://api.github.com/users/abretaud/orgs","repos_url":"https://api.github.com/users/abretaud/repos","events_url":"https://api.github.com/users/abretaud/events{/privacy}","received_events_url":"https://api.github.com/users/abretaud/received_events","type":"User","site_admin":false},"body":"Hi,\r\nAs discussed in https://github.com/bgruening/galaxytools/pull/660, here's a PR to condafy and update the glimmer tools that are currently in https://github.com/bgruening/galaxytools/\r\n\r\nIt uses a not-yet-merged new datatype: https://github.com/galaxyproject/galaxy/pull/5042\r\n\r\nI had to rename the tools because their id was invalid (`-` in their id), and as I did it, I created a proper tool suite. I kept the owner as bgruening in .shed.yml, but I guess it will be hard to keep the tool lineage... Any thought on that?\r\n\r\nAnthony","created_at":"2017-11-20T15:01:39Z","updated_at":"2017-11-28T14:02:43Z","closed_at":null,"merged_at":null,"merge_commit_sha":"d263783d6f45f4bb4b4a45cb7b27d45b43d25172","assignee":null,"assignees":[],"requested_reviewers":[],"milestone":null,"commits_url":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/1593/commits","review_comments_url":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/1593/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/1593/comments","statuses_url":"https://api.github.com/repos/galaxyproject/tools-iuc/statuses/ac1fc739bf053d6c1e63eaac70e56a5638024b0b","head":{"label":"abretaud:glimmer","ref":"glimmer","sha":"ac1fc739bf053d6c1e63eaac70e56a5638024b0b","user":{"login":"abretaud","id":238755,"avatar_url":"https://avatars3.githubusercontent.com/u/238755?v=4","gravatar_id":"","url":"https://api.github.com/users/abretaud","html_url":"https://github.com/abretaud","followers_url":"https://api.github.com/users/abretaud/followers","following_url":"https://api.github.com/users/abretaud/following{/other_user}","gists_url":"https://api.github.com/users/abretaud/gists{/gist_id}","starred_url":"https://api.github.com/users/abretaud/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/abretaud/subscriptions","organizations_url":"https://api.github.com/users/abretaud/orgs","repos_url":"https://api.github.com/users/abretaud/repos","events_url":"https://api.github.com/users/abretaud/events{/privacy}","received_events_url":"https://api.github.com/users/abretaud/received_events","type":"User","site_admin":false},"repo":{"id":45838293,"name":"tools-iuc","full_name":"abretaud/tools-iuc","owner":{"login":"abretaud","id":238755,"avatar_url":"https://avatars3.githubusercontent.com/u/238755?v=4","gravatar_id":"","url":"https://api.github.com/users/abretaud","html_url":"https://github.com/abretaud","followers_url":"https://api.github.com/users/abretaud/followers","following_url":"https://api.github.com/users/abretaud/following{/other_user}","gists_url":"https://api.github.com/users/abretaud/gists{/gist_id}","starred_url":"https://api.github.com/users/abretaud/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/abretaud/subscriptions","organizations_url":"https://api.github.com/users/abretaud/orgs","repos_url":"https://api.github.com/users/abretaud/repos","events_url":"https://api.github.com/users/abretaud/events{/privacy}","received_events_url":"https://api.github.com/users/abretaud/received_events","type":"User","site_admin":false},"private":false,"html_url":"https://github.com/abretaud/tools-iuc","description":"Tool Shed repositories maintained and developed by the Intergalactic Utilities Commission","fork":true,"url":"https://api.github.com/repos/abretaud/tools-iuc","forks_url":"https://api.github.com/repos/abretaud/tools-iuc/forks","keys_url":"https://api.github.com/repos/abretaud/tools-iuc/keys{/key_id}","collaborators_url":"https://api.github.com/repos/abretaud/tools-iuc/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/abretaud/tools-iuc/teams","hooks_url":"https://api.github.com/repos/abretaud/tools-iuc/hooks","issue_events_url":"https://api.github.com/repos/abretaud/tools-iuc/issues/events{/number}","events_url":"https://api.github.com/repos/abretaud/tools-iuc/events","assignees_url":"https://api.github.com/repos/abretaud/tools-iuc/assignees{/user}","branches_url":"https://api.github.com/repos/abretaud/tools-iuc/branches{/branch}","tags_url":"https://api.github.com/repos/abretaud/tools-iuc/tags","blobs_url":"https://api.github.com/repos/abretaud/tools-iuc/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/abretaud/tools-iuc/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/abretaud/tools-iuc/git/refs{/sha}","trees_url":"https://api.github.com/repos/abretaud/tools-iuc/git/trees{/sha}","statuses_url":"https://api.github.com/repos/abretaud/tools-iuc/statuses/{sha}","languages_url":"https://api.github.com/repos/abretaud/tools-iuc/languages","stargazers_url":"https://api.github.com/repos/abretaud/tools-iuc/stargazers","contributors_url":"https://api.github.com/repos/abretaud/tools-iuc/contributors","subscribers_url":"https://api.github.com/repos/abretaud/tools-iuc/subscribers","subscription_url":"https://api.github.com/repos/abretaud/tools-iuc/subscription","commits_url":"https://api.github.com/repos/abretaud/tools-iuc/commits{/sha}","git_commits_url":"https://api.github.com/repos/abretaud/tools-iuc/git/commits{/sha}","comments_url":"https://api.github.com/repos/abretaud/tools-iuc/comments{/number}","issue_comment_url":"https://api.github.com/repos/abretaud/tools-iuc/issues/comments{/number}","contents_url":"https://api.github.com/repos/abretaud/tools-iuc/contents/{+path}","compare_url":"https://api.github.com/repos/abretaud/tools-iuc/compare/{base}...{head}","merges_url":"https://api.github.com/repos/abretaud/tools-iuc/merges","archive_url":"https://api.github.com/repos/abretaud/tools-iuc/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/abretaud/tools-iuc/downloads","issues_url":"https://api.github.com/repos/abretaud/tools-iuc/issues{/number}","pulls_url":"https://api.github.com/repos/abretaud/tools-iuc/pulls{/number}","milestones_url":"https://api.github.com/repos/abretaud/tools-iuc/milestones{/number}","notifications_url":"https://api.github.com/repos/abretaud/tools-iuc/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/abretaud/tools-iuc/labels{/name}","releases_url":"https://api.github.com/repos/abretaud/tools-iuc/releases{/id}","deployments_url":"https://api.github.com/repos/abretaud/tools-iuc/deployments","created_at":"2015-11-09T13:03:49Z","updated_at":"2016-02-05T13:57:12Z","pushed_at":"2017-11-28T13:36:59Z","git_url":"git://github.com/abretaud/tools-iuc.git","ssh_url":"git@github.com:abretaud/tools-iuc.git","clone_url":"https://github.com/abretaud/tools-iuc.git","svn_url":"https://github.com/abretaud/tools-iuc","homepage":"https://wiki.galaxyproject.org/IUC","size":244751,"stargazers_count":0,"watchers_count":0,"language":"Python","has_issues":false,"has_projects":true,"has_downloads":true,"has_wiki":true,"has_pages":false,"forks_count":0,"mirror_url":null,"archived":false,"open_issues_count":0,"forks":0,"open_issues":0,"watchers":0,"default_branch":"master"}},"base":{"label":"galaxyproject:master","ref":"master","sha":"883d4cd19450fd7a09bbc8f9cf28570e65a202f2","user":{"login":"galaxyproject","id":7937847,"avatar_url":"https://avatars3.githubusercontent.com/u/7937847?v=4","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://avatars3.githubusercontent.com/u/7937847?v=4","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 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}","deployments_url":"https://api.github.com/repos/galaxyproject/tools-iuc/deployments","created_at":"2014-09-13T11:18:49Z","updated_at":"2017-11-20T17:37:35Z","pushed_at":"2017-11-28T13:37:01Z","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://galaxyproject.org/iuc","size":244174,"stargazers_count":48,"watchers_count":48,"language":"Python","has_issues":true,"has_projects":true,"has_downloads":true,"has_wiki":false,"has_pages":false,"forks_count":139,"mirror_url":null,"archived":false,"open_issues_count":196,"forks":139,"open_issues":196,"watchers":48,"default_branch":"master"}},"_links":{"self":{"href":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/1593"},"html":{"href":"https://github.com/galaxyproject/tools-iuc/pull/1593"},"issue":{"href":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/1593"},"comments":{"href":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/1593/comments"},"review_comments":{"href":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/1593/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/1593/commits"},"statuses":{"href":"https://api.github.com/repos/galaxyproject/tools-iuc/statuses/ac1fc739bf053d6c1e63eaac70e56a5638024b0b"}},"author_association":"CONTRIBUTOR"}}
{"actor":{"display_login":"bgruening"}}