{"action":"created","comment":{"url":"https://api.github.com/repos/genome/genome/pulls/comments/26695371","id":26695371,"diff_hunk":"@@ -9,24 +9,27 @@ use Path::Class qw();\n class Genome::Model::Tools::Transcriptome::ErccMapUnaligned {\n     is => 'Command::V2',\n     has_input => [\n+        model => {\n+            is => 'Text',\n+            doc => 'A RNASeq model that has ERCC transcripts spiked in.',\n+            is_optional => '1,',\n+        },\n         bam_file => {\n             is => 'FilePath',\n-            doc => 'An aligned BAM file to a reference genome without the ERCC transcripts spiked in.',\n+            doc => 'A path to a BAM file that has ERCC transcripts spiked in.',\n+            is_optional => '1,',\n         },\n         ercc_fasta_file => {\n             is => 'FilePath',\n             doc => 'The FASTA format sequence for all ERCC transcripts.',\n-            example_values => ['/gscmnt/gc13001/info/model_data/jwalker_scratch/ERCC/ERCC92.fa'],\n+            default_value => '/gscmnt/gc13001/info/model_data/jwalker_scratch/ERCC/ERCC92.fa',\n+            is_optional => '1',\n         },\n         ercc_spike_in_file => {\n             is => 'FilePath',\n             doc => 'The control analysis file provided by Agilent for the ERCC spike-in.',\n-            example_values => ['/gscmnt/gc13001/info/model_data/jwalker_scratch/ERCC/ERCC_Controls_Analysis.txt'],\n-        },\n-        ercc_spike_in_mix => {\n-            is => 'Integer',\n-            doc => 'The name of the Life Technologies ERCC spike-in mixture.',\n-            valid_values => [ '1', '2'],\n+            default_value => '/gscmnt/gc13001/info/model_data/jwalker_scratch/ERCC/ERCC_Controls_Analysis.txt',","path":"lib/perl/Genome/Model/Tools/Transcriptome/ErccMapUnaligned.pm","position":31,"original_position":31,"commit_id":"acd55e46cee0669ab0503f739d1cec040e350c25","original_commit_id":"acd55e46cee0669ab0503f739d1cec040e350c25","user":{"login":"jasonwalker80","id":884229,"avatar_url":"https://avatars.githubusercontent.com/u/884229?v=3","gravatar_id":"","url":"https://api.github.com/users/jasonwalker80","html_url":"https://github.com/jasonwalker80","followers_url":"https://api.github.com/users/jasonwalker80/followers","following_url":"https://api.github.com/users/jasonwalker80/following{/other_user}","gists_url":"https://api.github.com/users/jasonwalker80/gists{/gist_id}","starred_url":"https://api.github.com/users/jasonwalker80/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jasonwalker80/subscriptions","organizations_url":"https://api.github.com/users/jasonwalker80/orgs","repos_url":"https://api.github.com/users/jasonwalker80/repos","events_url":"https://api.github.com/users/jasonwalker80/events{/privacy}","received_events_url":"https://api.github.com/users/jasonwalker80/received_events","type":"User","site_admin":false},"body":"For the ERCC txt file:\r\n1. We could create a generic allocation, see `genome disk allocation create --help`\r\n2. Use an imported variation list : https://confluence.gsc.wustl.edu/display/BIO/GMS+-+Imported+Variation+List\r\n3. Create a genome db, see `genome db --help`\r\n\r\n@apregier, other suggestions?","created_at":"2015-03-18T18:56:05Z","updated_at":"2015-03-18T18:56:05Z","html_url":"https://github.com/genome/genome/pull/568#discussion_r26695371","pull_request_url":"https://api.github.com/repos/genome/genome/pulls/568","_links":{"self":{"href":"https://api.github.com/repos/genome/genome/pulls/comments/26695371"},"html":{"href":"https://github.com/genome/genome/pull/568#discussion_r26695371"},"pull_request":{"href":"https://api.github.com/repos/genome/genome/pulls/568"}}},"pull_request":{"url":"https://api.github.com/repos/genome/genome/pulls/568","id":31381796,"html_url":"https://github.com/genome/genome/pull/568","diff_url":"https://github.com/genome/genome/pull/568.diff","patch_url":"https://github.com/genome/genome/pull/568.patch","issue_url":"https://api.github.com/repos/genome/genome/issues/568","number":568,"state":"open","locked":false,"title":"ERCC-based Quality Control Screening for RNASeq: Part 2","user":{"login":"indraniel","id":42710,"avatar_url":"https://avatars.githubusercontent.com/u/42710?v=3","gravatar_id":"","url":"https://api.github.com/users/indraniel","html_url":"https://github.com/indraniel","followers_url":"https://api.github.com/users/indraniel/followers","following_url":"https://api.github.com/users/indraniel/following{/other_user}","gists_url":"https://api.github.com/users/indraniel/gists{/gist_id}","starred_url":"https://api.github.com/users/indraniel/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/indraniel/subscriptions","organizations_url":"https://api.github.com/users/indraniel/orgs","repos_url":"https://api.github.com/users/indraniel/repos","events_url":"https://api.github.com/users/indraniel/events{/privacy}","received_events_url":"https://api.github.com/users/indraniel/received_events","type":"User","site_admin":false},"body":"This is \"Part 2\" of a 2-part introduction of a RNASeq quality control tool to address a need mentioned in BIO-1345.  [Part 1][1] was focused on getting the tool infrastructure and plumbing setup.  Part 2 is focused on the analysis being done and what kind of inputs and outputs the end user will need to supply and observe respectively.\r\n\r\n## High-Level Summary of Perl Script Changes:\r\n\r\n* A user must supply either a model ID, or a specific BAM file path, but not both.\r\n* A number of required input parameters have been changed to optional and sensible default values have been placed for them.\r\n* There are two specific files created by the tool that the end-user will notice: a PDF file containing analysis plots and a TSV file containing the raw data used to make the PDF file.  Both these file names are auto-generated by what the user supplied as inputs.\r\n* The contents and structure of TSV file was changed for the R script.\r\n\r\n\r\n## High-Level Summary of R Script Changes:\r\n\r\n* Apply some software-engineering to the script.  Everything is modularized into functions.\r\n* Introduce a [goodness of fit test][2] to evaluate which ERCC Mixture (Mix 1 or 2) was used in the RNASeq dataset.\r\n* Remove 2 kinds of plots used in Part 1.  They were uninformative.\r\n* Add 2 new \"observed vs expected\" plots for ERCC Mixtures 1 and 2.  They let the end-user do a [goodness of fit][2] by their own eyes.\r\n* Add titles and axis labels on all the plots.\r\n* Display some useful alignment summary table statistics for the end user.\r\n* Tried to minimize the number of extraneous status & warnings messages issued by R.\r\n\r\n[1]: https://github.com/genome/genome/pull/557\r\n[2]: 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