{"action":"created","comment":{"url":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/comments/41171372","id":41171372,"diff_hunk":"@@ -0,0 +1,165 @@\n+<tool id=\"read_450k_IDAT\" name=\"Read Illumina 450k IDAT \" version=\"1.0\">\n+    <description>format to get Beta Values</description>\n+    <requirements>\n+        <requirement type=\"package\" version=\"1.15.7\">minfi</requirement>\n+    </requirements>\n+    <stdio>\n+        <exit_code range=\"1:\" />\n+    </stdio>\n+    <command>\n+      cp \"${minfi_get_files}\" $__new_file_path__/minfi_config.txt;\n+        Rscript \"${minfi_read_450k_script}\"\n+    </command>\n+       <configfiles>\n+        <configfile name=\"minfi_get_files\"><![CDATA[\n+          ### Parse the HDA's to get the path of each forward and reverse dataset\n+          #for $key in $control.keys()\n+          control $control[$key].forward  $control[$key].reverse $control[$key].name\n+          #end for\n+          #for $key in $case.keys()\n+          case  $case[$key].forward $case[$key].reverse $case[$key].name\n+          #end for\n+      ]]></configfile>\n+        <configfile name=\"minfi_read_450k_script\"><![CDATA[\n+\n+          ### Start time for code, approximate\n+          timeStart <- as.character(Sys.time())\n+          ### code chunk number 2: Load all required libraries\n+          library(minfi, quietly=TRUE, warn.conflicts=FALSE,verbose = FALSE)\n+          ### code chunk number 3: Update package version\n+          if (packageVersion(\"minfi\") < \"1.15.6\") {\n+            stop(\"Please update 'minfi' to version >= 1.15.7  to run this tool\")\n+          }\n+\n+          ### Parse cheetah code and make dataframe for creating tmp dir\n+          minfi_config_path = paste0(\"$__new_file_path__\",\"/minfi_config.txt\")\n+          minfi_config = read.table(minfi_config_path)\n+          colnames(minfi_config) = c(\"status\",\"green\",\"red\",\"name\")\n+\n+          ### Make the tmpdir for symlinking data\n+          base_dir = paste0(\"$__new_file_path__\",\"/base\")\n+          system(paste0(\"mkdir \",base_dir))\n+\n+          ### Make symlinks of files\n+          for (i in 1:nrow(minfi_config)){\n+            stopifnot(nrow(minfi_config) == nrow(minfi_config[\"name\"]))\n+\n+            ### Make green idat file symlinks\n+            file_green = paste0(base_dir,\"/\",as.character(minfi_config[i,\"name\"]),\"_Grn.idat\")\n+            cmd_green = paste(\"ln -s\",as.character(minfi_config[i,\"green\"]),file_green,sep=\" \")\n+            cat(\"Reading file \",i,\"GREEN Channel \", file_green)\n+            system(cmd_green)\n+\n+            ### Make red idat file symlinks\n+            file_red = paste0(base_dir,\"/\",as.character(minfi_config[i,\"name\"]),\"_Red.idat\")\n+            cmd_red = paste(\"ln -s\",as.character(minfi_config[i,\"red\"]),file_red,sep=\" \")\n+            cat(\"Reading file \",i,\"RED Channel \", file_red)\n+            system(cmd_red)\n+          }\n+\n+          ### Make dataframe with Basenames\n+          Basename = paste0(base_dir,\"/\",unique(substr(list.files(base_dir),1,17)))\n+          status = minfi_config[match(gsub(\".+/\",\"\",Basename), minfi_config\\$name),\"status\"]\n+          targets = data.frame(Basename=Basename,status=status)\n+\n+          targets\n+          ### Read 450k files\n+          RGset = read.450k.exp(targets=targets,verbose=T)\n+          RGset\n+\n+\n+          ## Preprocess data with the normalization method chosen\n+          if(\"${preprocess.preprocess_method}\" == \"quantile\"){\n+              normalized_RGset = preprocessQuantile(RGset)\n+          } else if (\"${preprocess.preprocess_method}\" == \"noob\"){\n+              normalized_RGset = preprocessNoob(RGset)\n+          } else if (\"${preprocess.preprocess_method}\" == \"raw\"){\n+              normalized_RGset = preprocessRaw(RGset)\n+          } else if (\"${preprocess.preprocess_method}\" == \"illumina\"){\n+              normalized_RGset = preprocessIllumina(RGset,bg.correct = TRUE, normalize = c(\"controls\", \"no\"),reference = 1)\n+          } else {\n+              normalized_RGset = RGset\n+          }\n+          ### else if (\"${preprocess.preprocess_method}\" == \"swan\"){\n+          ###    normalized_RGset = preprocessSWAN(RGset)\n+\n+\n+          ### Save file as RGset in the working directory OUTPUT-1\n+          getwd()\n+          save(RGset, file=\"RGset.RData\")\n+\n+\n+          ## Get beta values from Proprocessed data\n+          beta = getBeta(normalized_RGset)\n+          ## Save beta values OUTPUT-2\n+          write.table(beta,file = \"beta_values.txt\",quote=FALSE,row.names=FALSE)\n+\n+      ]]></configfile>\n+    </configfiles>\n+    <inputs>\n+        <param name=\"control\" type=\"data_collection\" format=\"idat\" label=\"Control\" collection_type=\"list:paired\"/>\n+        <param name=\"case\" type=\"data_collection\" format=\"idat\" label=\"Case\" collection_type=\"list:paired\"/>\n+        <conditional name=\"preprocess\">\n+           <param name=\"preprocess_method\" type=\"select\" label=\"Select Preprocessing Method\">\n+              <option value=\"no_normalization\">No Normalization</option>\n+              <option value=\"quantile\">Quantile Normalization</option>\n+              <option value=\"raw\">Raw Normalization</option>\n+              <option value=\"noob\">Noob Normalization</option>\n+              <option value=\"illumina\">Illumina:Genome Studio Normalization</option>\n+           </param>\n+        </conditional>\n+    </inputs>\n+    <outputs>\n+        <data name=\"RGset\" format=\"RData\" label=\"RGset from input IDAT files\" from_work_dir=\"RGset.RData\"/>\n+        <data name=\"beta_values\" format=\"txt\" label=\"Beta value matrix from input IDAT files\" from_work_dir=\"beta_values.txt\"/>\n+    </outputs>\n+    <!-- WRITE TESTS -->\n+    <help><![CDATA[\n+\n+**What it does**\n+\n+Reads in Illumina 450K file which are in IDAT format. Each sample needs both the Red and Green channel IDAT files.\n+\n+\n+**Input**:\n+\n+*Case* : Dataset collection with all samples which are of one phenotype (Example: Cancer, Disease state, Phenotype 1)\n+\n+*Control* : Dataset collection with all samples which are of base normal phenotype (Example: Normals, Non-Disease state, Phenotype 2)\n+\n+*Select Preprocessing Method*: Choose one of the many preprocessing methods available. For more information on the different preprocessing methods\n+refer to the minfi manual, https://www.bioconductor.org/packages/release/bioc/manuals/minfi/man/minfi.pdf\n+\n+**Output**:\n+\n+RData file, which contains the RGset for IDAT files. RGSet is a RGChannelSet object, which contains the raw data from the IDAT files: green intensities and red intensities.\n+\n+\n+Beta values, text file of all the beta values contained in the samples.\n+\n+**How to Use**\n+\n+IDAT files (Both Red and Green channel). Make paired dataset collections, with RED and GREEN channel IDAT files.\n+","path":"tool_collections/methylation_toolkit/minfi_tools/read_450k_IDAT.xml","position":143,"original_position":143,"commit_id":"9ab46773fe78d41285987286c1786cde52f549cb","original_commit_id":"9ab46773fe78d41285987286c1786cde52f549cb","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":"I'm not sure this should be part of a Tool. The interface and wording can change of Galaxy functionality, this wrappers needs to stay :)","created_at":"2015-10-05T17:23:13Z","updated_at":"2015-10-05T17:23:13Z","html_url":"https://github.com/galaxyproject/tools-iuc/pull/274#discussion_r41171372","pull_request_url":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/274","_links":{"self":{"href":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/comments/41171372"},"html":{"href":"https://github.com/galaxyproject/tools-iuc/pull/274#discussion_r41171372"},"pull_request":{"href":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/274"}}},"pull_request":{"url":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/274","id":45093544,"html_url":"https://github.com/galaxyproject/tools-iuc/pull/274","diff_url":"https://github.com/galaxyproject/tools-iuc/pull/274.diff","patch_url":"https://github.com/galaxyproject/tools-iuc/pull/274.patch","issue_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/274","number":274,"state":"open","locked":false,"title":"Methylation Toolkit (WIP)","user":{"login":"nitesh1989","id":2746443,"avatar_url":"https://avatars.githubusercontent.com/u/2746443?v=3","gravatar_id":"","url":"https://api.github.com/users/nitesh1989","html_url":"https://github.com/nitesh1989","followers_url":"https://api.github.com/users/nitesh1989/followers","following_url":"https://api.github.com/users/nitesh1989/following{/other_user}","gists_url":"https://api.github.com/users/nitesh1989/gists{/gist_id}","starred_url":"https://api.github.com/users/nitesh1989/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nitesh1989/subscriptions","organizations_url":"https://api.github.com/users/nitesh1989/orgs","repos_url":"https://api.github.com/users/nitesh1989/repos","events_url":"https://api.github.com/users/nitesh1989/events{/privacy}","received_events_url":"https://api.github.com/users/nitesh1989/received_events","type":"User","site_admin":false},"body":"Added \"Minfi\" methylation tool. \r\n\r\n -Need to add some test cases\r\n -Clean up some of the syntax \r\n -Write README documentation for tool usage\r\n\r\n_Upcoming:_\r\n\r\nMore methylation tools, starting with ELMER(bioconductor)\r\nFunctions in methylation toolkit which work with parallel packages in R, should work on galaxy. (Ex: bumphunter)\r\n","created_at":"2015-09-15T19:47:34Z","updated_at":"2015-10-05T17:23:13Z","closed_at":null,"merged_at":null,"merge_commit_sha":"9e828e3e00f4fe9646baeb00137fdacaaf5d8616","assignee":null,"milestone":null,"commits_url":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/274/commits","review_comments_url":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/274/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/274/comments","statuses_url":"https://api.github.com/repos/galaxyproject/tools-iuc/statuses/9ab46773fe78d41285987286c1786cde52f549cb","head":{"label":"nitesh1989:methylation","ref":"methylation","sha":"9ab46773fe78d41285987286c1786cde52f549cb","user":{"login":"nitesh1989","id":2746443,"avatar_url":"https://avatars.githubusercontent.com/u/2746443?v=3","gravatar_id":"","url":"https://api.github.com/users/nitesh1989","html_url":"https://github.com/nitesh1989","followers_url":"https://api.github.com/users/nitesh1989/followers","following_url":"https://api.github.com/users/nitesh1989/following{/other_user}","gists_url":"https://api.github.com/users/nitesh1989/gists{/gist_id}","starred_url":"https://api.github.com/users/nitesh1989/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nitesh1989/subscriptions","organizations_url":"https://api.github.com/users/nitesh1989/orgs","repos_url":"https://api.github.com/users/nitesh1989/repos","events_url":"https://api.github.com/users/nitesh1989/events{/privacy}","received_events_url":"https://api.github.com/users/nitesh1989/received_events","type":"User","site_admin":false},"repo":{"id":42542123,"name":"tools-iuc","full_name":"nitesh1989/tools-iuc","owner":{"login":"nitesh1989","id":2746443,"avatar_url":"https://avatars.githubusercontent.com/u/2746443?v=3","gravatar_id":"","url":"https://api.github.com/users/nitesh1989","html_url":"https://github.com/nitesh1989","followers_url":"https://api.github.com/users/nitesh1989/followers","following_url":"https://api.github.com/users/nitesh1989/following{/other_user}","gists_url":"https://api.github.com/users/nitesh1989/gists{/gist_id}","starred_url":"https://api.github.com/users/nitesh1989/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nitesh1989/subscriptions","organizations_url":"https://api.github.com/users/nitesh1989/orgs","repos_url":"https://api.github.com/users/nitesh1989/repos","events_url":"https://api.github.com/users/nitesh1989/events{/privacy}","received_events_url":"https://api.github.com/users/nitesh1989/received_events","type":"User","site_admin":false},"private":false,"html_url":"https://github.com/nitesh1989/tools-iuc","description":"Tool 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