function create_annotation_form(content){initWorkArea("Create annotation","");var idannotater_form=FC_Form("create_annotation","",{action:"Executer",help:"http://docs.bioinfo.cipf.es/projects/babelomics/wiki/Create_annotation_input"});idannotater_form.add(FC_Hidden("sessionid",wc_getSessionCookie()));var data_set=FC_Set("data_set","Select your data",{headered:true});var type_forall=FC_CheckBox("all_genome","All genome",true,{checked:true});data_set.add(type_forall);var datalist=FC_DataBox("listfile",
"ID list file",{},["idlist"]);var listfile=datalist.child("listfile");var listfile_messages=datalist.child("listfile_messages");data_set.add(datalist);idannotater_form.add(data_set);var db_set=FC_Set("db_set","Databases",{headered:true});var fdb=FC_Functional_Databases();var species=fdb.child("species");var annotations=fdb.child("annotations");db_set.add(fdb);idannotater_form.add(db_set);var outformat_set=FC_Set("method_set","Output format",{headered:true});var outformat_rg=FC_RadioGroup("output_format",
"",{});outformat_rg.addOption("Compact","compact");outformat_rg.addOption("Extended","extended",{checked:true});outformat_set.add(outformat_rg);idannotater_form.add(outformat_set);var job_set=FC_Set("job_set","Job",{headered:true});var jobname_tb=FC_Textbox("jobname","Job name:","jobname",{});var jobdescription_ta=FC_TextArea("jobdescription","Job description","",{});job_set.add(jobname_tb);job_set.add(jobdescription_ta);idannotater_form.add(job_set);var submit=FC_Submit("submit_button","Run",{});
idannotater_form.add(submit);listfile.addDisabilityRule("all_genome");listfile_messages.addValidationRule("!all_genome listfile=='none'","","","","select file");species.addValidationRule("species=='none'","go_bp","","","select a valid species for selected databases");species.addValidationRule("species=='none'","go_mf","","","select a valid species for selected databases");species.addValidationRule("species=='none'","go_cc","","","select a valid species for selected databases");species.addValidationRule("species=='none'",
"go_slim","","","select a valid species for selected databases");species.addValidationRule("species=='none'","interpro","","","select a valid species for selected databases");species.addValidationRule("species=='none'","kegg","","","select a valid species for selected databases");species.addValidationRule("species=='none'","reactome","","","select a valid species for selected databases");species.addValidationRule("species=='none'","biocarta","","","select a valid species for selected databases");
species.addValidationRule("species=='none'","mirna","","","select a valid species for selected databases");species.addValidationRule("species=='none'","jaspar","","","select a valid species for selected databases");species.addValidationRule("species=='none'","oreganno","","","select a valid species for selected databases");db_set.addValidationRule("!go_bp !go_mf !go_cc !go_slim !interpro !kegg !reactome !biocarta !mirna !jaspar !oreganno","","","","no database selected");idannotater_form.render("work-area-content");
$("#your_annotations_hp").hide();fc_fillForm(content);loadExamples("create_annotation");loadFeedByTags(["babelomics"],"create_annotation")};function agilent_cgh_normalization_form(content){initWorkArea("Agilent CGH Normalization","");var cgh_agi_normalization_form=FC_Form("agilent_cgh_normalization","",{action:"Executer",help:"javascript:void(0)"});cgh_agi_normalization_form.add(FC_Hidden("sessionid",wc_getSessionCookie()));var data_set=FC_Set("data_set","Select your data",{headered:true});var datalist=FC_DataBox("compressed_file","Gene expression file",{},["CGH"]);data_set.add(datalist);cgh_agi_normalization_form.add(data_set);var analysis_set=
FC_Set("analysis_set","Background correction",{headered:true});var bg_correction=FC_RadioGroup("bg_correction","",{});bg_correction.addOption("None","none",false);bg_correction.addOption("Substract","substract",false);bg_correction.addOption("Half","half",false);bg_correction.addOption("Minimum","minimum",true);bg_correction.addOption("Movingmin","movingmin",false);bg_correction.addOption("Edwards","edwards",false);bg_correction.addOption("Normexp","normexp",false);analysis_set.add(bg_correction);
cgh_agi_normalization_form.add(analysis_set);var job_set=FC_Set("job_set","Job",{headered:true});var jobname_tb=FC_Textbox("jobname","Job name:","sample name",{});var jobdescription_ta=FC_TextArea("jobdescription","Job description","",{});job_set.add(jobname_tb);job_set.add(jobdescription_ta);cgh_agi_normalization_form.add(job_set);var submit=FC_Submit("submit_button","Run",{});cgh_agi_normalization_form.add(submit);data_set.addValidationRule("compressed_file=='none'","","","","select file");cgh_agi_normalization_form.render("work-area-content");
fc_fillForm(content);loadExamples("agilent_cgh_normalization");loadFeedByTags(["gepas"],"agilent_cgh_normalization")};function genotype_form(content){initWorkArea("Genotype data preprocessing","");var geno_form=FC_Form("genotype","",{action:"Executer",help:"javascript:void(0)"});var data_set=FC_Set("data_set","Select your data",{headered:true});var list1_hp=FC_HorizontalPanel("list1_hp","",{});var list1_label=FC_Label("list1_label","Gene expression file:",{});list1_hp.add(list1_label);var list1_set=FC_Set("list1_set","",{});var list1=FC_ComboBox("list1","","none",{});list1.addOption("--","data1",{checked:true});
list1.addOption("Dataset1","data1");list1.addOption("Dataset2","data2");list1.addOption("Dataset3","data3");list1.addOption("Dataset4","data4");list1_set.add(list1);list1_hp.add(list1_set);data_set.add(list1_hp);geno_form.add(data_set);var test_set=FC_Set("comparisontest_set","Select test",{headered:true});var comparison=FC_RadioGroup("comparison","",{});comparison.addOption("Affymetrix 500k","affy500",true);comparison.addOption("Affymetrix 6.0","affy6");test_set.add(comparison);var comparisontest=
FC_CheckBox("rem_duplicates","Remove duplicates",true,{});test_set.add(comparisontest);geno_form.add(test_set);var job_set=FC_Set("job_set","Job",{headered:true});var jobname=FC_Textbox("jobname","job name:","sample name",{});job_set.add(jobname);geno_form.add(job_set);var submit=FC_Submit("submit_button","Run",{});geno_form.add(submit);geno_form.render("work-area-content");fc_fillForm(content);loadExamples("genotype");loadFeedByTags(["gepas"],"genotype")};function id_converter_form(content){$("#work-area-title").html("ID converter");$("#work-area-content").empty();var idconverter_form=FC_Form("id_converter","",{action:"Executer",help:"javascript:void(0)"});idconverter_form.add(FC_Hidden("sessionid",wc_getSessionCookie()));idconverter_form.add(FC_Hidden("db_names",""));var data_set=FC_Set("data_set","Select your data",{headered:true});var datalist=FC_DataBox("listfile","ID list file",{},["idlist"]);var datalist_messages=datalist.child("listfile_messages");
data_set.add(datalist);idconverter_form.add(data_set);var organism_set=FC_Set("organism_set","Select your organism",{headered:true});var organism=FC_ComboBox("species","Organism","none",{});organism.addOption("Select an organism","hsa",{checked:true});organism.addOption("Human (homo sapiens)","hsa");organism.addOption("Mouse (mus musculus)","mmu");organism.addOption("Rat (rattus norvegicus)","rno");organism.addOption("Chicken (gallus gallus)","gga");organism.addOption("Fruitfly (drosophila melanogaster)",
"dme");organism.addOption("Cow (bos taurus)","bta");organism.addOption("Zebrafish (danio rerio)","dre");organism.addOption("Anopheles gambiae","aga");organism.addOption("Saccharomyces cerevisiae","sce");organism.addOption("Caenorhabditis elegans","cel");organism.addOption("Arabidopsis thaliana","ath");organism_set.add(organism);idconverter_form.add(organism_set);var refs_set=FC_Set("refs_set","Select output IDs",{headered:true});idconverter_form.add(refs_set);var outformat_set=FC_Set("method_set",
"Output format",{headered:true});var outformat_rg=FC_RadioGroup("output_format","",{});outformat_rg.addOption("Compact","compact");outformat_rg.addOption("Extended","extended",{checked:true});outformat_set.add(outformat_rg);idconverter_form.add(outformat_set);var job_set=FC_Set("job_set","Job",{headered:true});var jobname_tb=FC_Textbox("jobname","Job name:","jobname",{});var jobdescription_ta=FC_TextArea("jobdescription","Job description","",{});job_set.add(jobname_tb);job_set.add(jobdescription_ta);
idconverter_form.add(job_set);var submit=FC_Submit("submit_button","Run",{});idconverter_form.add(submit);datalist_messages.addValidationRule("listfile=='none'","","","","select a valid option");organism.addValidationRule("species=='none'","","","","select a valid species for selected databases");refs_set.addValidationRule("==''","","","","check some output IDs");idconverter_form.render("work-area-content");fc_fillForm(content);loadExamples("id_converter");loadFeedByTags(["babelomics"],"id_converter");
$("#submit_button").click(function(){$("#db_names").val("");$(".fc-checkbox").each(function(){if(this.checked)$("#db_names").val($("#db_names").val()+","+this.value)});$("#db_names").val($("#db_names").val().substr(1))});$("#species").change(function(){var success=function(data){var object=eval("("+data+")");var categories=object.categories;for(var i=0;i<refs_set.children.length;i++)$("#"+refs_set.children[i].id+"_container").remove();refs_set.children=[];if(categories.length>0)for(var i=0;i<categories.length;i++){var category_set=
FC_Set("category_"+i+"_set",categories[i].name.toUpperCase(),{headered:false});for(var j=0;j<categories[i].dbnames.length;j++)category_set.add(FC_CheckBox(categories[i].dbnames[j].name,categories[i].dbnames[j].label,categories[i].dbnames[j].name,{}));refs_set.add(category_set)}if(refs_set.children.length<=0)refs_set.add(FC_Label("no_ids_found","No IDs found",{}));for(var i=0;i<refs_set.children.length;i++)refs_set.children[i].render()};var error=function(data){for(var i=0;i<refs_set.children.length;i++)$("#"+
refs_set.children[i].id+"_container").remove();refs_set.children=[];refs_set.add(FC_Label("no_ids_found","No IDs found",{}));for(var i=0;i<refs_set.children.length;i++)refs_set.children[i].render()};var url="InfraredInspector?cmd=get_dbnames&species="+$("#species").val()+"&sessionid="+wc_getSessionCookie();callGetServer(url,success,error)});$("#species").change()};function preprocessing_form(content){initWorkArea("Normalized data preprocesing","");var prep_form=FC_Form("preprocessing","",{action:"Executer",help:"http://docs.bioinfo.cipf.es/projects/babelomics/wiki/Preprocessing_data_matrix_input"});prep_form.add(FC_Hidden("sessionid",wc_getSessionCookie()));var data_set=FC_Set("data_set","Select your data",{headered:true});var datalist=FC_DataBox("dataset","Gene expression file",{},["datamatrix"]);data_set.add(datalist);prep_form.add(data_set);var comparison_set=
FC_Set("log_transform_set","Log-transform",{headered:true});var comparison=FC_RadioGroup("logarithm_base","",{});comparison.addOption("none","none",true);comparison.addOption("Log 2","2");comparison.addOption("Log e","e");comparison.addOption("Log 10","10");comparison_set.add(comparison);prep_form.add(comparison_set);var exp_set=FC_Set("exponential_function_set","Exponential function",{headered:true});var exp_rg=FC_RadioGroup("exp","",{});exp_rg.addOption("none","none",true);exp_rg.addOption("2",
"2");exp_rg.addOption("e","e");exp_rg.addOption("10","10");exp_set.add(exp_rg);prep_form.add(exp_set);var comparison_set2=FC_Set("comparison_set2","Merge replicates",{headered:true});var comparison2=FC_RadioGroup("merge_replicates","",{});comparison2.addOption("none","none",true);comparison2.addOption("Average","mean");comparison2.addOption("Median","median");comparison_set2.add(comparison2);prep_form.add(comparison_set2);var test_set=FC_Set("comparisontest_set","Filter missing values",{headered:true});
var comparisontest=FC_CheckBox("filter_missing","Check to apply this filter",true,{});var go_int=FC_Int("min_perc_int","Minimum percentage of existing values (%) ",70,{});test_set.add(comparisontest);test_set.add(go_int);go_int.addDisabilityRule("!filter_missing");prep_form.add(test_set);var comparison_set3=FC_Set("comparison_set3","Impute missing values",{headered:true});var comparison3=FC_RadioGroup("impute_missing","",{});comparison3.addOption("Do not impute","none",true);comparison3.addOption("KNN imputation",
"knn");comparison3.addOption("Row mean imputation","mean");comparison3.addOption("Row median imputation","median");comparison3.addOption("Impute with zeros","zero");comparison_set3.add(comparison3);var kvalue_int=FC_Int("kvalue","K-value ",15,{});kvalue_int.addDisabilityRule("impute_missing!='knn'");comparison_set3.add(kvalue_int);prep_form.add(comparison_set3);var extract_ids_set=FC_Set("extract_ids_set","Extract IDs from dataset and save into a file",{headered:true});var id_cb=FC_CheckBox("extract_ids",
"Check to extract IDs",true,{});extract_ids_set.add(id_cb);prep_form.add(extract_ids_set);var comparison_set4=FC_Set("comparison_set4","Filter genes by names",{headered:true});var list1=FC_DataBox("gene_file_filter","List of valid genes",{},["idlist","gene"]);comparison_set4.add(list1);prep_form.add(comparison_set4);var job_set=FC_Set("job_set","Job",{headered:true});var jobname_tb=FC_Textbox("jobname","Job name:","sample name",{});var jobdescription_ta=FC_TextArea("jobdescription","Job description",
"",{});job_set.add(jobname_tb);job_set.add(jobdescription_ta);prep_form.add(job_set);var submit=FC_Submit("submit_button","Run",{});prep_form.add(submit);data_set.addValidationRule("dataset=='none'","","","","select file");prep_form.render("work-area-content");fc_fillForm(content);loadExamples("preprocessing");loadFeedByTags(["gepas"],"preprocessing")};