# oneChannelGUI Menu Definitions

# last modified 10 07 2007 RA Calogero 

# Based on Rcmdr-menus.txt from the Rcmdr package by John Fox, 

#   type    menu/item      operation/parent label                                                          command/menu

    menu    NGSMenu         topMenu         ""                                                              ""
    item    NGSMenu         command         "oneChannelGUI: miRNAs fq linker trimming"                                            adaptorTrimm
    item    NGSMenu        separator       ""                                                              ""
    item    NGSMenu         command         "oneChannelGUI: New RNA-seq project"                                            NewLimmaFileNGS
    item    NGSMenu         command         "oneChannelGUI: Open    Ctrl+O"                                 OpenLimmaFile
    item    NGSMenu         command         "oneChannelGUI: Save As"                                        SaveAsLimmaFile
    item    NGSMenu        separator       ""                                                              ""
    item    NGSMenu        command         "oneChannelGUI: Info about the loaded data set"                 showDataset
    item    NGSMenu        command         "oneChannelGUI: Export Normalized Expression Values"            ExportNormalizedExpressionValues1
    item    NGSMenu        separator       ""                                                              ""
    item    NGSMenu        command         "affylmGUI: Working Directory"                                  SetWD
    item    NGSMenu        separator       ""                                                              ""
    item    NGSMenu        command         "affylmGUI: Exit"                                               onExit
    item    topMenu         cascade         "File (RNA-seq)"                                               NGSMenu
    
    menu    fileMenu        topMenu         ""                                                              ""
    item    fileMenu        command         "oneChannelGUI: New     Ctrl+N"                                 NewLimmaFile
    item    fileMenu        command         "oneChannelGUI: Open    Ctrl+O"                                 OpenLimmaFile
    item    fileMenu        command         "oneChannelGUI: Save As"                                        SaveAsLimmaFile
    item    fileMenu        separator       ""                                                              ""
    item    fileMenu        command         "oneChannelGUI: Info about the loaded data set"                 showDataset
    item    fileMenu        separator       ""                                                              ""
    item    fileMenu        command         "affylmGUI: Working Directory"                                  SetWD
    item    fileMenu        separator       ""                                                              ""
    item    fileMenu        command         "affylmGUI: Exit"                                               onExit
    item    topMenu         cascade         "File (Microarray)"                                                          fileMenu

    menu    RNATargetsMenu  topMenu         ""                                                              ""
    item    RNATargetsMenu  command         "affylmGUI: View RNA Targets"                                   ViewRNATargets
    item    topMenu         cascade         "RNA Targets"                                                   RNATargetsMenu

    menu    miRNAMenu  topMenu         ""                                                              ""
    item    miRNAMenu  command         "oneChannelGUI: miRNA differential expression"                                   miRNAde
    item    miRNAMenu  command         "oneChannelGUI: miRNA DE filtering"                                   deseq2Processing
    item    miRNAMenu   command         "oneChannelGUI: Predicted miRNA-targets enrichment analysis"                          mirPath
    item    topMenu         cascade         "miRNA DESeq2"                                                   miRNAMenu

    menu    tuxedoMenu   topMenu         ""                                                              ""
    item    tuxedoMenu   command         "oneChannelGUI: Create a folder for each sample described in a target file"                          createDir
    item    tuxedoMenu   command         "oneChannelGUI: Execute tophat for one sample, exec in background"                          tophat
    item    tuxedoMenu   command         "oneChannelGUI: Execute cufflinks for all samples, exec in background"               cufflinks
    item    tuxedoMenu   command         "oneChannelGUI: Merge cufflinks results, exec in background"                          cuffmerge
    item    tuxedoMenu   command         "oneChannelGUI: Detect differential expression, exec in background"                 cuffdiff
    item    tuxedoMenu   separator       ""                                                              ""
    item    tuxedoMenu   command         "oneChannelGUI: Extract gene differential expression"                   geneDiff
    item    tuxedoMenu   command         "oneChannelGUI: Extract isoforms differential expression"                   isoDiff
 #   item    tuxedoMenu   command         "oneChannelGUI: Extract CDSs differential expression"                   cdsDiff
    item    tuxedoMenu   separator       ""                                                              ""
    item    tuxedoMenu   command         "oneChannelGUI: Open pdf output"                          openPdf
    item    tuxedoMenu   command         "oneChannelGUI: Close pdf output"                          closePdf

    item    topMenu         cascade         "TopHat and CuffLinks"                                             tuxedoMenu

    menu    dexMenu   topMenu         ""                                                              ""
    item    dexMenu   command         "oneChannelGUI: Create a folder for each sample described in a target file"                 createDir
    item    dexMenu   command         "oneChannelGUI: Execute tophat for one sample, exec in background"                          tophat
    item    dexMenu   command         "oneChannelGUI: Converting a bam in sam file"                          makeSam
    item    dexMenu   separator       ""                                                              ""
    item    dexMenu   command         "oneChannelGUI: Creating exon-level counts files"                          dexCounts
    item    dexMenu   command         "oneChannelGUI: Differential expression analysis at exon-level"                          dexExons
    item    dexMenu   command         "oneChannelGUI: Filter and save differentially expressed exons"                       topTable.exons
    item    dexMenu   command         "oneChannelGUI: Plot splicing (one gene only)"                          plotDE.exons
    item    dexMenu   separator       ""                                                              ""
#    item    dexMenu   command         "oneChannelGUI: Creating gene-level counts files"                          desCounts
#    item    dexMenu   command         "oneChannelGUI: Differential expression analysis at gene-level"                          desGenes
#    item    dexMenu   command         "oneChannelGUI: Filter and save differentially expressed genes"                       topTable.genes
    item    dexMenu   separator       ""                                                              ""
    item    dexMenu   command         "oneChannelGUI: Open pdf output"                          openPdf
    item    dexMenu   command         "oneChannelGUI: Close pdf output"                          closePdf
    item    topMenu         cascade         "DEXSeq"                                             dexMenu

    menu    chimeraMenu   topMenu         ""                                                              ""
    item    chimeraMenu   command         "oneChannelGUI: Import fusion data"                 importfusions
    item    chimeraMenu   command         "oneChannelGUI: Extract fusion names"                          fusionNS
    item    chimeraMenu   command         "oneChannelGUI: Filter fusions"                          fusionfilter
    item    chimeraMenu   command         "oneChannelGUI: Add sequence data to a fusion object"                          chimeraseq
    item    chimeraMenu   command         "oneChannelGUI: Generate coverage data"                          tophatrun
    item    chimeraMenu   command         "oneChannelGUI: Add coverage data to a fusion object"                       addga
    item    chimeraMenu   command         "oneChannelGUI: Plot fusion coverage"                          plotcoverage
    item    chimeraMenu   command         "oneChannelGUI: Generate fusion Information"                          fusionpeptides
    item    topMenu         cascade         "Chimera analysis"                                             chimeraMenu



    menu    plotMenu        topMenu         ""                                              ""
    item    plotMenu        command         "oneChannelGUI: Samples QC (PCA/HCL)"                               ocPlotPCA
    item    plotMenu        command         "oneChannelGUI: Multidimensional scaling plot (edgeR package)"                               qcMDS
    item    plotMenu        command         "oneChannelGUI: Box plot of peaks counts"                               normBoxplot
    item    plotMenu        separator       ""                                              ""
    item    plotMenu        command         "fastq Quality Analysis"                               fastQC
#    item    plotMenu        command         "EDASeq Quality plot"                               EDAplotQuality
#    item    plotMenu        command         "EDASeq Reads number plot"                               EDAreadNumber
#    item    plotMenu        command         "EDASeq Nt frequency plot"                               EDANtFreq
#    item    plotMenu        command         "EDASeq Boxplot plot"                               EDAboxplot
#    item    plotMenu        command         "EDASeq Bias plot"                                  EDAbiasPlot
#    item    plotMenu        separator       ""                                              ""
    item    plotMenu        command         "affylmGUI: Options"                                       PlotOptionsv1
    item    topMenu         cascade         "QC"                                       plotMenu


    menu    filteringMenu   topMenu         ""                                                              ""
    item    filteringMenu   command         "oneChannelGUI: Filtering by counts threshold"            intensityFilter
    item    filteringMenu   command         "oneChannelGUI: Filtering using a list of probe sets"          listFilter
    item    filteringMenu   command         "oneChannelGUI: Recovering unfiltered data"                     recoverUnfiltered
    item    filteringMenu   separator       ""                                              ""
    item    filteringMenu   command         "oneChannelGUI: Info about the loaded data set"                 showDataset
    item    filteringMenu   command         "oneChannelGUI: Export counts Values"                          ExportNormalizedExpressionValues1
    item    filteringMenu   command         "oneChannelGUI: Exporting peaks ids"            ExportfeatureNames
    item    filteringMenu   command         "oneChannelGUI: Exporting counts Values reformatted for meV software"           eSet4meV
    item    topMenu         cascade         "Filtering"                                                     filteringMenu

    menu    statsMenu topMenu         ""                                                              ""
    item    statsMenu    command         "oneChannelGUI: edgeR"                          edgerInterface
    item    statsMenu    command         "oneChannelGUI: baySeq"                          bayseqInterface
    item    statsMenu    command         "oneChannelGUI: DESeq"                          DESeqInterface
    item    topMenu         cascade         "Statistics"                                                    statsMenu

    menu    toptableMenu    topMenu         ""                                                              ""
    item    toptableMenu    command         "oneChannelGUI: Adding annotation to NGS data set"                              annotateNGSeset
    item    toptableMenu    command         "oneChannelGUI: Starting meV clustering software"                      startmeV
    item    toptableMenu    separator       ""                                                              ""
    item    toptableMenu    command         "oneChannelGUI: GO enrichment via goseq"                      goseqInterface
    item    toptableMenu    separator       ""                                                              ""
    item    toptableMenu    command         "oneChannelGUI: Detecting miR targets via RmiR package"                      RmiRInterface
    item    toptableMenu    command         "oneChannelGUI: Extract miR targets from RmiR output"                      extractmirTargets
    item    toptableMenu    command         "oneChannelGUI: Retrieve miR targets from RmiR.Hs.miRNA"                      retrieveMirTargets
    item    topMenu         cascade         "Biological Interpretation"                                                       toptableMenu

    menu    generalToolsMenu  topMenu         ""                                                            ""
    item    generalToolsMenu  command       "oneChannelGUI: Filtering a tab delimited file"                 filteringTable
    item    generalToolsMenu  command       "oneChannelGUI: Extract a column from a tab delimited file"                                colExtract
    item    generalToolsMenu command         "oneChannelGUI: Venn Diagram between probe set lists"          VennDiagram
    item    generalToolsMenu        separator       ""                                                              ""
#    item    generalToolsMenu command         "oneChannelGUI: Setting Tuxedo suite"          tuxedoSetup
#    item    generalToolsMenu command         "oneChannelGUI: Install NGS perl scripts"          ngsperlDownload
    item    generalToolsMenu command         "oneChannelGUI: Set bin folder"          setBinDir
    item    generalToolsMenu command         "oneChannelGUI: Set Java folder"          javaFolder
    item    generalToolsMenu command         "oneChannelGUI: Install Bowtie and Picard tools"          bowtieDownload
    item    generalToolsMenu command         "oneChannelGUI: Install SHRiMP Aligner"          downloadShrimp
    item    generalToolsMenu command         "oneChannelGUI: Download and build hs, mm, rn bowtie reference sets (slow)"          bowtieGenomes
    item    generalToolsMenu command         "oneChannelGUI: Download built hs, mm, rn bowtie reference sets (fast)"          bowtieBuilt
    item    generalToolsMenu        separator       ""                                                              ""
    item    generalToolsMenu command         "oneChannelGUI: Set library folder, installing Affy gene/Exon libs and miRNAs refs for RNA-seq"          geneExonLibs
    item    generalToolsMenu command         "oneChannelGUI: Set Affymetrix apt tools folder"          aptFolder
    item    generalToolsMenu        separator       ""                                                              ""
    item    generalToolsMenu    command         "oneChannelGUI: Installing meV clustering software"                              meVDownload
    item    generalToolsMenu    command         "oneChannelGUI: Information on external software and data connected to oneChannelGUI"                              extPckInfo
    item    generalToolsMenu        separator       ""                                                              ""
item    generalToolsMenu command         "oneChannelGUI: Reformat Genome Studio exported files"          genomeStudioReformat
    item    generalToolsMenu command         "oneChannelGUI: Update gene-level annotation via Netaffx"          buildingLocalAnnotation
     item    generalToolsMenu command         "oneChannelGUI: Update The UCSC tables linking exon-level probsets to variant exons"          variantExons
#    item    generalToolsMenu command         "oneChannelGUI: Retrieve Reference Sequences fasta file from NCBI"          refseqDownload
    item    generalToolsMenu command         "oneChannelGUI: Reset Local Data info"          deleteLocalData
    item    generalToolsMenu    command         "oneChannelGUI: Export non-coding RNA fasta reference file for ncRNA-seq quantitative analysis"                              exportFASTA
    item    generalToolsMenu    command         "affylmGUI: Evaluate R Code"                                evalRcode
    item    topMenu         cascade         "General Tools"                                                 generalToolsMenu

    menu    helpMenu        topMenu         ""                                                              ""
    item    helpMenu        command         "oneChannelGUI Help"                                            oneChannelGUIHelp
    item    helpMenu        command         "oneChannelGUI: About oneChannelGUI"                            AboutextendedaffylmGUI
    item    helpMenu        command         "affylmGUI: Citations"                                          showCitations
    item    topMenu         cascade         "Help"                                                          helpMenu
