# 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    tuxedoMenu   topMenu         ""                                                              ""
    item    tuxedoMenu   command         "oneChannelGUI: Create a folder for each sample 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    topMenu         cascade         "TopHat and CuffLinks"                                             tuxedoMenu

    menu    normalizeMenu   topMenu         ""                                                              ""
    item    normalizeMenu   command         "oneChannelGUI: Refining peaks"                          refiningPeaks
    item    normalizeMenu   command         "oneChannelGUI: Log2 transformation of reads counts"               log2Conversion
    item    normalizeMenu   command         "oneChannelGUI: Scale/normalize NGS data"                          edgeRNorm
    item    normalizeMenu   command         "oneChannelGUI: Info about the loaded data set"                 showDataset
    item    normalizeMenu   separator       ""                                                              ""
    item    normalizeMenu   command         "EDASeq: Within-lane Normalization"                   EDAwithinLane
    item    normalizeMenu   command         "EDASeq: between-lanes Normalization"                 EDAbetweenLane

    item    topMenu         cascade         "Refining NGS peaks"                                             normalizeMenu

    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         "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: Installing all external software needed for RNA-seq"          wrapNGS
#    item    generalToolsMenu command         "oneChannelGUI: Install NGS perl scripts"          ngsperlDownload
    item    generalToolsMenu command         "oneChannelGUI: Set Java folder"          javaFolder
    item    generalToolsMenu command         "oneChannelGUI: Install Bowtie and Picard tools"          bowtieDownload
    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
