!~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
!
! definition of command line options for SRS programs
!
!~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


#command /name=srsbuild 
    /usage="libName [libName]"
{
    #arg /name="-help" /type=help /comment="this message"
    #arg /name="-w"    /parameter=showWarnings 
    #arg /name="-c"    /parameter=compress
    #arg /name="-t"    /parameter=touchIndex
    #arg /name="-f"    /parameter=fieldList 
    #arg /name="-b"    /parameter=buildIndex 
    #arg /name="-d"    /parameter=parseTest
    #arg /name="-l"    /parameter=readLink
    #arg /name="-r"    /parameter=relocateLib
    #arg /name="-i"    /parameter=indexLink
    #arg /name="-xdir" /parameter=indexDirName
    #arg /name="-odir" /parameter="outDirName"
    #arg /name="-info" /parameter=printLibInfo
    #arg /name="-libs" /parameter=printLibs
    #arg /name="-rel" /parameter=releaseName
    #arg /name="-env" /parameter=environment
}

#command /name=wgetz
    /usage="'queryExpression'"
{
    #arg /name="-help" /comment="this message" /type=help
    #arg /name="-lo" /parameter="linkToLibs"
    #arg /name="-id"   /parameter="userId"
    #arg /name="-qm"   /parameter="queryManager"
    #arg /name="-qf"   /parameter="doQueryForm"
    #arg /name="-top"   /parameter="topPage"
    #arg /name="-rep"   /parameter="doRepeat"
    #arg /name="-info"   /parameter="libInfo"
    #arg /name="-linfo"   /parameter="linkInfo"
    #arg /name="-blast"   /parameter="prepBlastSearch"
    #arg /name="-ht" /parameter="printHelpTopic"
    #arg /name="-viv" /parameter="visitIndexValue"
    #arg /name="-f"    /parameter=fieldList 
    #arg /name="-bl"    /parameter=listEntriesStartN
    #arg /name="-ll"    /parameter=listEntriesChunkSize
    #arg /name="-bv"    /parameter=viewEntriesStartN
    #arg /name="-lv"    /parameter=viewEntriesChunkSize
    #arg /name="-lset"  /parameter=listSetNumber
    #arg /name="-vset"  /parameter=viewSetNumber
    #arg /name="-lquery"  /parameter=listQuery
    #arg /name="-msg"  /parameter=getMessage    
    #arg /name="-sf"   /parameter="seqFormat" 
    #arg /name="-subn" /parameter=subEntryN
    #arg /name="-tr" /parameter=translateSequence
    #arg /name="-libs" /parameter=printLibs
    #arg /name="-network" /parameter=printNetwork
    #arg /name="-ls" /parameter=linkLibSelect
    #arg /name="-link" /parameter=printLinkTable 
    #arg /name="-odd" /parameter=getOddFile
    #arg /name="-env" /parameter=environment
}

#command /name=getz
    /usage="'queryExpression'"
{
    #arg /name="-help" /comment="this message" /type=help
    #arg /name="-t"    /parameter="printText"
    #arg /name="-d"    /parameter="printData"
    #arg /name="-fse"  /parameter="listFSE"     ! dgg added
    #arg /name="-tdir"  /parameter="tempDirName"     ! dgg added
    #arg /name="-f"    /parameter="fieldList"
    #arg /name="-l"    /parameter="libList" 
    #arg /name="-w"    /parameter="makeWild"
    #arg /name="-r"    /parameter="doQueryReport" 
    #arg /name="-rep"    /parameter="doOnlyQueryReport" 
    #arg /name="-pmin" /parameter="printMinOccur" 
    #arg /name="-qf"   /parameter=queryFileName
    #arg /name="-xdir" /parameter=indexDirName
    #arg /name="-info" /parameter=printLibInfo
    #arg /name="-libs" /parameter=printLibs
    #arg /name="-fosn" /parameter=listFOSN
    #arg /name="-fil"    /parameter=printToFile
    #arg /name="-sf"   /parameter="seqFormat" 
    #arg /name="-pos"  /parameter=fosnWithPos
    #arg /name="-link" /parameter=linkTable
    #arg /name="-si"   /parameter=getStartupInfo

    #arg /name="options for retrieval of sequence features" /type=title

    #arg /name="-fbegs"     /parameter=shiftbeginpos
    #arg /name="-fends"     /parameter=shiftendpos
    #arg /name="-fbegsrend" /parameter=isshiftbeginrelend
    #arg /name="-fendsrbeg" /parameter=isshiftendrelbegin
    #arg /name="-takeuncf"  /parameter=takeuncompletefeature
    #arg /name="-takeuncsf" /parameter=takeuncompleteshiftfeature
    #arg /name="-env" /parameter=environment
}

#command /name=trembl
    /usage=""
{
    #arg /name="-help" /comment="this message" /type=help
    #arg /name="-l"    /parameter=libName
    #arg /name="-f"    /parameter=tremblInFile
    #arg /name="-c"    /parameter=findAccNoCommand
    #arg /name="-sf"   /parameter=inputSeqFile
}

#command /name=srscheck
    /usage=""
{
    #arg /name="-help"   /type=help /comment="this message"
    #arg /name="-xdir"   /parameter=indexDirName
    #arg /name="-odir"   /parameter="outDirName"
    #arg /name="-info"   /parameter=printLibInfo
    #arg /name="-e"      /parameter=etcDir
    #arg /name="-s"      /parameter=procIndexSize
    #arg /name="-l"      /parameter=checkLibList
    #arg /name="-L"      /parameter=notCheckLibList
    #arg /name="-header" /parameter=srsEnvHeader
    #arg /name="-o"      /parameter=updateScriptName
    #arg /name="-env" /parameter=environment
}

#command /name=srs
    /usage=""
{
    #arg /name="-help" /type=help /comment="this message"
    #arg /name="-v" /type=bool /parameter="printVersion"
         /comment="print version numbers of all modules and quits"
    #arg /name="-p" /type=bool /parameter="noProfile"
         /comment="does not read and write user defined parameters"
    #arg /name="-lmax" /type=number /parameter="listEntriesMaxN"
         /comment="maximum number of entries that can be listed"
    #arg /name="-pmax" /type=number /parameter="printEntriesMaxN"
         /comment="maximum number of entries that can be printed"
}

#command /name=reflink
    /usage="libName"
{
    #arg /name="-help" /type=help /comment="this message"
    #arg /name="-r" /parameter="readLib"
    #arg /name="-s" /parameter="searchLib"
    #arg /name="-jf" /parameter="journalListFile"
    #arg /name="-j"  /parameter="doJournalList"
    #arg /name="-m" /parameter="doMergeJournalLists"
    #arg /name="-l" /parameter="doRefLink"
    #arg /name="-p" /parameter="doRefLinkFile"
}