Content-type: biocompute/command # tacg.command # d.gilbert, dec'97 # for use of Harry Mangalam tacg restriction mapping program # # this is a hasty, not final, selection of tagc command options # command = { id = tacg menu = "Restriction Map|tacg" filepath = data/methods datapath = data/prefs ## server only config ------- transport = local: #transport = iiop://chipmunk.bio.indiana.edu:7000/Bopper action= "$filepath/tacg $REBASE $orderout $REselect $circular $linear \ $codon.u $codon.v $codon.d $codon.sc $codon.sp $codon.nc $codon.hp $codon.c \ $fragunsort $fragsort $frag3 $gelmap $laddermap $linearmap $summary $sites " # -R $filepath/rebase.data ## ---------------------- parlist = { par = { id = TITLE value.title = "tacg restriction map" } par = { id = HELP label = "Help with tacg" #value.url = http://chipmunk.bio.indiana.edu/bopper/help/tacg2.main.html value.url = file://$filepath/tacg2.main.html } par = { id = INFO label = "About tacg" value.title = "tacg analyzes a DNA sequence for restriction enzyme sites, \ nucleic acid patterns version 2, by Harry Mangalam" } par = { id = IOfiles label = "Input/Output files" value.container = { required = false parlist = { par={ id= STDIN; label="Input"; value.data={dataflow= input; datatype= biosequence/fasta; flavor= stdin; filename= tacg.inseq;} } par={ id= STDOUT; label="Output"; value.data={dataflow= output; datatype= text/plain; flavor= stdout; filename= tacg.map;} } ## not getting filepath/datapath set right !!! par={ id= REBASE; label="Restrict. Enzyme table"; value.data={dataflow= output; datatype= text/gcg; flavor= serverlocal; filename= "$filepath/rebase.data"; } runSwitch= "-R $value" } par={ id= STDERR; label="Errors"; value.data={dataflow= output;datatype= text/plain; flavor= stderr; filename= tacg.err;} } } } } par = { id = Options label = "Options" value.container = { required = false parlist = { par = { id = orderout runSwitch = "-c" value.boolean = false label = "order the output by # of cuts/fragments by each RE, and thence alphabetic" } par = { id = laddermap runSwitch = "-l" value.boolean = false label = "a 'ladder' map of selected enzymes" } par = { id = linearmap runSwitch = "-L" value.boolean = false label = "if you WANT a linear map. This spews the most output" } par = { id = summary runSwitch = "-s" value.boolean = false label = "print the summary of site information" } par = { id = sites runSwitch = "-S" value.boolean = false label = "print the the actual cut sites in tabular form" } par = { id = 98 label = "Print/Sort Fragments" value.choice = { multipleChoices = false parlist = { par = { id= 988; label=Omit; value.boolean=true; } par = { id= fragunsort; label="Print unsorted"; value.boolean=false; runSwitch = "-F1"; } par = { id= fragsort; label="Print sorted"; value.boolean=false; runSwitch = "-F2"; } par = { id= frag3; label="Print sorted & unsorted"; value.boolean=false; runSwitch = "-F3"; } } } } par = { id = 96 label = "pseudo-gel map graphic" value.container = { required = false parlist = { par= { id= gelmap; label="do map"; value.boolean= false; runSwitch = "-g$gelmapval"; } par= { id= gelmapval; label="map val"; value.int= 10; } } } } par = { id = 99 label = "form (or topology) of DNA " value.choice = { multipleChoices = false parlist = { par = { id= circular; label=Circular; value.boolean=false; runSwitch = "-f0"; } par = { id= linear; label=Linear; value.boolean=true; runSwitch = "-f1"; } } } } par = { id= 100 label= "Codon usage" value.choice = { multipleChoices = false parlist = { par = { id = codon.u; label= "Universal"; value.boolean= true; runSwitch = -C0; } par = { id = codon.v; label= "Mito.Vertebrates"; value.boolean= false; runSwitch = -C1; } par = { id = codon.d; label= "Mito.Drosophila "; value.boolean= false; runSwitch = -C2; } par = { id = codon.sc; label= "Mito.S.Cervisiae "; value.boolean= false; runSwitch = -C3 } par = { id = codon.sp; label= "Mito.S.Pombe "; value.boolean= false; runSwitch = -C4; } par = { id = codon.nc; label= "Mito.N.crassa "; value.boolean= false; runSwitch = -C5; } par = { id = codon.hp; label= "Mito.Higher.Plants "; value.boolean= false; runSwitch = -C6; } par = { id = codon.c; label= "Mito.Ciliates "; value.boolean= false; runSwitch = -C7; } } } } } } } par= { id = REnzymes label = "Restriction Enzymes" value.container = { required = false parlist = { par = { id = REselect label = "Select specific r. enzymes" runSwitch = "-r $RElist" value.boolean = false } par = { id = RElist label = "List of enzymes to select" value.list = "AatII|AccI|AceIII|AciI|AclI|AflII|AflIII|AhdI|AluI|AlwI|AlwNI|\ ApaI|ApaLI|ApoI|AscI|AvaI|AvaII|AvrII|BaeI|BaeI|BamHI|\ BanI|BanII|BbsI|BbvI|BccI|Bce83I|BcefI|BcgI|BcgI|BciVI|\ BclI|BfaI|BfiI|BglI|BglII|BmgI|BplI|BpmI|Bpu10I|Bpu1102I|\ BsaI|BsaAI|BsaBI|BsaHI|BsaJI|BsaWI|BsaXI|BsbI|BscGI|BseMII|\ BseRI|BsgI|BsiEI|BsiHKAI|BslI|BsmI|BsmAI|BsmBI|BsmFI|Bsp24I|\ Bsp24I|Bsp1286I|BspEI|BspGI|BspLU11I|BspMI|BsrI|BsrBI|BsrDI|BsrFI|\ BsrGI|BssHII|BssSI|Bst4CI|BstAPI|BstDSI|BstEII|BstXI|BstYI|BstZ17I|\ Bsu36I|Cac8I|CjeI|CjeI|CjePI|CjePI|ClaI|CviJI|CviRI|DdeI|\ DpnI|DraI|DraIII|DrdI|DrdII|EaeI|EagI|EarI|EciI|Eco47III|\ Eco57I|EcoNI|EcoO109I|EcoRI|EcoRII|EcoRV|FauI|Fnu4HI|FokI|FseI|\ FspI|GdiII|HaeI|HaeII|HaeIII|HgaI|HgiEII|HhaI|Hin4I|HincII|HindIII|HinfI|HpaI|HphI|KpnI|\ MaeIII|MboII|MluI|MmeI|MnlI|MscI|MseI|MslI|MspI|MspA1I|\ MunI|MwoI|NarI|NciI|NcoI|NdeI|NgoAIV|NheI|NlaIII|NlaIV|\ NotI|NruI|NsiI|NspI|NspV|PacI|Pfl1108I|PflMI|PinAI|PleI|\ PmeI|PmlI|PshAI|Psp5II|PstI|PvuI|PvuII|RcaI|RleAI|RsaI|\ RsrII|SacI|SacII|SalI|SanDI|SapI|Sau96I|Sau3AI|SbfI|ScaI|\ ScrFI|SexAI|SfaNI|SfcI|SfiI|SgfI|SgrAI|SimI|SmaI|SmiI|\ SmlI|SnaBI|SpeI|SphI|SrfI|Sse8647I|SspI|StuI|StyI|SunI|\ TaiI|TaqI|TaqII|TaqII|TatI|TauI|TfiI|ThaI|TseI|Tsp45I|\ Tsp509I|TspRI|Tth111I|Tth111II|UbaDI|UbaEI|VspI|XbaI|XcmI|XhoI|XmnI" } } } } } # end parameters } # end command