Parsing command-line arguments by Getopt::Long

Later the Perl script is executed with the command-line arguments that user specified. The options are parsed and saved into a json file. Parsingcommand-lineargumentsbyGetopt::Long ZuguangGu([email protected]) 2020-12-15 TherearealreadyseveralRpackageswhichparsecommand-lineargumentssuchasgetopt,optparse,argparse,docopt.HereGetoptLongisanothercommand-lineargumentparser(actuallyitwasdevelopedveryearly,thefirstCRANversionwasin2013)whichwrapsthepowerfulPerlmoduleGetopt::Long.GetoptLongpackagealsoprovidessomeadaptationsforeasieruseinR. UsingGetoptLongissimpleespeciallyforusershavingPerlexperience(Oops,ageexposed:))becausethespecificationisalmostthesameasinPerl.TheoriginalwebsiteofGetopt::Longisalwaysyourbestreference. Note:tousethispackage,Perlshouldbeinstalled. Workflowofthewrapping TheGetoptLongRpackageautomaticallygeneratesaPerlscriptaccordingtothespecificationsintheRscript.LaterthePerlscriptisexecutedwiththecommand-lineargumentsthatuserspecified.Theoptionsareparsedandsavedintoajsonfile.FinallyRreadsbackthejsonfileandformatsthemasRvariables. FollowingfigureshowshowtheRpackageworksforparsingthecommand-linearguments. Aquickexample Specifyasavector ThefollowingexamplegivesyousomefeelsofusingGetoptLongpackage.ThefollowingcodeissavedintoanRscriptnamedfoo.R. library(GetoptLong) cutoff=0.05 GetoptLong( "number=i","Numberofitems.", "cutoff=f","Cutoffforfilteringresults.", "verbose","Printmessage." ) TheRscriptcanbeexecutedas: ~\>Rscriptfoo.R--number4--cutoff0.01--verbose ~\>Rscriptfoo.R--number=4--cutoff=0.01--verbose ~\>Rscriptfoo.R-n4-c0.01-v ~\>Rscriptfoo.R-n4--verbose Inthisexample,numberisamandatoryoptionanditshouldonlybeinintegermode.cutoffisoptionalanditalreadyhasadefaultvalue0.05.verboseisalogicaloption.Ifparsingissuccessful,twovariablesnumberandverbosewillbeimportedintotheworkingenvironmentwiththespecifiedvalues.Valueforcutoffwillbeupdatedifitisspecifiedincommand-line. Datatypesareautomaticallychecked.E.g.,ifcutoffisspecifiedwithacharacter,anerrorwillbethrown. Theoptionusagetriggeredby--helpisautomaticallygenerated.Therearetwostyles: Theone-columnstyle: Usage:Rscriptfoo.R[options] Options: --number,-ninteger Numberofitems. --cutoff,-cnumeric Cutoffforfilteringresults. [default:0.05] --verbose Printmessage. --help,-h Printhelpmessageandexit. --version Printversioninformationandexit. Orthetwo-columnstyle: Usage:Rscriptfoo.R[options] Options: --number,-nNumberofitems. [type:int] --cutoff,-cCutoffforfilteringresults. [type:num][default:0.05] --verbosePrintmessage. --help,-hPrinthelpmessageandexit. --versionPrintversioninformationandexit. Youcanfindtheshortoptionnames(insingleletters)areautomaticallyadded.Theinformationofdefaultvaluesisaddedaswell. Specifyasatemplate Thespecificationcanalsobesetasatemplatewherethespecificationsaremarkedby<>. spec=" Thisisanexampleofusingtemplatetospecifyoptions. Usage:Rscriptfoo.R[options] Options: Numberofitems. Cutoffforfilteringresults. Printmessages. Contact:name@address " GetoptLong(spec,template_control=list(opt_width=21)) Theparameteropt_widthcontrolsthemaximalwidthoftheoptiondescription(i.e.,--number,-ninteger,--cutoff,-cnumericand--verbose). CallingRscriptfoo.R--helpgeneratesthefollowingmessage: Thisisanexampleofusingtemplatetospecifyoptions. Usage:Rscriptfoo.R[options] Options: --number,-nintegerNumberofitems. --cutoff,-cnumericCutoffforfilteringresults. --verbosePrintmessages. Contact:name@address Advantages Thereareseveraladvantagescomparedtoothercommand-lineargumentparserpackages.ThemajoradvantagecomesfromtheGetopt::LongPerlmodulewhichactuallyparsestheoptions.TheGetopt::Longmoduleprovidesaflexible,smartandcompactwayforspecifyingcommand-linearguments.Themajorfeaturesare: Variousformatsofspecifyingoptionswithvalues,suchas -s24-s24 or --size24--size=24-size24-size=24 Single-letteroptionscanbebundled: -a-b-c-abs Optionswithmultiplenames.Withthefollowingspecification,--length,--heightarethesame. length|height=f Automaticallysupportsingle-letteroptions.Ifthefirstletterofanoptionisuniquetoallotheroptions,thefirstlettercanbeusedasanoptionaloptionname.Forexample,iflandhareunique,--length,--height,-land-hsetthesameoption. length|height=f--length--height-l-h Richoptiondatatypes,includingscalar,vector(arrayinPerl),list(hashinPerl).Forexample: length=iasingleintegerscalar name=sasinglecharacterscalar canbespecifiedas: --length1--namea or length=i@aintegervector name=s@acharactervector length=i{2,}aintegervector,atleasttwoelements name=s{2,}acharactervector,atleasttwoelements canbespecifiedas: --length123--nameabc or length=i%name-valuepair,valuesshouldbeintegers name=s%name-valuepair,valuesshouldbecharacters tobespecifiedas: --lengthfoo=1bar=3--namefoo=abar=b ThefeaturesfromRpartare: Itautomaticllygeneratesoptionusageintwostyles.Thedatatypeanddefaultvalueofoptionsareautomaticallydetectedandincluded. Itsupportsspecifyingtheusageinatemplatewhichallowsmorecomplextextofoptionusage. Itallowsgroupingoptions. Itprovidesanaturalandconvenientwaytospecifydefaults. Customizethespecifications Eachspecifierinoptionsconsistsoftwoparts:thenamespecificationandtheargumentspecification: length|size|l=i@ Herelength|size|lisalistofalternativenamesseparatedby|.Theremainingpartisargumentspecificationwhichdefinesthemodeandamountofarguments. Specifyanyofalternativeoptionnamefromcommand-lineisokanditdoesn’tmatterwhetherusingoneortwoslashinfrontoftheoptionname.Sometimesyouevendon’tneedtospecifycompleteoptionnames,youonlyneedtomakesurethepartialnamematchisunique.Ifthepartialmatchisnotuniqe,itwillthrowanerror.Foraboveexample,wecanspecifytheargumentlike: ~\>Rscriptfoo.R--length1 ~\>Rscriptfoo.R--length=1#adding"="isalsook ~\>Rscriptfoo.R-len1 ~\>Rscriptfoo.R-lengt1#thisisalsook,butnotsuggested ~\>Rscriptfoo.R--size1 ~\>Rscriptfoo.R-l1 Optionsforargumentspecificationare: noargumentspecification:takingnoargument.Optionsarelogical. !:takingnoargument.Optionsarelogical.Youcansetitsopositevaluebyaddingitwithnoorno-.E.g.,foo!allows--fooaswellas--nofooand--no-foo. =type[desttype][repeat]:optionsshouldhavearguments(oroptionsshouldhavevaluesspecified).E.g.tag=i@whereicorrespondstotype,and@correspondstodesttype,ortag=i{2,}where{2,}correspondstorepeat. Pleasenote:[type][desttype]isnotsupportedhere.Weuseanotherwaytodefinemandatoryoptionsandoptionaloptions.Ifyoudon’tknowwhatitis,justignorethisparagraph. Availabletypeoptionsare: s:strings i:integers F:realnumbers o:extendedinteger,anoctalstring(0followedby0,1..7),orahexadecimalstring(0xfollowedby0..9,A..F,caseinsensitive),orabinarystring(0bfollowedbyaseriesof0and1). Availabledesttypesettingsare: @:array,allowmorethanoneargumentsforanoption. %:hash,allowargumentslikename=value. nothing:scalar,singleargumentforsingleoption. Availablerepeatsettingsareformattedas{\d,\d}.Notethereisnospacecharacterinside: {2}:exactly2argumentsforanoption. {2,}:atleast2argumentsforanoption. {,4}:atmost4argumentsforanoption. {2,5}:minimal2andmaximal5argumentsforanoption. Notedesttypeandrepeatcannotbeusedatthesametime. InthePerlmodule,tag=i@onlyallows,e.g.,specificationof--tag1--tag2while--tag12isnotallowedwhichisonlypossiblebytag=i{1,}.IntheRpackage,[email protected],tag=i%onlyallows--tagname1=value1--tagname2=value2inthePerlmodule.IntheRpackage,italsoallows--tagname1=value1name2=value2. Followingtablecontainsexamplesforeachtypeofoptionspecification: Options Command-linearguments Valueoftag tag=i –tag1 1 –tag=1 1 -t1 1 –tag1–tag2 2.Hereonlytakethelastone –tag0.1 Error:Value“0.1”invalidforoptiontag(numberexpected) –taga Error:Value“a”invalidforoptiontag(numberexpected) –tag Error:Optiontagrequiresanargument noargument tagismandatory,pleasespecifyit tag=s –tag1 “1”.Heredoublequoteisusedbecauseitisspecifiedasastring. –tag0.1 “0.1” –taga “a” tag=f –tag1 1 –tag0.1 0.1 –taga Error:Value“a”invalidforoptiontag(realnumberexpected) tag=o –tag1 1 –tag0b001001 9 –tag0721 465 –tag0xaf2 2802 -tag0.1 Error:Value“0.1”invalidforoptiontag(extendednumberexpected) –taga Error:Value“a”invalidforoptiontag(extendednumberexpected) tag –tag1 TRUE –tag0 TRUE,itdoesn’tcarethevaluefortheoption. –tag0.1 TRUE –taga TRUE –tag TRUE noargument FALSE tag! –tag TRUE –no-tag FALSE tag=i@ –tag1 1 –tag12 c(1,2) –tag1–tag2 c(1,2) –tag=1–tag=2 c(1,2) tag=i% –tag1 Error:Optiontag,key“1”,requiresavalue –tagfoo=1–tagbar=2 list(foo=1,bar=2),tagisalist. –tagfoo=1bar=2 list(foo=1,bar=2),tagisalist. tag=i{2} –tag1 Error:Insufficientargumentsforoptiontag –tag12 c(1,2) –tag1–tag2 Error:Value“–tag”invalidforoptiontag tag=i{2,} –tag1 Error:Insufficientargumentsforoptiontag –tag12 c(1,2) –tag123 c(1,2,3) tag=i{,2} –tag1 1 –tag12 c(1,2) –tag123 c(1,2) Wheredotheoptionvaluesgo Optionswillbeimportedintouser’senvironmentasRvariablesbydefault.Thefirstoptionnameinallalternativenameswillbetakenasthenameofthevariable,(e.g.forspecificationoflength|size=s,lengthwillbeusedasthevariablename.),whichmeans,itmustbeavalidRvariablename.AnydefinitionofthesevariablesinfrontofGetoptLong()willbetreatedasdefaultvaluesforthecorrespondingoptions.Ifoptionsalreadyhavedefaultvalues,theyareoptionalincommand-line.IfthevariableisdefinedasafunctionbeforeGetoptLong()iscalled,itistreatedasundefined.Pleasenoteyouroptionnamesshouldnotstartwiththedot.AlthoughitisvalidforRvariablesbutitisnotallowedforGetopt::Longmodule. Forthefollowingexample: library(GetoptLong) cutoff=0.05 GetoptLong( "number=i{1,}","Numberofitems.", "cutoff=f","Cutoffforfilteringresults.", "param=s%","Parametersspecifiedbyname=valuepairs.", "verbose","Printmessage." ) print(number) print(cutoff) print(param) print(verbose) acallingfromcommand-line: Rscriptfoo.R--number12--paramvar1=avar2=b--verbose willprint [1]12 [1]0.05 $var1 [1]"a" $var2 [1]"b" [1]TRUE Therearetwowaystospecifylogicaloptions,e.g.,verboseandverbose!.verbosealwaystakesFALSEasdefaultandyoucannotsetdefaultvalueforit,whileyoucansetdefaultforverbose!.E.g.: verbose=TRUE GetoptLong( "verbose!","Printmessage." ) If--verbose/--no-verboseisnotspecified,thevariableverboseisTRUE.If--verboseisspecified,verboseisTRUEandif--no-verboseisspecified,verboseisFALSE. Ifyoudon’twanttodirectlyexportoptionsasvariables,youcanassignenvirargumentwithanenvironmentvariablesothatalltheoptionvaluesgothere. opt=new.env() opt$cutoff=0.05 GetoptLong( "number=i@","Numberofitems.", "cutoff=f","Cutoffforfilteringresults.", "param=s%","Parametersspecifiedbyname=valuepairs.", "verbose","Printmessage.", envir=opt ) print(as.list(opt)) acallingfromcommand-line: Rscriptfoo.R--number12--paramvar1=avar2=b--verbose willprint $cutoff [1]0.05 $number [1]12 $param $param$var1 [1]"a" $param$var2 [1]"b" $verbose [1]TRUE Helpoption helpisareservedoption,whichmeans,youcannotuseitasyours. Optionusageisautomaticallygeneratedandcanberetrievedbysetting--helpinthecommand.Infollowingexample,Icreateanoptionspecificationthatcontainsalltypesofoptions(withlongdescriptions): GetoptLong( "count=i",paste("Thisisacount.Thisisacount.Thisisacount.", "Thisisacount.Thisisacount.Thisisacount."), "number=f",paste("Thisisanumber.Thisisanumber.Thisisanumber.", "Thisisanumber.Thisisanumber.Thisisanumber."), "array=f@",paste("Thisisanarray.Thisisanarray.Thisisanarray.", "Thisisanarray.Thisisanarray.Thisisanarray."), "hash=s%",paste("Thisisahash.Thisisahash.Thisisahash.", "Thisisahash.Thisisahash.Thisisahash."), "verbose!","Whethershowmessages", "flag","anon-senseoption" ) Theoptionusageisasfollows.Here,forexample,thesingle-letteroption-cfor--countisautomaticallyextractedwhilenotfor--helpbecausehmatchestwooptions. Usage:Rscriptfoo.R[options] Options: --count,-cinteger Thisisacount.Thisisacount.Thisisacount.Thisisacount.Thisis acount.Thisisacount. --number,-nnumeric Thisisanumber.Thisisanumber.Thisisanumber.Thisisanumber.This isanumber.Thisisanumber. --array,-a[numeric,...] Thisisanarray.Thisisanarray.Thisisanarray.Thisisanarray.This isanarray.Thisisanarray. --hash{name=character,...} Thisisahash.Thisisahash.Thisisahash.Thisisahash.Thisisa hash.Thisisahash. --verbose,-no-verbose Whethershowmessages [default:off] --flag,-f anon-senseoption --help Printhelpmessageandexit. --version Printversioninformationandexit. Ifdefaultvaluesforoptionsareprovided,theyareproperlyinsertedtotheusagemessage. count=1 number=0.1 array=c(1,2) hash=list("foo"="a","bar"="b") verbose=TRUE GetoptLong( ... ) Usage:Rscriptfoo.R[options] Options: --count,-cinteger Thisisacount.Thisisacount.Thisisacount.Thisisacount.Thisis acount.Thisisacount. [default:1] --number,-nnumeric Thisisanumber.Thisisanumber.Thisisanumber.Thisisanumber.This isanumber.Thisisanumber. [default:0.1] --array,-a[numeric,...] Thisisanarray.Thisisanarray.Thisisanarray.Thisisanarray.This isanarray.Thisisanarray. [default:1,2] --hash{name=character,...} Thisisahash.Thisisahash.Thisisahash.Thisisahash.Thisisa hash.Thisisahash. [default:foo=a,bar=b] --verbose,-no-verbose Whethershowmessages [default:on] --flag,-f anon-senseoption --help Printhelpmessageandexit. --version Printversioninformationandexit. Theglobalparametershelp_stylecanbesettotwo-columntochangetoanotherstyle: GetoptLong.options(help_style="two-column") #specifyingthedefaults GetoptLong{ ... } Usage:Rscriptfoo.R[options] Options: --count,-cThisisacount.Thisisacount.Thisisacount. [type:int]Thisisacount.Thisisacount.Thisisacount. [default:1] --number,-nThisisanumber.Thisisanumber.Thisisa [type:num]number.Thisisanumber.Thisisanumber.Thisis anumber. [default:0.1] --array,-aThisisanarray.Thisisanarray.Thisisan [type:[num,...]]array.Thisisanarray.Thisisanarray.Thisis anarray. [default:1,2] --hashThisisahash.Thisisahash.Thisisahash.This [type:{name=chr,...}]isahash.Thisisahash.Thisisahash. [default:foo=a,bar=b] --verbose,-no-verboseWhethershowmessages [default:on] --flag,-fanon-senseoption --helpPrinthelpmessageandexit. --versionPrintversioninformationandexit. Whenoptionsarespecifiedasname-valuepairs,thesesuboptionscanbedocumentedasfollows.Notethespecificationsofe.g.foo$name1areonlyfortheusagemessage. foo=list(a=1,b=2) GetoptLong( "foo=i%",paste("Thisisfoo.Thisisfoo.Thisisfoo.Thisisfoo.", "Thisisfoo.Thisisfoo.Thisisfoo.Thisisfoo."), "foo$name1",paste("name1infoo.name1infoo.name1infoo.name1infoo.", "name1infoo.name1infoo.name1infoo.name1infoo."), "foo$name2",paste("name2infoo.name2infoo.name2infoo.name2infoo.", "name2infoo.name2infoo.name2infoo.name2infoo."), "bar=s%",paste("Thisisbar.Thisisbar.Thisisbar.Thisisbar.", "Thisisbar.Thisisbar.Thisisbar.Thisisbar."), "bar$name3",paste("name3inbar.name3inbar.name3inbar.name3inbar.", "name3inbar.name3inbar.name3inbar.name3inbar."), "bar$name4",paste("name4inbar.name4inbar.name4inbar.name4inbar.", "name4inbar.name4inbar.name4inbar.name4inbar.") ) Usage:Rscriptfoo.R[options] Options: --foo,-f{name=integer,...} Thisisfoo.Thisisfoo.Thisisfoo.Thisisfoo.Thisisfoo.Thisis foo.Thisisfoo.Thisisfoo. [default:a=1,b=2] Subnamedoptions: name1=integername1infoo.name1infoo.name1infoo.name1infoo.name1 infoo.name1infoo.name1infoo.name1infoo. name2=integername2infoo.name2infoo.name2infoo.name2infoo.name2 infoo.name2infoo.name2infoo.name2infoo. --bar,-b{name=character,...} Thisisbar.Thisisbar.Thisisbar.Thisisbar.Thisisbar.Thisis bar.Thisisbar.Thisisbar. Subnamedoptions: name3=charactername3inbar.name3inbar.name3inbar.name3inbar.name3 inbar.name3inbar.name3inbar.name3inbar. name4=charactername4inbar.name4inbar.name4inbar.name4inbar.name4 inbar.name4inbar.name4inbar.name4inbar. --help,-h Printhelpmessageandexit. --version,-v Printversioninformationandexit. Andthetwo-columnstyleforthesuboptions. GetoptLong.options(help_style="two-column") GetoptLong{ ... } Usage:Rscriptfoo.R[options] Options: --foo,-fThisisfoo.Thisisfoo.Thisisfoo.Thisisfoo. [type:{name=int,...}]Thisisfoo.Thisisfoo.Thisisfoo.Thisisfoo. [default:a=1,b=2] Subnamedoptions: name1=intname1infoo.name1infoo.name1infoo. name1infoo.name1infoo.name1infoo. name1infoo.name1infoo. name2=intname2infoo.name2infoo.name2infoo. name2infoo.name2infoo.name2infoo. name2infoo.name2infoo. --bar,-bThisisbar.Thisisbar.Thisisbar.Thisisbar. [type:{name=chr,...}]Thisisbar.Thisisbar.Thisisbar.Thisisbar. Subnamedoptions: name3=chrname3inbar.name3inbar.name3inbar. name3inbar.name3inbar.name3inbar. name3inbar.name3inbar. name4=chrname4inbar.name4inbar.name4inbar. name4inbar.name4inbar.name4inbar. name4inbar.name4inbar. --help,-hPrinthelpmessageandexit. --version,-vPrintversioninformationandexit. Extratextsuchheadandfootoftheusagemessagecanbesetwithhelp_headandhelp_footarguments: GetoptLong( help_head="Thisisademonstrationofaddingusageheadandfoot.", "number=i","Numberofitems.", "cutoff=f","Cutoffforfilteringresults.", "verbose","Printmessage.", help_foot="Pleasecontactname@address." ) Thisisademonstrationofaddingusageheadandfoot. Usage:Rscriptfoo.R[options] Options: --number,-ninteger Numberofitems. --cutoff,-cnumeric Cutoffforfilteringresults. --verbose Printmessage. --help,-h Printhelpmessageandexit. --version Printversioninformationandexit. Pleasecontactname@address. Theoptionsintheusagetextcanbegroupedbysettingseparatorlines.Theseparatorlineshouldcontaintwoelements:theseparatorandthedescription.Theseparatorcanbeanycharacterin-+=#%withanylength. count=1 array=c(0.1,0.2) GetoptLong( "--------","Binaryoptions:", "verbose!","Whethershowmessages", "flag","anon-senseoption", "-------","Single-valueoptions:", "count=i",paste("Thisisacount.Thisisacount.Thisisacount.", "Thisisacount.Thisisacount.Thisisacount."), "number=f",paste("Thisisanumber.Thisisanumber.Thisisanumber.", "Thisisanumber.Thisisanumber.Thisisanumber."), "--------",paste("Multiple-vlaueoptions:longtextlongtextlongtext", "longtextlongtextlongtextlongtextlongtext"), "array=f@",paste("Thisisanarray.Thisisanarray.Thisisanarray.", "Thisisanarray.Thisisanarray.Thisisanarray."), "hash=s%",paste("Thisisahash.Thisisahash.Thisisahash.", "Thisisahash.Thisisahash.Thisisahash."), "-------","Otheroptions:" ) Usage:Rscriptfoo.R[options] Binaryoptions: --verbose,-no-verbose Whethershowmessages [default:off] --flag,-f anon-senseoption Single-valueoptions: --count,-cinteger Thisisacount.Thisisacount.Thisisacount.Thisisacount.Thisis acount.Thisisacount. [default:1] --number,-nnumeric Thisisanumber.Thisisanumber.Thisisanumber.Thisisanumber.This isanumber.Thisisanumber. Multiple-vlaueoptions:longtextlongtextlongtextlongtextlongtextlong textlongtextlongtext --array,-a[numeric,...] Thisisanarray.Thisisanarray.Thisisanarray.Thisisanarray.This isanarray.Thisisanarray. [default:0.1,0.2] --hash{name=character,...} Thisisahash.Thisisahash.Thisisahash.Thisisahash.Thisisa hash.Thisisahash. Otheroptions: --help Printhelpmessageandexit. --version Printversioninformationandexit. Andthetwo-columnstyleforthegroupedoptions. GetoptLong.options(help_style="two-column") GetoptLong{ ... } Usage:Rscriptfoo.R[options] Binaryoptions: --verbose,-no-verboseWhethershowmessages [default:off] --flag,-fanon-senseoption Single-valueoptions: --count,-cThisisacount.Thisisacount.Thisisacount.Thisisa [type:int]count.Thisisacount.Thisisacount. [default:1] --number,-nThisisanumber.Thisisanumber.Thisisanumber.Thisis [type:num]anumber.Thisisanumber.Thisisanumber. Multiple-vlaueoptions:longtextlongtextlongtextlongtextlongtextlong textlongtextlongtext --array,-aThisisanarray.Thisisanarray.Thisisan [type:[num,...]]array.Thisisanarray.Thisisanarray.Thisis anarray. [default:0.1,0.2] --hashThisisahash.Thisisahash.Thisisahash.This [type:{name=chr,...}]isahash.Thisisahash.Thisisahash. Otheroptions: --helpPrinthelpmessageandexit. --versionPrintversioninformationandexit. TheglobaloptionGetoptLong.options$help_widthcontrolsthemaximalwidthoftheusagemessage. Thespecificationcanalsobesetasatemplatewhichprovidesmoreflexibilitiesfortheusagemessage.Hereoptionspecificationsaremakedby<>wherethespecificationswillbeextractedandthetextwillbereplacedbytheoptiondescription.ThemarkcanbesetbyGetoptLong.options$template_tagglobaloption. Theoptiondescriptionshavedifferentwidths.Toproperlyalignthetext,youneedtomanuallyadjustthewidth(spacesarefilledifthewidthislargerthantheoptiondescription)bysettingopt_widthparameterviatemplate_controlargument.Seethefollowingexample. GetoptLong(" Thisisademonstrationofusingtemplateastheoptionspecification. Usage:Rscriptfoo.R[options] Binaryoptions: Whethershowmessages Anon-senseoption Single-valueoptions: Thisisacount.Thisisacount. Thisisanumber.Thisisanumber. Multiple-vlaueoptions: Thisisanarray.Thisisanarray. Thisisahash.Thisisahash. Questions,pleasecontactyour.name@email ",template_control=list(opt_width=c(verbose=23,flag=23, count=22,number=22, array=30,hash=30) )) Thisisademonstrationofusingtemplateastheoptionspecification. Usage:Rscriptfoo.R[options] Binaryoptions: --verbose,-no-verboseWhethershowmessages --flag,-fAnon-senseoption Single-valueoptions: --count,-cintegerThisisacount.Thisisacount. --number,-nnumericThisisanumber.Thisisanumber. Multiple-vlaueoptions: --array,-a[numeric,...]Thisisanarray.Thisisanarray. --hash{name=character,...}Thisisahash.Thisisahash. Questions,pleasecontactyour.name@email Iftheoptionexplanationliesinmorethanonelines,infrontfromthesecondline,youshouldaddataginformofwheretagistheoptionnameofthecurrentoptionblock,sothatproperspacesinfrontofthetextcanbecalculatedandthetextwillbeproperlyaligned.Seethefollowingexample: GetoptLong(" Usage:Rscriptfoo.R[options] Thisisacount.Thisisacount.Thisisacount. Thisisacount.Thisisacount. Thisisanumber.Thisisanumber.Thisisanumber. Thisisanumber.Thisisanumber. ",template_control=list(opt_width=c(count=28,number=28)) ) Usage:Rscriptfoo.R[options] --count,-c[integer,...]Thisisacount.Thisisacount.Thisisacount. Thisisacount.Thisisacount. --number,-nnumericThisisanumber.Thisisanumber.Thisisanumber. Thisisanumber.Thisisanumber. Versionoption versionisalsoareservedoption. VersionshouldbestoredinavariableVERSIONbeforethecallofGetoptLong(),then--versionprintsthecorrespondingversionvalue. VERSION="0.0.1" GetoptLong( "tag=i","...", ) ~\>Rscriptfoo.R--version 0.0.1 ConfiguringGetopt::Long ConfigurationofGetopt::LongcanbesetbyGetoptLong.options("config"): GetoptLong.options("config"="bundling") GetoptLong.options("config"=c("no_ignore_case","bundling")) Withdifferentconfigurations,itcansupportmoretypesofoptionspecifications: -a-b-c-abc -s24-s24-s=24 PleaserefertowebsiteofGetopt::Longformoreinformation. SpecifypathofPerlincommandline InsomeconditionsthatpathofbinaryPerlisnotinthePATHenvironmentvariableandyoudonothavepermissiontomodifyPATH.YoucanspecifyyourPerlpathfromcommandlinelike: ~\>Rscriptfoo.R-a-b-c--/your/perl/bin/perl Sinceargumentsfollowingafter--willbeignoredbyGetopt::Long,wetakethefirstargumentnextto--asthepathofuser-specifiedPerlpath. Specifycommand-lineoptionswithinRsession WheninaninteractiveRsession,argumentscanbesetwhencallingsource_script(),soitwouldbeconvinienttoloadexternalRscriptswithdifferentcomand-linearguments.E.g.: source_script("foo.R",argv_str="--cutoff0.01--inputfile=foo.txt--verbose") Sessioninfo sessionInfo() Rversion4.0.2(2020-06-22) Platform:x86_64-apple-darwin17.0(64-bit) Runningunder:macOSCatalina10.15.5 Matrixproducts:default BLAS:/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib LAPACK:/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib locale: [1]C/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attachedbasepackages: [1]statsgraphicsgrDevicesutilsdatasetsmethodsbase otherattachedpackages: [1]GetoptLong_1.0.5knitr_1.30 loadedviaanamespace(andnotattached): [1]compiler_4.0.2rjson_0.2.20magrittr_2.0.1 [4]htmltools_0.5.0tools_4.0.2GlobalOptions_0.1.2 [7]yaml_2.2.1crayon_1.3.4stringi_1.5.3 [10]rmarkdown_2.5stringr_1.4.0digest_0.6.27 [13]xfun_0.19rlang_0.4.8evaluate_0.14