samplepack expath=/bio/mb/bin/ filepath=/bio/mb/ datapath=/bio/mb/data/ TACGLIB=/bio/mb/data/ docpath=/bio/mb/docs/ stderr=childapp.stderr stdout=childapp.stdout samplebix About|Bio App Samples TITLE Bioinformatics Application samples INFO About HELP Help http://iubio.bio.indiana.edu/grid/runner/ bixinfo About|Bix command language TITLE BIX - BioInformatics application/command Xml INFO About bix.DTD - BioInformatics application/command Xml rewrite of clustal.command (BOP structure format) d.gilbert, dec97 rewrite of clustal.html (seqpup) and clustalw.config (seqlab) as general parseable structure for specifying app parameters for use w/ a corba client=server interface magic string for this format is "Content=type: biocompute/command" format key = value key = { structured.value } newlines or ';' separate key=value pairs in a structure values that include white space need to be quoted with "" or '' see bopper.idl and ReadCommand.java for current key words (these may change) key words match fields in the bopper.idl, and are case=insensitive commandKeys = { "id", "transport", "action", "filepath", "parlist", "command" }; parameterKeys = { "id", "label", "value", "ifelseRules", "runSwitch" }; containerKeys = { "required", "parlist" }; choiceKeys = { "multiple", "minToShow", "parlist" }; dataKeys = { "datatype", "dataflow", "filename", "flavor", "data" }; ID values are case=sensitive, unique strings. reference IDs and other variables as $ID $serverurl, $tempdir, and $tempname are variables that are set by server (remote or local) at runtime TITLE, INFO and HELP are special par ids ]]> HELP Help http://iubio.bio.indiana.edu/grid/runner/docs/bix.dtd clustalw Sequence Alignment|Clustal multiple alignment local: ${expath}clustalw $INFILE $OUTFILE $ALIGN $TREE $QUICK $BOOT $GAPEXT $GAPOPEN $200 $220 $100 $PAIRGAP $KTUP $TOPDIAGS $WINDOW $PWGAPOPEN $PWGAPEXT $PWMATRIX $300 $221 $211 $212 $213 TITLE Clustal W Alignment INFO About Clustal W Clustal W - for multiple sequence alignment by Des Higgins and colleagues. Clustal W is a general purpose multiple alignment program for DNA or proteins. globalrules -300,+200,+210,+220,+221,+211,+212,+213 +300,-200,-210,-220,-221,-211,-212,-213 main Clustal W - A multiple sequence alignment program true HELP Help with Clustal W http://www-igbmc.u-strasbg.fr/BioInfo/ClustalW/ ALIGN Do full multiple align true -align IOfiles Input/Output files false INFILE Input sequences input biosequence/nbrf clustalw.pir input -infile=$value OUTFILE Output aligned sequences output biosequence/gcg clustalw.msf output -outfile=$value -output=GCG TreeFile Tree file output biotree/newick output clustalw.dnd STDOUT Command output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} treeoptions Tree options false TREE Calculate NJ tree false -tree BOOT Bootstrap NJ tree false -bootstrap=$BOOTVAL BOOTVAL No. of boostraps 1000 pairoptions Pairwise alignment options false 100 false 2 QUICK Perform fast, approximate pair-wise alignments false -quicktree +KTUP,+WINDOW,+PAIRGAP,+TOPDIAGS,-PWMATRIX,-USERDEF SLOW Perform slow, accurate pair-wise alignments true -pairwise -KTUP,-WINDOW,-PAIRGAP,-TOPDIAGS,+PWMATRIX,+USERDEF -KTUP,-WINDOW,-PAIRGAP,-TOPDIAGS,-PWMATRIX,-USERDEF PAIRGAP Gap penalty 3,1,500,1 5,1,50,1 -pairgap=$value KTUP Wordsize (ktuple) 1,1,2,1 2,1,4,1 -ktuple=$value TOPDIAGS Number of best diagonals 5,1,50,1 4,1,50,1 -topdiags=$value WINDOW Window size 5,1,50,1 4,1,50,1 -window=$value PWGAPOPEN Window Gap penalty 10.0,0,100,0.1 -pwgapopen=$value PWGAPEXT Window Gap extension 0.1,0,10,0.1 5.0,0,10,0.1 -pwgapext=$value PWMATRIX Pair-wise scoring matrix false 6 1 BLOSUM30 true -pwmatrix=blosum 2 PAM350 false -pwmatrix=pam 3 Gonnet250 false -pwmatrix=gonnet 4 Identity Matrix false -pwmatrix=id 5 User Defined false -matrix=$USERDEF USERDEF Scoring Matrix file name multalign Multiple sequence alignment options false GAPOPEN Gap opening penalty 10.0,0,100,1.0 -gapopen=$value GAPEXT Gap extension penalty 0.05,0,10,0.1 5.0,0,10,0.1 -gapext=$value 300 Do NOT Weight Transitions false -transitions 220 Delay divergent sequences 40,0,100,1 -maxdiv=$value 221 Use a negative matrix false -negative 200 Protein scoring matrices false 6 BLOSUM true -matrix=blosum 7 Identity Matrix false -matrix=id 8 PAM false -matrix=pam 9 User Defined false -matrix=$210 210 Scoring Matrix file name 211 Turn Off Residue-Specific Gap Penalties false -nopgap 212 Turn Off Hydrophilic Gap Penalties false -nohgap 213 List of Hydrophilic Residues GPSNDQEKR -hgapresidues=$value cap Sequence Alignment|CAP contig assembly local: ${expath}cap $INFILE $OUTFILE $MIN_OVERLAP $PERCENT_MATCH TITLE CAP Contig Assembly INFO About CAP A gel Contig Assembly Program by Xiaoqiu Huang main CAP contig assembly true MIN_OVERLAP Minimum base overlap for contig alignment 20 $value PERCENT_MATCH Percent match for alignment 85,0,100,1 $value IOfiles Input/Output files false INFILE Input sequences input input biosequence/fasta cap-data.fasta $value OUTFILE Output aligned sequences output output biosequence/fasta cap-out.fasta $value STDOUT Command output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} fastdnaml Phylogeny|FastDNAml local: ${expath}fastDNAml $TREEFILE TITLE FastDNAml INFO About FastDNAml A faster DNA maximum likelihood phylogeny estimator. fastDNAml is a program derived from Joseph Felsenstein version 3.3 DNAML (part of his PHYLIP package). Users should consult the documentation for DNAML before using this program. Produced by Gary Olsen, Hideo Matsuda, Ray Hagstrom, and Ross Overbeek. main fastDNAml phylogeny analysis true HELP Help with FastDNAml http://geta.life.uiuc.edu/~gary/programs/fastDNAml.html IOfiles Input/Output files false STDIN Input input biosequence/phylip stdin fastdnaml.phylip STDOUT Output output text/plain stdout ${stdout} TREEFILE Tree file output biotree/newick output $filepath/treefile.0 STDERR Errors output text/plain stderr ${stderr} Options Options false optNotice NOTICE These option selections are not yet implemented in the local versions of seqpup bootstrap false bootstrap bootseed 987 bootstrap seed categories false use categories catnum 1 Number of categories catlist category values for each site frequencies false use frequencies freqlist 0.24 0.28 0.27 0.21 empirical base frequencies (A,C,G,T) global false Global rearrangements Global1 Global1: the number of branches to cross in rearrangements of the completed tree Global2 Global2: the number of branches to cross in testing rearrangements jumble false Jumble jumbleseed 987 jumble seed outgroup false use outgroup outval 1 outgroup number quickadd false use Quickadd option transitions false use transitions/transversion ratio transval 2.0 transition/transversion ratio weights false use weights weightlist weighting values per site tacg Restriction Map/tacg ${expath}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 $sites TITLE tacg restriction map HELP Help with tacg file:${docpath}tacg3.main.html INFO About tacg tacg analyzes a DNA sequence for restriction enzyme sites, nucleic acid patterns version 3, by Harry Mangalam IOfiles Input/Output files false STDIN Input input biosequence/fasta stdin globin.gb STDOUT Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} REBASE Restrict. Enzyme table input text/gcg serverlocal $datapath/rebase.data -R $value Options Options false orderout -c false order the output by # of cuts/fragments by each RE, and thence alphabetic laddermap -l true a 'ladder' map of selected enzymes linearmap -L false if you WANT a linear map. This spews the most output summary -s true print the summary of site information sites -S false print the the actual cut sites in tabular form 98 Print/Sort Fragments false 988 Omit true fragunsort Print unsorted false -F1 fragsort Print sorted true -F2 frag3 Print sorted & unsorted false -F3 96 pseudo-gel map graphic false gelmap do map false -g$gelmapval gelmapval map val 10 99 form (or topology) of DNA false circular Circular false -f0 linear Linear true -f1 100 Codon usage false codon.u Standard true -C0 codon.v Vert_Mito false -C1 codon.d Yeast_Mito false -C2 codon.sc Mold_Mito false -C3 codon.sp Invert_Mito false -C4 codon.nc Ciliate_Mito false -C5 codon.hp Echino_Mito false -C6 codon.c Euplotid_Nuclear false -C7 codon.b Bacterial false -C8 codon.alty Alt_Yeast false -C9 codon.ascm Ascidian_Mito false -C10 codon.flat Flatworm false -C11 codon.blep Blepharisma false -C12 REnzymes Restriction Enzymes false REselect Select specific r. enzymes -r $RElist false RElist List of enzymes to select AarI|AatII|Acc65I|AccI|AciI|AclI|AfeI|AflII|AflIII|AgeI| AhdI|AloI|AluI|AlwI|AlwNI|ApaI|ApaLI|ApoI|AscI|AseI| AvaI|AvaII|AvrII|BaeI|BamHI|BanI|BanII|BbeI|BbsI|BbvCI| BbvI|BceAI|BcgI|BciVI|BclI|BfaI|BfrBI|BglI|BglII|BlpI| Bme1580I|BmrI|BplI|BpmI|Bpu10I|BsaAI|BsaBI|BsaHI|BsaI|BsaJI| BsaWI|BsaXI|BseMII|BseRI|BsgI|BsiEI|BsiHKAI|BsiWI|BslI|BsmAI| BsmBI|BsmFI|BsmI|Bsp1286I|BspCNI|BspEI|BspHI|BspMI|BsrBI|BsrDI| BsrFI|BsrGI|BsrI|BssHII|BssKI|BssSI|BstAPI|BstBI|BstEII|BstF5I| BstKTI|BstNI|BstUI|BstXI|BstYI|BstZ17I|Bsu36I|BtgI|BtrI|BtsI| Cac8I|ClaI|Csp6I|CviJI|DdeI|DpnI|DraI|DraIII|DrdI|EaeI| EagI|EarI|EciI|Ecl136II|Eco57I|Eco57MI|EcoNI|EcoO109I|EcoRI|EcoRV| FalI|FatI|FauI|Fnu4HI|FokI|FseI|FspAI|FspI|HaeII|HaeIII| HgaI|HhaI|Hin4I|HinP1I|HincII|HindIII|HinfI|HpaI|HpaII|HphI| Hpy188I|Hpy188III|Hpy8I|Hpy99I|HpyCH4III|HpyCH4IV|HpyCH4V|KasI|KpnI|MaeIII| MboI|MboII|MfeI|MluI|MlyI|MnlI|MscI|MseI|MslI|MspA1I| MwoI|NaeI|NarI|NciI|NcoI|NdeI|NgoMIV|NheI|NlaIII|NlaIV| NotI|NruI|NsiI|NspI|OliI|PacI|PciI|PflMI|PleI|PmeI| PmlI|PpiI|Ppu10I|PpuMI|PshAI|PsiI|PspGI|PspOMI|PsrI|PstI| PvuI|PvuII|RsaI|RsrII|SacI|SacII|SalI|SanDI|SapI|Sau96I| SbfI|ScaI|ScrFI|SexAI|SfaNI|SfcI|SfiI|SfoI|SgfI|SgrAI| SmaI|SmlI|SnaBI|SpeI|SphI|SrfI|SspI|StuI|StyI|SwaI| TaqI|TaqII|TatI|TauI|TfiI|TscI|TseI|Tsp45I|Tsp509I|TspGWI| TspRI|Tth111I|XbaI|XcmI|XhoI|XmaI|XmnI|ZraI