arb_item:Clustalv Alignment (DNA)
itemmethod:(tr '"%//' '>' <in1 >clus_in; RUN_IN_WINDOW((clustalv /output=PIR /infile=clus_in /align /ktuple=$KTUP /window=$WIN $Trans /fixedgap=$FIXED /floatgap=$FLOAT;cat clus_in.pir |sed "s/^>DL;/#/g" |sed "s/^>P1;/%/g" |sed "s/^\*$//g" >out1; )); /bin/rm -f clus_in* in1)

itemhelp:clustal_help

arg:KTUP
argtype:slider
arglabel:K-tuple size for fast pairwise search 
argmin:1
argmax:10
argvalue:2

arg:WIN
argtype:slider
arglabel:Window size
argmin:1
argmax:10
argvalue:4

arg:Trans
argtype:chooser
arglabel:Transitions weighted?
argchoice:Yes:/TRANSIT
argchoice:No:

arg:FIXED
argtype:slider
arglabel:Fixed gap penalty
argmin:1
argmax:100
argvalue:10

arg:FLOAT
arglabel:Floating gap penalty
argtype:slider
argmin:1
argmax:100
argvalue:10

in:in1
informat:flat
insave:

out:out1
outformat:flat


item:Clustalw DNA Alignment
itemmethod:(tr '"%//' '>' <in1 >clus_in;RUN_IN_WINDOW((clustalw -output=PIR -infile=clus_in -align -ktuple=$KTUP_ -window=$WIN_ -topdiags=$WIN_ $MATRIX_  -gapopen=$FIXED_ -gapext=$FLOAT_ -transweight=0.5 -type=DNA -DNAMATRIX=$MATRIX_;cat clus_in.pir |sed "s/^>DL;/#/g" |sed "s/^>P1;/%/g" |sed "s/^\*$//g" >out1; )); /bin/rm -f clus_in* in1)

itemhelp:clustal.help

arg:KTUP
argtype:slider
arglabel:K-tuple size for fast pairwise search
argmin:1
argmax:10
argvalue:2

arg:WIN
argtype:slider
arglabel:Window size for fast pairwise search
argmin:1
argmax:10
argvalue:4

arg:MATRIX_
argtype:chooser
arglabel:Weighting matrix
argchoice:BLOSUM:BLOSUM
argchoice:PAM:PAM
argchoice:GONNET:GONNET
argchoice:ID:ID

arg:FIXED_
argtype:slider
arglabel:Gap Open Panelty
argmin:1
argmax:100
argvalue:8.7
 
arg:FLOAT_
arglabel:Gap Extend Panelty
argtype:slider
argmin:.001
argmax:1
argvalue:.1


in:in1
informat:flat
insave:

out:out1
outformat:flat


item:Clustalw Protein Alignment
itemmethod:(tr '"%//' '>' <in1 >clus_in;RUN_IN_WINDOW((clustalw -output=PIR -infile=clus_in -align -ktuple=$KTUP_ -window=$WIN_ -topdiags=$WIN_ $MATRIX_  -gapopen=$FIXED_ -gapext=$FLOAT_ -type=PROTEIN;cat clus_in.pir |sed "s/^>DL;/#/g" |sed "s/^>P1;/%/g" |sed "s/^\*$//g" >out1; ));\/bin/rm -f clus_in* in1)


itemhelp:clustalw.help

arg:KTUP_
argtype:slider
arglabel:K-tuple size for fast pairwise search
argmin:1
argmax:10
argvalue:2

arg:WIN_
argtype:slider
arglabel:Window size and top diagonals for fast alignment
argmin:1
argmax:10
argvalue:4

arg:MATRIX_
argtype:chooser
arglabel:Weighting matrix
argchoice:BLOSUM:BLOSUM
argchoice:PAM:PAM
argchoice:GONNET:GONNET
argchoice:ID:ID

arg:FIXED_
argtype:slider
arglabel:Gap Open Panelty
argmin:1
argmax:100
argvalue:8.7
 
arg:FLOAT_
arglabel:Gap Extend Panelty
argtype:slider
argmin:.001
argmax:1
argvalue:.1


 
in:in1
informat:flat
insave:

out:out1
outformat:flat

item:Assemble Contigs
itemmethod: (tr '"%//' '>' <in1 >in1.tmp;CAP2 in1.tmp $OVERLAP $PMATCH >  out1;/bin/rm -f in1.tmp)
itemhelp:CAP2.help

arg:OVERLAP
argtype:slider
arglabel:Minimum overlap?
argmin:5
argmax:100
argvalue:20

arg:PMATCH
argtype:slider
arglabel:Percent match required within overlap
argmin:25
argmax:100
argvalue:90

in:in1
informat:flat

out:out1
outformat:gde