#-------------------------- Clustalw protein alignment -------------------- 
item:Clustal Protein Alignment
itemmethod:(tr '%#' '>'<in1>clus_in;clustalw -output=GDE -infile=clus_in -align  > in1.rpt;sed "s/>DL;/#/g" < clus_in.gde> in1;$REPORT gde clus_in.gde;/bin/rm -f clus_in* in1*   )&


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

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

arg:Matrx
argtype:chooser
arglabel:Weighting matrix
argchoice:PAM 250:PAM250
argchoice:PAM 100:PAM100
argchoice:Identity:ID

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

arg:REPORT
argtype:chooser
arglabel:View assembly report?
argchoice:No:
argchoice:Yes:textedit in1.rpt&
 
in:in1
informat:flat
insave: