source: branches/help/SH/arb_phyml

#!/bin/bash -x

showinput() {
    echo '------------------'
    cat -
    echo '------------------'
}

switchmodel() {
    if [ $1 = 0 ]; then
        echo ""
    else
        echo "m `switchmodel $[$1-1]`"
    fi
}

PHYML=$ARBHOME/bin/phyml
if [ \! -x $PHYML ]; then
    arb_message 'Error: You have to install phyml and link it into $ARBHOME/bin\n(e.g.: cd ARBHOME/bin; ln -s /path/to/your/phyml .)'
else
    INFILE=$1; shift
    DATATYPE=$1; shift
    MODEL=$1; shift

    if [ "$DATATYPE" = "DNA" ]; then
        OPTFREQ=$1; shift
        BASEFREQEST=$1; shift
        TSTVRATIO=$1; shift
        PINVAR=$1; shift
    else
        if [ "$DATATYPE" = "AA" ]; then
            PINVAR=$1; shift
        else
            arb_message "Invalid datatype '$DATATYPE'"
            exit 1
        fi
    fi
    INTERACTIVE=$1; shift

    if [ -z $INTERACTIVE -o \! -z $1 ]; then
        echo 'Usage: arb_phyml seqfile DNA substmodel optfreq basefreqest tstvratio pinvar interactive'
        echo 'Usage: arb_phyml seqfile AA  substmodel pinvar interactive'
    else
        # echo "INFILE='$INFILE'"
        # echo "DATATYPE='$DATATYPE'"
        # echo "MODEL='$MODEL'"
        # echo "OPTFREQ='$OPTFREQ'"
        # echo "BASEFREQEST='$BASEFREQEST'"
        # echo "TSTVRATIO='$TSTVRATIO'"
        # echo "PINVAR='$PINVAR'"
        # echo "INTERACTIVE='$INTERACTIVE'"
        
        ARGS=$INFILE
        SETMODEL=`switchmodel $MODEL`
        if [ "$DATATYPE" = "AA" ]; then
            ARGS="$ARGS d $SETMODEL"
            if [ $PINVAR = 1 ]; then
                ARGS="$ARGS v y"
            fi
        else
            ARGS="$ARGS $SETMODEL"
            if [ $OPTFREQ = 1 ]; then
                if [ $MODEL = 4 ]; then
                    ARGS="$ARGS e"
                else
                    arb_message "'Optimize equilibrium frequencies' only applies to 'custom' model. Ignored."
                fi
            fi
            if [ $BASEFREQEST = 1 ]; then
                if [ $MODEL = 5 -o $MODEL = 6 -o $MODEL = 4 ]; then
                    arb_message "'Base frequency estimates' does not apply to chosen model. Ignored."
                else
                    ARGS="$ARGS e"
                fi
            fi
            if [ $TSTVRATIO = 1 ]; then
                if [ $MODEL = 3 -o $MODEL = 4 -o $MODEL = 5 -o $MODEL = 7 ]; then
                    arb_message "'Ts/tv ratio' does not apply to chosen model. Ignored."
                else
                    ARGS="$ARGS t y"
                fi
            fi
            if [ $PINVAR = 1 ]; then
                if [ $MODEL = 4 ]; then
                    arb_message "'Proportion of invariable sites' does not apply to chosen model. Ignored."
                else
                    ARGS="$ARGS v y"
                fi
            fi
        fi

        # PHYML=showinput
        if [ $INTERACTIVE = 1 ]; then
            (arb_echo $ARGS; cat -) | $PHYML
        else
            arb_echo $ARGS y | $PHYML
        fi
        
        TREEFILE=infile_phyml_tree.txt
        if [ \! -s $TREEFILE ]; then
            arb_message "'$TREEFILE' was not generated or is empty"
            false
        else
            echo >arb_read_tree_args
            mv $TREEFILE outtree
        fi
    fi
fi