Mercurial > repos > dereeper > haplophyle
diff Haplophyle.sh @ 0:6f11162b6fa2 draft
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
author | dereeper |
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date | Tue, 14 Aug 2018 08:04:23 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Haplophyle.sh Tue Aug 14 08:04:23 2018 -0400 @@ -0,0 +1,36 @@ +#!/bin/bash + +# Config ####### +maxsizeseq=500 +maxnumseq=200 +################ + +tool_path=$(dirname $0) + +filein=$1 +fileout=$2 +dotfile=$3 +logfile=$4 +filein2=$5 +groups=$6 + +nbline=$(sed -n '$=' $filein) +let "nbseq = $nbline / 2" +seq=$(sed -n 2p $filein) +sizeseq=${#seq} + +if [ $nbseq -lt $maxnumseq ] +then + if [ $sizeseq -lt $maxsizeseq ] + then + perl $tool_path/Haplophyle.pl --input $filein --groups $groups --stats $filein2 --dot $dotfile --out $fileout --tool_path $tool_path >>$logfile 2>&1 + else + echo "Sequence size: $sizeseq" + echo "Input Sequences bust have a length < $maxsizeseq" + exit 1 + fi +else + echo "$nbseq sequences in the file" + echo "Input file must have less than $maxnumseq sequences" + exit 1 +fi