diff Haplophyle.sh @ 0:6f11162b6fa2 draft

planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f

--- /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