comparison processMAF.sh @ 3:d49b9759e294 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit 3abc213e109bb564de7dee75d71d90eb1bf78c7e

2:434332033e82

ref=""
last=0

if [[ ! -z "$tabular" ]]; then
	echo -e "HSS #\tFrame\tLength\tFrom\tTo\tName\tStart\tEnd\tScore\tP" >> ${outfile:-/dev/stdout}
fi

tmpif=$(mktemp -p '.')
tmpof=$(mktemp -p '.')
tmpd=$(mktemp -d -p '.')

while read line
do
	if [[ "$line" =~ ^# ]]; then
		echo -n > ${tmpif}
	elif [[ "$line" =~ ^$ ]]; then
		run_rnacode ${args[@]} ${tmpif}
		# >> ${outfile:-/dev/stdout}
		echo -n > ${tmpif}
	else
                if [[ -z $ref && "$line" =~ ^s ]]; then
			if [[ -z "$gtf" ]]; then
				ref=`echo $line | cut -d" " -f 2`

		echo $line >> ${tmpif}
	fi
done < ${file:-/dev/stdin}
# if there is something left -> process it
if [[ "`cat ${tmpif} | wc -l`" -gt "0" ]]; then
	run_rnacode ${args[@]} ${tmpif}
       #	>> ${outfile:-/dev/stdout} 
fi

if [[ ! -z "$eps" ]]; then
	mv ${tmpd}/*eps ${epsdir:-eps}/
fi

3:d49b9759e294

ref=""
last=0

if [[ ! -z "$tabular" ]]; then
	echo -e "HSS #\tStrand\tFrame\tLength\tFrom\tTo\tName\tStart\tEnd\tScore\tP" >> ${outfile:-/dev/stdout}
fi

tmpif=$(mktemp -p '.')
tmpof=$(mktemp -p '.')
tmpd=$(mktemp -d -p '.')

while read line
do
	if [[ "$line" =~ ^# ]]; then
		echo -n > ${tmpif}
	elif [[ "$line" =~ ^$ ]]; then
		run_rnacode ${args[@]} ${tmpif} >> ${outfile:-/dev/stdout}
		echo -n > ${tmpif}
	else
                if [[ -z $ref && "$line" =~ ^s ]]; then
			if [[ -z "$gtf" ]]; then
				ref=`echo $line | cut -d" " -f 2`

		echo $line >> ${tmpif}
	fi
done < ${file:-/dev/stdin}
# if there is something left -> process it
if [[ "`cat ${tmpif} | wc -l`" -gt "0" ]]; then
	run_rnacode ${args[@]} ${tmpif} >> ${outfile:-/dev/stdout} 
fi

if [[ ! -z "$eps" ]]; then
	mv ${tmpd}/*eps ${epsdir:-eps}/
fi