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comparison processMAF.sh @ 3:d49b9759e294 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit 3abc213e109bb564de7dee75d71d90eb1bf78c7e
author rnateam
date Thu, 15 Nov 2018 01:24:06 -0500
parents 434332033e82
children
comparison
equal deleted inserted replaced
2:434332033e82 3:d49b9759e294
131 131
132 ref="" 132 ref=""
133 last=0 133 last=0
134 134
135 if [[ ! -z "$tabular" ]]; then 135 if [[ ! -z "$tabular" ]]; then
136 echo -e "HSS #\tFrame\tLength\tFrom\tTo\tName\tStart\tEnd\tScore\tP" >> ${outfile:-/dev/stdout} 136 echo -e "HSS #\tStrand\tFrame\tLength\tFrom\tTo\tName\tStart\tEnd\tScore\tP" >> ${outfile:-/dev/stdout}
137 fi 137 fi
138 138
139 tmpif=$(mktemp -p '.') 139 tmpif=$(mktemp -p '.')
140 tmpof=$(mktemp -p '.') 140 tmpof=$(mktemp -p '.')
141 tmpd=$(mktemp -d -p '.') 141 tmpd=$(mktemp -d -p '.')
149 while read line 149 while read line
150 do 150 do
151 if [[ "$line" =~ ^# ]]; then 151 if [[ "$line" =~ ^# ]]; then
152 echo -n > ${tmpif} 152 echo -n > ${tmpif}
153 elif [[ "$line" =~ ^$ ]]; then 153 elif [[ "$line" =~ ^$ ]]; then
154 run_rnacode ${args[@]} ${tmpif} 154 run_rnacode ${args[@]} ${tmpif} >> ${outfile:-/dev/stdout}
155 # >> ${outfile:-/dev/stdout}
156 echo -n > ${tmpif} 155 echo -n > ${tmpif}
157 else 156 else
158 if [[ -z $ref && "$line" =~ ^s ]]; then 157 if [[ -z $ref && "$line" =~ ^s ]]; then
159 if [[ -z "$gtf" ]]; then 158 if [[ -z "$gtf" ]]; then
160 ref=`echo $line | cut -d" " -f 2` 159 ref=`echo $line | cut -d" " -f 2`
165 echo $line >> ${tmpif} 164 echo $line >> ${tmpif}
166 fi 165 fi
167 done < ${file:-/dev/stdin} 166 done < ${file:-/dev/stdin}
168 # if there is something left -> process it 167 # if there is something left -> process it
169 if [[ "`cat ${tmpif} | wc -l`" -gt "0" ]]; then 168 if [[ "`cat ${tmpif} | wc -l`" -gt "0" ]]; then
170 run_rnacode ${args[@]} ${tmpif} 169 run_rnacode ${args[@]} ${tmpif} >> ${outfile:-/dev/stdout}
171 # >> ${outfile:-/dev/stdout}
172 fi 170 fi
173 171
174 if [[ ! -z "$eps" ]]; then 172 if [[ ! -z "$eps" ]]; then
175 mv ${tmpd}/*eps ${epsdir:-eps}/ 173 mv ${tmpd}/*eps ${epsdir:-eps}/
176 fi 174 fi