Mercurial > repos > nml > smalt_map
comparison smalt_map.sh @ 0:77cc50d982c0 draft default tip
planemo upload for repository https://sourceforge.net/projects/smalt/ commit 008f4667b70be22e9ddf496738b3f74bb942ed28
| author | nml |
|---|---|
| date | Tue, 19 Sep 2017 16:40:17 -0400 |
| parents | |
| children |
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| -1:000000000000 | 0:77cc50d982c0 |
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| 1 #/bin/bash | |
| 2 | |
| 3 | |
| 4 smi=$1 | |
| 5 shift | |
| 6 sma=$1 | |
| 7 shift | |
| 8 #get format type so we can do extra work if it is a bam file | |
| 9 format=$1 | |
| 10 shift | |
| 11 | |
| 12 #get working directory so we can find the output files | |
| 13 CUR_DIR=`pwd` | |
| 14 | |
| 15 | |
| 16 cp "$smi" "$CUR_DIR/temp.smi" | |
| 17 cp "$sma" "$CUR_DIR/temp.sma" | |
| 18 | |
| 19 #determine if we have 1 or 2 | |
| 20 num_inputs=$1 | |
| 21 shift | |
| 22 | |
| 23 inputs=() | |
| 24 | |
| 25 #determine how many fasta/fastq were given. Needs to be provided by user | |
| 26 if [ $num_inputs -eq 1 ]; then | |
| 27 inputs+=$1 | |
| 28 shift | |
| 29 elif [ $num_inputs -eq 2 ]; then | |
| 30 inputs+=$1 | |
| 31 shift | |
| 32 inputs+=' ' | |
| 33 inputs+=$1 | |
| 34 shift | |
| 35 else | |
| 36 exit 1 | |
| 37 fi | |
| 38 | |
| 39 smaltout=$2 | |
| 40 | |
| 41 smalt map $@ 'temp' $inputs | |
| 42 | |
| 43 | |
| 44 if [ "$format" == "bam" ]; then | |
| 45 if [ $GALAXY_SLOTS ] | |
| 46 then | |
| 47 samtools sort -@ $GALAXY_SLOTS $smaltout 'temp2' | |
| 48 else | |
| 49 samtools sort $smaltout 'temp2' | |
| 50 fi | |
| 51 mv 'temp2.bam' $smaltout | |
| 52 fi | |
| 53 | |
| 54 #remove index files | |
| 55 rm "$CUR_DIR/temp.smi" | |
| 56 rm "$CUR_DIR/temp.sma" | |
| 57 | |
| 58 exit 0 |