Mercurial > repos > drosofff > repenrich
comparison test-data/tool_wrapper.sh @ 0:1435d142041b draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
| author | drosofff |
|---|---|
| date | Tue, 23 May 2017 18:37:22 -0400 |
| parents | |
| children | 54a3f3a195d6 |
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| -1:000000000000 | 0:1435d142041b |
|---|---|
| 1 input_base=$1 | |
| 2 baseReference=$2 | |
| 3 | |
| 4 bowtie-build ${baseReference}.fa ${baseReference} | |
| 5 | |
| 6 python RepEnrich_setup.py ${baseReference}_repeatmasker.txt ${baseReference}.fa \ | |
| 7 setup_folder_${baseReference} | |
| 8 | |
| 9 bowtie $baseReference -p 16 -t -m 1 -S --max ${input_base}_multimap.fastq \ | |
| 10 ${input_base}.fastq ${input_base}_unique.sam | |
| 11 | |
| 12 samtools view -bS ${input_base}_unique.sam > ${input_base}_unique.bam | |
| 13 samtools sort ${input_base}_unique.bam ${input_base}_unique_sorted | |
| 14 mv ${input_base}_unique_sorted.bam ${input_base}_unique.bam | |
| 15 samtools index ${input_base}_unique.bam | |
| 16 rm ${input_base}_unique.sam | |
| 17 | |
| 18 python RepEnrich.py ${baseReference}_repeatmasker.txt ${input_base} ${input_base} \ | |
| 19 setup_folder_${baseReference} ${input_base}_multimap.fastq ${input_base}_unique.bam --cpus 16 |