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view test-data/tool_wrapper.sh @ 8:5dd4791c7b70 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ccf4b178d13aeedf7214f2400e7411bcfa3e73b4
author artbio
date Tue, 11 Dec 2018 12:43:07 -0500
parents f6f0f1e5e940
children
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input_base=Samp
baseReference=chrM

bowtie-build ${baseReference}.fa ${baseReference}

python RepEnrich_setup.py ${baseReference}_repeatmasker.txt ${baseReference}.fa \
       setup_folder_${baseReference}

bowtie $baseReference -p 16 -t -m 1 -S --max ${input_base}_multimap.fastq \
       ${input_base}.fastq ${input_base}_unique.sam

samtools view -bS ${input_base}_unique.sam > ${input_base}_unique.bam
samtools sort ${input_base}_unique.bam ${input_base}_unique_sorted
mv ${input_base}_unique_sorted.bam ${input_base}_unique.bam
samtools index ${input_base}_unique.bam
rm ${input_base}_unique.sam

python RepEnrich.py ${baseReference}_repeatmasker.txt ${input_base} ${input_base} \
        setup_folder_${baseReference} ${input_base}_multimap.fastq ${input_base}_unique.bam --cpus 16