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view test-data/tool_wrapper.sh @ 0:1435d142041b draft

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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
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children 54a3f3a195d6
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input_base=$1
baseReference=$2

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