Mercurial > repos > drosofff > repenrich
view test-data/tool_wrapper.sh @ 4:4850fb47c45c draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 5bd2ca88fb31e5e836f41bc3c70b9d559bcdb52f
author | drosofff |
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date | Mon, 29 May 2017 17:09:00 -0400 |
parents | 89968ee4bf95 |
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