Mercurial > repos > drosofff > repenrich
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tool_wrapper.sh Tue May 23 18:37:22 2017 -0400 @@ -0,0 +1,19 @@ +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