Mercurial > repos > drosofff > repenrich

diff test-data/tool_wrapper.sh @ 0:041de602103e draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
author drosofff
date Tue, 23 May 2017 03:08:45 -0400
parents
children 89968ee4bf95
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tool_wrapper.sh	Tue May 23 03:08:45 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