Mercurial > repos > artbio > repenrich2

diff test-data/tool_wrapper.sh @ 0:4905a332a094 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
author artbio
date Sat, 20 Apr 2024 11:56:53 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tool_wrapper.sh	Sat Apr 20 11:56:53 2024 +0000
@@ -0,0 +1,19 @@
+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