Mercurial > repos > artbio > repenrich

diff test-data/tool_wrapper.sh @ 0:f6f0f1e5e940 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
author artbio
date Wed, 02 Aug 2017 05:17:29 -0400
parents
children
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tool_wrapper.sh	Wed Aug 02 05:17:29 2017 -0400
@@ -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