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#!/bin/sh -e
pkg=adapterremoval
if [ "$AUTOPKGTEST_TMP" = "" ] ; then
AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
fi
cd $AUTOPKGTEST_TMP
cp -a /usr/share/doc/${pkg}/examples/* .
find . -name "*.gz" -exec gunzip \{\} \;
# examples from README.html
AdapterRemoval --file1 reads_1.fq --basename output_single --trimns --trimqualities --gzip
AdapterRemoval --file1 reads_1.fq --file2 reads_2.fq --basename output_paired --trimns --trimqualities --collapse
AdapterRemoval --interleaved --file1 interleaved.fq --basename output_interleaved
AdapterRemoval --qualitybase 64 --file1 reads_q64.fq --basename phred_64_encoded
AdapterRemoval --qualitybase 64 --qualitybase-output 33 --file1 reads_q64.fq --basename phred_33_encoded
## The documentation has the --collapsed argument which leads to
# AdapterRemoval --qualitymax 50 --file1 reads_1.fq --file2 reads_2.fq --collapsed --basename collapsed_q50
# ERROR: Unknown argument: '--collapsed'
# so leaving out --collapsed
AdapterRemoval --qualitymax 50 --file1 reads_1.fq --file2 reads_2.fq --basename collapsed_q50
AdapterRemoval --file1 reads_1.fq --file2 reads_2.fq --basename output_multi --trimns --trimqualities --collapse --adapter-list adapters.txt
AdapterRemoval --identify-adapters --file1 reads_1.fq --file2 reads_2.fq
AdapterRemoval --file1 demux_1.fq --file2 demux_2.fq --basename output_dumux --barcode-list barcodes.txt
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