#!/bin/sh
set -e

pkg=metaphlan

CUR_DIR=`pwd`

if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
  AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
  trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
fi

cp ${CUR_DIR}/debian-tests-data/* -a "${AUTOPKGTEST_TMP}"

cd "${AUTOPKGTEST_TMP}"

# Run metaphlan using the test fastq file from the copied data
metaphlan Test.fastq \
    --input_type fastq \
    --bowtie2db . \
    --index mpa_vFeb24_CDIFF_CHOCOPhlAnSGB_20240910 \
    -o result.txt

# Check if result.txt is not empty
if [ -s result.txt ]; then
    echo "MetaPhlAn test passed"
else
    echo "MetaPhlAn test failed"
    exit 1
fi

