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#!/bin/bash
set -e
pkg=tombo
export LC_ALL=C.UTF-8
if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
fi
cd "${AUTOPKGTEST_TMP}"
printf "********* Testing help commands **********\n"
tombo -h || { echo 'Main tombo help failed. Likely a syntax error.' ; exit 1; }
tombo resquiggle -h
tombo preprocess annotate_raw_with_fastqs -h
tombo filter clear_filters -h
tombo filter stuck -h
tombo filter level_coverage -h
tombo filter q_score -h
tombo filter raw_signal_matching -h
tombo filter genome_locations -h
tombo detect_modifications de_novo -h
tombo detect_modifications alternative_model -h
tombo detect_modifications model_sample_compare -h
tombo detect_modifications level_sample_compare -h
tombo detect_modifications aggregate_per_read_stats -h
tombo text_output browser_files -h
tombo text_output signif_sequence_context -h
tombo plot max_coverage -h
tombo plot genome_locations -h
tombo plot motif_centered -h
tombo plot max_difference -h
tombo plot most_significant -h
tombo plot motif_with_stats -h
tombo plot per_read -h
tombo plot roc -h
tombo plot per_read_roc -h
tombo plot kmer -h
tombo plot cluster_most_significant -h
tombo build_model estimate_scale -h
tombo build_model event_resquiggle -h
tombo build_model estimate_reference -h
tombo build_model estimate_alt_reference -h
cat <<EOT
This test only tests the help system
There is an extensive test in
tombo/tests/shell_tests.sh
but this requires to download larger data
sets which is not done for the moment.
EOT
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