annotate test/test-multi @ 4:5526f8258e8a draft default tip

planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 0f382a5296aae9bfc77df06b0a5ad493eb3c01f3

#!/bin/bash

# Constants {{{1
################################################################

PROG_PATH=$(dirname $0)

# MAIN {{{1
################################################################

$PROG_PATH/../multivariate_wrapper.R dataMatrix_in $PROG_PATH/../test-data/input-dataMatrix.tsv sampleMetadata_in $PROG_PATH/../test-data/input-sampleMetadata.tsv variableMetadata_in $PROG_PATH/../test-data/input-variableMetadata.tsv respC age predI 1 orthoI 1 testL FALSE sampleMetadata_out $PROG_PATH/outputSampleMetadata.tsv variableMetadata_out $PROG_PATH/outputVariableMetadata.tsv

# Computed numbers are not always the same. We cannot use diff directly on files.

# 0) Check they have the same number of lines
nlines=$(wc -l <"$PROG_PATH/outputSampleMetadata.tsv")
ref_nlines=$(wc -l <"$PROG_PATH/../test-data/output-sampleMetadata.tsv")
if [ $nlines != $ref_nlines ] ; then
	echo "Incorrect output sample metadata." >&2
	exit 1
fi

# 1) We check the header line
head -n 1 "$PROG_PATH/outputSampleMetadata.tsv" > "$PROG_PATH/header.tsv"
head -n 1 "$PROG_PATH/../test-data/output-sampleMetadata.tsv" > "$PROG_PATH/ref_header.tsv"
if ! diff "$PROG_PATH/header.tsv" "$PROG_PATH/ref_header.tsv" ; then
	echo "Incorrect output sample metadata." >&2
	exit 1
fi

# 2) We remove computed values and compare what's left
awk 'BEGIN{FS=OFS="\t"} {$7=$8=$9="";sub("\t\t","\t")}1' "$PROG_PATH/outputSampleMetadata.tsv" > "$PROG_PATH/nocomput.tsv"
awk 'BEGIN{FS=OFS="\t"} {$7=$8=$9="";sub("\t\t","\t")}1' "$PROG_PATH/../test-data/output-sampleMetadata.tsv" > "$PROG_PATH/ref_nocomput.tsv"
if ! diff "$PROG_PATH/nocomput.tsv" "$PROG_PATH/ref_nocomput.tsv" ; then
	echo "Incorrect output sample metadata." >&2
	exit 1
fi