<commit_before>#!/bin/bash
TIMESTAMP=$(date +%s)
SCRIPT_DIR=$(dirname ${BASH_SOURCE[0]})

CODEDIR="${SCRIPT_DIR}/.."
INPUTDIR="${SCRIPT_DIR}/../test-data"
OUTPUTDIR="$(pwd)/output_${TIMESTAMP}"
mkdir -p ${OUTPUTDIR}

/modulated_modularity_clustering.py \
		-i  $INPUTDIR/ST000006_data.tsv \
		-d  $INPUTDIR/ST000006_design.tsv \
		-id Retention_Index \
                -c pearson \
         	-o $OUTPUTDIR/ST000006_modulated_modularity_clustering_out.tsv \
	        -f $OUTPUTDIR/ST000006_modulated_modularity_clustering_figure.pdf 







: '

The piece of code below is the test for the xml file.

    <tests>
     <test>
        <param name="input"   value="ST000006_data.tsv"/>
        <param name="design"  value="ST000006_design.tsv"/>
        <param name="uniqID"  value="Retention_Index" />
        <param name="corr"    value="pearson" />
        <output name="output" file="ST000006_modulated_modularity_clustering_out.tsv" compare="sim_size" delta="10000"/>
        <output name="figure" file="ST000006_modulated_modularity_clustering_figure.pdf" compare="sim_size" delta="10000" />
     </test>
    </tests>

'


<commit_msg>Update modulated_modularity_clustering test script to pass red/green test<commit_after>#!/bin/bash
#     <test>
#        <param name="input"   value="ST000006_data.tsv"/>
#        <param name="design"  value="ST000006_design.tsv"/>
#        <param name="uniqID"  value="Retention_Index" />
#        <param name="corr"    value="pearson" />
#        <output name="output" file="ST000006_modulated_modularity_clustering_out.tsv" compare="sim_size" delta="10000"/>
#        <output name="figure" file="ST000006_modulated_modularity_clustering_figure.pdf" compare="sim_size" delta="10000" />
#     </test>

SCRIPT=$(basename "${BASH_SOURCE[0]}");
TEST="${SCRIPT%.*}"
TESTDIR="testout/${TEST}"
INPUT_DIR="galaxy/test-data"
OUTPUT_DIR=$TESTDIR
rm -rf "${TESTDIR}"
mkdir -p "${TESTDIR}"
echo "### Starting test: ${TEST}"
if [[ $# -gt 0 ]]; then OUTPUT_DIR=$1 ; fi
mkdir -p "${OUTPUT_DIR}"

modulated_modularity_clustering.py \
    -i  "$INPUT_DIR/ST000006_data.tsv" \
    -d  "$INPUT_DIR/ST000006_design.tsv" \
    -id Retention_Index \
    -c pearson \
    -o "$OUTPUT_DIR/ST000006_modulated_modularity_clustering_out.tsv" \
    -f "$OUTPUT_DIR/ST000006_modulated_modularity_clustering_figure.pdf"

echo "### Finished test: ${TEST} on $(date)"
{'fraction_non_alphanumeric': 0.15796124684077506, 'fraction_numerical': 0.05054759898904802, 'mean_word_length': 3.9479166666666665, 'pattern_counts': {'":': 0, '<': 21, '<?xml version=': 0, '>': 21, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 1}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '7046269', 'n_tokens_mistral': 975, 'n_tokens_neox': 855, 'n_words': 138}