view shell-script-template.sh @ 10:ec906e72784d draft

planemo upload commit e2f267840cded7ba17bb75a074796a4babbaab5b-dirty

# SHELL_SCRIPT file name
SHELL_SCRIPT='htseq-count.sh'

# run SHELL_SCRIPT within tool outputs directory
cd ${REPORT_FILES_PATH}

# build job-script.sh
cat >${SHELL_SCRIPT} <<EOF

  htseq-count \\
    $(echo ${X_A} | sed 's/,/ /g') \\
    ${X_G} \\
    -f ${X_f} \\
    -r ${X_r} \\
    -s ${X_S} \\
    -a ${X_a} \\
    -t ${X_T} \\
    -i ${X_i} \\
    -m ${X_m} > htseq-counts-raw.txt 
    
  grep -v '__no_feature\|__ambiguous\|__too_low_aQual\|__not_aligned\|__alignment_not_unique' htseq-counts-raw.txt > counts.txt

EOF

# run SHELL_SCRIPT
sh ${SHELL_SCRIPT}