Mercurial > repos > mingchen0919 > aurora_htseq
view shell-script-template.sh @ 9:578a96df8690 draft
planemo upload commit 1cb2dd80dcb431563edbe1e763b3dde3a1adb2ae-dirty
author | mingchen0919 |
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date | Wed, 25 Apr 2018 14:22:32 -0400 |
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children | ec906e72784d |
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# 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 #------------ BELOW IS WHERE YOU WRITE YOUR OWN SHELL SCRIPT -------------- 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 #------------ END OF SHELL SCRIPT ------------------------------------------ EOF # run SHELL_SCRIPT sh ${SHELL_SCRIPT}