Mercurial > repos > mingchen0919 > aurora_star_site

annotate expose-outputs-to-galaxy-history.sh @ 0:c12e291895ff draft

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planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
author mingchen0919
date Tue, 01 May 2018 10:45:22 -0400
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c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
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1 # change directory to tool outputs directory
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
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2 cd ${REPORT_FILES_PATH}
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
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3
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
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4 # copy outputs from tool outputs directory to corresponding galaxy output path
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
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5 if [ -e "rmarkdown_report.html" ]; then
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
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6 cp rmarkdown_report.html ${REPORT}
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
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7 fi
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
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8
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
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9 if [ -e "index.html" ]; then
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
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10 cp index.html ${REPORT}
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
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11 fi
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
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12
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
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13 cp Aligned.out.sorted.bam ${X_S}