Mercurial > repos > mingchen0919 > aurora_star

annotate expose-outputs-to-galaxy-history.sh @ 0:25602263cff0 draft default tip

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planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
author mingchen0919
date Sun, 30 Dec 2018 13:11:48 -0500
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25602263cff0 planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
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1 # change directory to tool outputs directory
25602263cff0 planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
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2 cd ${REPORT_FILES_PATH}
25602263cff0 planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
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3
25602263cff0 planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
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4 # copy outputs from tool outputs directory to corresponding galaxy output path
25602263cff0 planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
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5 if [ -e "rmarkdown_report.html" ]; then
25602263cff0 planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
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6 cp rmarkdown_report.html ${REPORT}
25602263cff0 planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
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7 fi
25602263cff0 planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
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8
25602263cff0 planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
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9 if [ -e "index.html" ]; then
25602263cff0 planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
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10 cp index.html ${REPORT}
25602263cff0 planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
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11 fi
25602263cff0 planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
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12
25602263cff0 planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
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13 cp Aligned.out.sorted.bam ${X_S}