Mercurial > repos > mingchen0919 > aurora_skewer

annotate expose-outputs-to-galaxy-history.sh @ 0:0358f6f78adf draft

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planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
author mingchen0919
date Fri, 14 Dec 2018 00:40:15 -0500
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0358f6f78adf planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
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1 # change directory to tool outputs directory
0358f6f78adf planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
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2 cd ${REPORT_FILES_PATH}
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3
0358f6f78adf planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
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4 # copy outputs from tool outputs directory to corresponding galaxy output path
0358f6f78adf planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
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5 if [ -e "rmarkdown_report.html" ]; then
0358f6f78adf planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
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6 cp rmarkdown_report.html ${REPORT}
0358f6f78adf planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
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7 fi
0358f6f78adf planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
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8
0358f6f78adf planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
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9 if [ -e "index.html" ]; then
0358f6f78adf planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
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10 cp index.html ${REPORT}
0358f6f78adf planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
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11 fi
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12
0358f6f78adf planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
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13
0358f6f78adf planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
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14 if [ -e trim-trimmed-pair1.fastq ]; then
0358f6f78adf planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
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15 cp trim-trimmed-pair1.fastq ${X_1}
0358f6f78adf planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
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16 fi
0358f6f78adf planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
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17
0358f6f78adf planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
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18 if [ -e trim-trimmed-pair2.fastq ]; then
0358f6f78adf planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
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19 cp trim-trimmed-pair2.fastq ${X_2}
0358f6f78adf planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
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20 fi
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21
0358f6f78adf planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
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22 if [ -e trim-trimmed.fastq ]; then
0358f6f78adf planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
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23 cp trim-trimmed.fastq ${X_3}
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mingchen0919
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24 fi