Mercurial > repos > mingchen0919 > aurora_skewer

annotate expose-outputs.sh @ 5:2c663ddb8488 draft

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planemo upload commit f0ae5255b6c75f69c85319bba8da742be83f27d2-dirty
author mingchen0919
date Wed, 25 Apr 2018 16:47:59 -0400
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children 5b07e567864b
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2c663ddb8488 planemo upload commit f0ae5255b6c75f69c85319bba8da742be83f27d2-dirty
mingchen0919
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1 # change directory to tool outputs directory
2c663ddb8488 planemo upload commit f0ae5255b6c75f69c85319bba8da742be83f27d2-dirty
mingchen0919
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2 cd ${REPORT_FILES_PATH}
2c663ddb8488 planemo upload commit f0ae5255b6c75f69c85319bba8da742be83f27d2-dirty
mingchen0919
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3
2c663ddb8488 planemo upload commit f0ae5255b6c75f69c85319bba8da742be83f27d2-dirty
mingchen0919
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4 # copy outputs from tool outputs directory to corresponding galaxy output path
2c663ddb8488 planemo upload commit f0ae5255b6c75f69c85319bba8da742be83f27d2-dirty
mingchen0919
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5 cp skewer.html ${REPORT}
2c663ddb8488 planemo upload commit f0ae5255b6c75f69c85319bba8da742be83f27d2-dirty
mingchen0919
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6
2c663ddb8488 planemo upload commit f0ae5255b6c75f69c85319bba8da742be83f27d2-dirty
mingchen0919
parents:
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7 if [ -e trim-trimmed-pair1.fastq ]; then
2c663ddb8488 planemo upload commit f0ae5255b6c75f69c85319bba8da742be83f27d2-dirty
mingchen0919
parents:
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8 cp trim-trimmed-pair1.fastq ${X_1}
2c663ddb8488 planemo upload commit f0ae5255b6c75f69c85319bba8da742be83f27d2-dirty
mingchen0919
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9 fi
2c663ddb8488 planemo upload commit f0ae5255b6c75f69c85319bba8da742be83f27d2-dirty
mingchen0919
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10
2c663ddb8488 planemo upload commit f0ae5255b6c75f69c85319bba8da742be83f27d2-dirty
mingchen0919
parents:
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11 if [ -e trim-trimmed-pair2.fastq ]; then
2c663ddb8488 planemo upload commit f0ae5255b6c75f69c85319bba8da742be83f27d2-dirty
mingchen0919
parents:
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12 cp trim-trimmed-pair2.fastq ${X_2}
2c663ddb8488 planemo upload commit f0ae5255b6c75f69c85319bba8da742be83f27d2-dirty
mingchen0919
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13 fi
2c663ddb8488 planemo upload commit f0ae5255b6c75f69c85319bba8da742be83f27d2-dirty
mingchen0919
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14
2c663ddb8488 planemo upload commit f0ae5255b6c75f69c85319bba8da742be83f27d2-dirty
mingchen0919
parents:
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15 if [ -e trim-trimmed.fastq ]; then
2c663ddb8488 planemo upload commit f0ae5255b6c75f69c85319bba8da742be83f27d2-dirty
mingchen0919
parents:
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16 cp trim-trimmed.fastq ${X_3}
2c663ddb8488 planemo upload commit f0ae5255b6c75f69c85319bba8da742be83f27d2-dirty
mingchen0919
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17 fi