Mercurial > repos > mingchen0919 > aurora_skewer

annotate expose-outputs.sh @ 9:c0e57c994deb draft

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planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
author mingchen0919
date Thu, 26 Apr 2018 14:10:58 -0400
parents 7c9170b7d9f6
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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2c663ddb8488 planemo upload commit f0ae5255b6c75f69c85319bba8da742be83f27d2-dirty
mingchen0919
parents:
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1 # change directory to tool outputs directory
2c663ddb8488 planemo upload commit f0ae5255b6c75f69c85319bba8da742be83f27d2-dirty
mingchen0919
parents:
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2 cd ${REPORT_FILES_PATH}
2c663ddb8488 planemo upload commit f0ae5255b6c75f69c85319bba8da742be83f27d2-dirty
mingchen0919
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2c663ddb8488 planemo upload commit f0ae5255b6c75f69c85319bba8da742be83f27d2-dirty
mingchen0919
parents:
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4 # copy outputs from tool outputs directory to corresponding galaxy output path
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c0e57c994deb planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents: 8
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5 cp skewer.html ${REPORT}
c0e57c994deb planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents: 8
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c0e57c994deb planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents: 8
diff changeset
7 if [ -e trim-trimmed-pair1.fastq ]; then
c0e57c994deb planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents: 8
diff changeset
8 cp trim-trimmed-pair1.fastq ${X_1}
c0e57c994deb planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents: 8
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9 fi
c0e57c994deb planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents: 8
diff changeset
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c0e57c994deb planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents: 8
diff changeset
11 if [ -e trim-trimmed-pair2.fastq ]; then
c0e57c994deb planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents: 8
diff changeset
12 cp trim-trimmed-pair2.fastq ${X_2}
c0e57c994deb planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents: 8
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13 fi
c0e57c994deb planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents: 8
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c0e57c994deb planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents: 8
diff changeset
15 if [ -e trim-trimmed.fastq ]; then
c0e57c994deb planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents: 8
diff changeset
16 cp trim-trimmed.fastq ${X_3}
c0e57c994deb planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
mingchen0919
parents: 8
diff changeset
17 fi