Mercurial > repos > bcclaywell > microbiome_pplacer_suite

annotate pplacer-wrapper.sh @ 8:35f9b833e12b draft default tip

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planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
author bcclaywell
date Mon, 12 Oct 2015 16:09:02 -0400
parents d4690e65afcd
children
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1 #!/bin/bash
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2
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3 source $(dirname $0)/util.sh
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4 source $1
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5
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6 QUERY_SEQS=$(extify fasta ${QUERY_SEQS})
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7 PPLACER_DEFAULT_ARGS="-j ${GALAXY_SLOTS:-4} -p --inform-prior --prior-lower 0.01 --map-identity"
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8
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9 pplacer \
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10 ${PPLACER_DEFAULT_ARGS} \
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11 -c ${REFPKG} \
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12 -o ${PLACED_SEQS} \
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13 ${QUERY_SEQS}