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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 2a0f9aee1c61e12ab9f0e25a6ba7db5c08b67fe6
author artbio
date Thu, 09 Oct 2025 17:14:30 +0000
parents 86bcdc94b008
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3a185b812f46 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 3c440a9075507e077fc8c82244d0313cb6478a01
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1 <macros>
3a185b812f46 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 3c440a9075507e077fc8c82244d0313cb6478a01
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2 <token name="@pipefail@"><![CDATA[set -o | grep -q pipefail && set -o pipefail;]]></token>
3a185b812f46 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 3c440a9075507e077fc8c82244d0313cb6478a01
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3 <token name="@TOOL_VERSION@">0.6.2</token>
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e8a8a4910e32 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 2a0f9aee1c61e12ab9f0e25a6ba7db5c08b67fe6
artbio
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4 <token name="@VERSION_SUFFIX@">8</token>
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3a185b812f46 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 3c440a9075507e077fc8c82244d0313cb6478a01
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5 <token name="@PROFILE@">23.0</token>
3a185b812f46 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 3c440a9075507e077fc8c82244d0313cb6478a01
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6 <xml name="requirements">
3a185b812f46 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 3c440a9075507e077fc8c82244d0313cb6478a01
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7 <requirements>
3a185b812f46 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 3c440a9075507e077fc8c82244d0313cb6478a01
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8 <requirement type="package" version="0.6.2">snp-pileup</requirement>
3a185b812f46 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 3c440a9075507e077fc8c82244d0313cb6478a01
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9 <requirement type="package" version="1.22">bcftools</requirement>
3a185b812f46 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 3c440a9075507e077fc8c82244d0313cb6478a01
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10 <requirement type="package" version="1.22.1">samtools</requirement>
3a185b812f46 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 3c440a9075507e077fc8c82244d0313cb6478a01
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11 <requirement type="package" version="1.22.1">htslib</requirement>
3a185b812f46 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 3c440a9075507e077fc8c82244d0313cb6478a01
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12 <requirement type="package" version="20250822">parallel</requirement>
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8e1fb7253c1d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 613efcbc9de2f712eb2ad9540e3e63f7b968640c
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13 <requirement type="package" version="9.5">coreutils</requirement>
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66a56502199d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 0176d2cc4f1caf0ab948ef72efb25ccce735461e
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14 <requirement type="package" version="0.6.2">r-facets</requirement>
66a56502199d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 0176d2cc4f1caf0ab948ef72efb25ccce735461e
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15 <requirement type="package" version="2.2.5">r-argparse</requirement>
66a56502199d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 0176d2cc4f1caf0ab948ef72efb25ccce735461e
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16
0
3a185b812f46 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 3c440a9075507e077fc8c82244d0313cb6478a01
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17 </requirements>
3a185b812f46 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 3c440a9075507e077fc8c82244d0313cb6478a01
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18 </xml> <xml name="citations">
3a185b812f46 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 3c440a9075507e077fc8c82244d0313cb6478a01
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19 <citations>
3a185b812f46 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 3c440a9075507e077fc8c82244d0313cb6478a01
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20 <citation type="bibtex">
3a185b812f46 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 3c440a9075507e077fc8c82244d0313cb6478a01
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21 @article{shen2016facets,
3a185b812f46 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 3c440a9075507e077fc8c82244d0313cb6478a01
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22 title={FACETS: allele-specific copy number and clonal heterogeneity analysis tool for cancer sequencing data},
3a185b812f46 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 3c440a9075507e077fc8c82244d0313cb6478a01
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23 author={Shen, Ronglai and Seshan, Venkatraman E},
3a185b812f46 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 3c440a9075507e077fc8c82244d0313cb6478a01
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24 journal={Nucleic acids research},
3a185b812f46 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 3c440a9075507e077fc8c82244d0313cb6478a01
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25 volume={44},
3a185b812f46 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 3c440a9075507e077fc8c82244d0313cb6478a01
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26 number={12},
3a185b812f46 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 3c440a9075507e077fc8c82244d0313cb6478a01
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27 pages={e131--e131},
3a185b812f46 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 3c440a9075507e077fc8c82244d0313cb6478a01
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28 year={2016},
3a185b812f46 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 3c440a9075507e077fc8c82244d0313cb6478a01
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29 publisher={Oxford University Press}
3a185b812f46 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 3c440a9075507e077fc8c82244d0313cb6478a01
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30 }
3a185b812f46 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 3c440a9075507e077fc8c82244d0313cb6478a01
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31 </citation>
3a185b812f46 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 3c440a9075507e077fc8c82244d0313cb6478a01
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32 </citations>
3a185b812f46 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 3c440a9075507e077fc8c82244d0313cb6478a01
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33 </xml>
3a185b812f46 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 3c440a9075507e077fc8c82244d0313cb6478a01
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3a185b812f46 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 3c440a9075507e077fc8c82244d0313cb6478a01
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35 <xml name="stdio">
3a185b812f46 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 3c440a9075507e077fc8c82244d0313cb6478a01
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36 <stdio>
3a185b812f46 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 3c440a9075507e077fc8c82244d0313cb6478a01
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37 <exit_code range="1:" level="fatal" description="Error during script execution." />
3a185b812f46 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 3c440a9075507e077fc8c82244d0313cb6478a01
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38 </stdio>
3a185b812f46 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 3c440a9075507e077fc8c82244d0313cb6478a01
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39 </xml>
3a185b812f46 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 3c440a9075507e077fc8c82244d0313cb6478a01
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3a185b812f46 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 3c440a9075507e077fc8c82244d0313cb6478a01
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41 </macros>