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annotate macros.xml @ 20:92678fcb1a5f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 20bce2a5482efb97b9176bfceeb527ef36ddbe4b
author iuc
date Mon, 18 Mar 2024 16:43:36 +0000
parents be1d967337e4
children 5cc34c3f440d
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037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
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1 <macros>
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92678fcb1a5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 20bce2a5482efb97b9176bfceeb527ef36ddbe4b
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2 <token name="@TOOL_VERSION@">2.27</token>
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3 <token name="@VERSION_SUFFIX@">0</token>
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037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
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4 <xml name="edam_ontology">
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5 <edam_topics>
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
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6 <edam_topic>topic_0102</edam_topic>
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
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7 </edam_topics>
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
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8 <edam_operations>
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
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9 <edam_operation>operation_0292</edam_operation>
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
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10 </edam_operations>
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
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11 </xml>
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
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12 <xml name="requirements">
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
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13 <requirements>
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
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14 <requirement type="package" version="@TOOL_VERSION@">minimap2</requirement>
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92678fcb1a5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 20bce2a5482efb97b9176bfceeb527ef36ddbe4b
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15 <requirement type="package" version="1.19.2">samtools</requirement>
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037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
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16 </requirements>
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
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17 </xml>
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
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18 <xml name="pe_anaylsis_fixed_selector">
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
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19 <param name="analysis_type_selector" type="select"
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
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20 label="Presets for PE reads alignment"
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
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21 help="These are the minimap2 preset options for PE alignment of short reads. You can customize these and other settings in the indexing, mapping and alignment options sections below.">
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
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22 <option value="sr">Short reads without splicing (-k21 -w11 --sr -F800 -A2 -B8 -O12,32 -E2,1 -r50 -p.5 -N20 -f1000,5000 -n2 -m20 -s40 -g200 -2K50m --heap-sort=yes --secondary=no) (sr)</option>
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
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23 </param>
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
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24 </xml>
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
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25 <xml name="citations">
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
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26 <citations>
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27 <citation type="doi">10.1093/bioinformatics/btp324</citation>
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28 <citation type="doi">10.1093/bioinformatics/btp698</citation>
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29 <citation type="bibtex">@misc{1303.3997,
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30 Author = {Heng Li},
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31 Title = {Minimap2: fast pairwise alignment for long nucleotide sequences},
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32 Year = {2017},
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33 Eprint = {arXiv:1708.01492},
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34 url = {https://arxiv.org/abs/1708.01492},
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35 }</citation>
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36 </citations>
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
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37 </xml>
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38 </macros>