Mercurial > repos > iuc > minimap2

annotate macros.xml @ 21:5cc34c3f440d draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d69f5cd1711d0c0bc2121d69dd168631f29ceeba
author iuc
date Wed, 03 Apr 2024 16:26:11 +0000
parents 92678fcb1a5f
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
12
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
iuc
parents:
diff changeset
1 <macros>
21
5cc34c3f440d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d69f5cd1711d0c0bc2121d69dd168631f29ceeba
iuc
parents: 20
diff changeset
2 <token name="@TOOL_VERSION@">2.28</token>
16
6b1e195506a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 6cc565120a57667abd303b9104d51443edec4860"
iuc
parents: 15
diff changeset
3 <token name="@VERSION_SUFFIX@">0</token>
12
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
iuc
parents:
diff changeset
4 <xml name="edam_ontology">
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
iuc
parents:
diff changeset
5 <edam_topics>
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
iuc
parents:
diff changeset
6 <edam_topic>topic_0102</edam_topic>
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
iuc
parents:
diff changeset
7 </edam_topics>
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
iuc
parents:
diff changeset
8 <edam_operations>
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
iuc
parents:
diff changeset
9 <edam_operation>operation_0292</edam_operation>
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
iuc
parents:
diff changeset
10 </edam_operations>
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
iuc
parents:
diff changeset
11 </xml>
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
iuc
parents:
diff changeset
12 <xml name="requirements">
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
iuc
parents:
diff changeset
13 <requirements>
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
iuc
parents:
diff changeset
14 <requirement type="package" version="@TOOL_VERSION@">minimap2</requirement>
20
92678fcb1a5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 20bce2a5482efb97b9176bfceeb527ef36ddbe4b
iuc
parents: 19
diff changeset
15 <requirement type="package" version="1.19.2">samtools</requirement>
12
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
iuc
parents:
diff changeset
16 </requirements>
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
iuc
parents:
diff changeset
17 </xml>
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
iuc
parents:
diff changeset
18 <xml name="pe_anaylsis_fixed_selector">
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
iuc
parents:
diff changeset
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"
iuc
parents:
diff changeset
20 label="Presets for PE reads alignment"
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
iuc
parents:
diff changeset
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"
iuc
parents:
diff changeset
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"
iuc
parents:
diff changeset
23 </param>
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
iuc
parents:
diff changeset
24 </xml>
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
iuc
parents:
diff changeset
25 <xml name="citations">
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
iuc
parents:
diff changeset
26 <citations>
13
1f06dccdc5d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit c8aee6bdc2b4254df523c05890b4e3c4de5928f8"
iuc
parents: 12
diff changeset
27 <citation type="doi">10.1093/bioinformatics/btp324</citation>
1f06dccdc5d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit c8aee6bdc2b4254df523c05890b4e3c4de5928f8"
iuc
parents: 12
diff changeset
28 <citation type="doi">10.1093/bioinformatics/btp698</citation>
1f06dccdc5d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit c8aee6bdc2b4254df523c05890b4e3c4de5928f8"
iuc
parents: 12
diff changeset
29 <citation type="bibtex">@misc{1303.3997,
1f06dccdc5d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit c8aee6bdc2b4254df523c05890b4e3c4de5928f8"
iuc
parents: 12
diff changeset
30 Author = {Heng Li},
1f06dccdc5d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit c8aee6bdc2b4254df523c05890b4e3c4de5928f8"
iuc
parents: 12
diff changeset
31 Title = {Minimap2: fast pairwise alignment for long nucleotide sequences},
1f06dccdc5d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit c8aee6bdc2b4254df523c05890b4e3c4de5928f8"
iuc
parents: 12
diff changeset
32 Year = {2017},
1f06dccdc5d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit c8aee6bdc2b4254df523c05890b4e3c4de5928f8"
iuc
parents: 12
diff changeset
33 Eprint = {arXiv:1708.01492},
1f06dccdc5d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit c8aee6bdc2b4254df523c05890b4e3c4de5928f8"
iuc
parents: 12
diff changeset
34 url = {https://arxiv.org/abs/1708.01492},
1f06dccdc5d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit c8aee6bdc2b4254df523c05890b4e3c4de5928f8"
iuc
parents: 12
diff changeset
35 }</citation>
12
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
iuc
parents:
diff changeset
36 </citations>
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
iuc
parents:
diff changeset
37 </xml>
13
1f06dccdc5d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit c8aee6bdc2b4254df523c05890b4e3c4de5928f8"
iuc
parents: 12
diff changeset
38 </macros>