Mercurial > repos > iuc > trycycler_subsample

annotate macros.xml @ 7:b9b0246a2be3 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/trycycler commit 9da13f57f93e69fd463f6245af45674fe011b861
author iuc
date Wed, 06 Nov 2024 13:31:34 +0000
parents 6bfab4a4a988
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
85658cabbbed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
1 <macros>
6
6bfab4a4a988 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e9abd8b86133e530d0395d85bca320a1af27a9b6
iuc
parents: 5
diff changeset
2 <token name="@TOOL_VERSION@">0.5.5</token>
0
85658cabbbed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
3 <token name="@PIPELINE@">
85658cabbbed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
4 **Trycycler pipeline**
85658cabbbed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
5
85658cabbbed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
6 ::
85658cabbbed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
7
85658cabbbed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
8 Trycycler subsample: make maximally-independent read subsets of an appropriate depth.
85658cabbbed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
9 ⬇
85658cabbbed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
10 Trycycler cluster: carries out complete-linkage clustering of all contig sequences.
85658cabbbed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
11 ⬇
85658cabbbed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
12 Trycycler reconcile/msa: reconcile the contigs within each cluster and perform a multiple sequence alignment.
85658cabbbed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
13 ⬇
85658cabbbed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
14 Trycycler partition: split the reads between the different clusters.
85658cabbbed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
15 ⬇
85658cabbbed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
16 Trycycler consensus: generate a consensus contig sequence for each cluster.
85658cabbbed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
17
85658cabbbed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
18 </token>
7
b9b0246a2be3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9da13f57f93e69fd463f6245af45674fe011b861
iuc
parents: 6
diff changeset
19 <xml name="biotools">
b9b0246a2be3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9da13f57f93e69fd463f6245af45674fe011b861
iuc
parents: 6
diff changeset
20 <xrefs>
b9b0246a2be3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9da13f57f93e69fd463f6245af45674fe011b861
iuc
parents: 6
diff changeset
21 <xref type="bio.tools">trycycler</xref>
b9b0246a2be3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9da13f57f93e69fd463f6245af45674fe011b861
iuc
parents: 6
diff changeset
22 </xrefs>
b9b0246a2be3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9da13f57f93e69fd463f6245af45674fe011b861
iuc
parents: 6
diff changeset
23 </xml>
0
85658cabbbed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
24 <xml name="edam_ontology">
85658cabbbed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
25 <edam_topics>
85658cabbbed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
26 <edam_topic>topic_0196</edam_topic>
85658cabbbed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
27 </edam_topics>
85658cabbbed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
28 <edam_operations>
85658cabbbed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
29 <edam_operation>operation_0525</edam_operation>
85658cabbbed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
30 </edam_operations>
85658cabbbed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
31 </xml>
85658cabbbed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
32 <xml name="requirements">
85658cabbbed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
33 <requirements>
85658cabbbed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
34 <requirement type="package" version="@TOOL_VERSION@">trycycler</requirement>
85658cabbbed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
35 </requirements>
85658cabbbed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
36 </xml>
85658cabbbed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
37 <xml name="citations">
85658cabbbed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
38 <citations>
85658cabbbed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
39 <citation type="bibtex">
85658cabbbed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
40 @misc{githubTrycycler,
85658cabbbed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
41 author = {Ryan, Wick},
85658cabbbed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
42 year = {2020},
85658cabbbed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
43 title = {Trycycler},
85658cabbbed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
44 publisher = {GitHub},
85658cabbbed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
45 journal = {GitHub repository},
85658cabbbed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
46 url = {https://github.com/rrwick/Trycycler},
85658cabbbed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
47 }
85658cabbbed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
48 </citation>
85658cabbbed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
49 </citations>
85658cabbbed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
50 </xml>
85658cabbbed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff changeset
51 </macros>