Mercurial > repos > iuc > trycycler_consensus
annotate macros.xml @ 4:43af166bc01e draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e093c3f4fa599c1cb5cfc6f98e11ff1070ce440f"
author | iuc |
---|---|
date | Mon, 13 Dec 2021 21:17:36 +0000 |
parents | d40ed4eb0c0e |
children | 19bdfd1e6fe3 |
rev | line source |
---|---|
0
93c6a7423090
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff
changeset
|
1 <macros> |
4
43af166bc01e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e093c3f4fa599c1cb5cfc6f98e11ff1070ce440f"
iuc
parents:
3
diff
changeset
|
2 <token name="@TOOL_VERSION@">0.5.3</token> |
0
93c6a7423090
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff
changeset
|
3 <token name="@PIPELINE@"> |
93c6a7423090
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff
changeset
|
4 **Trycycler pipeline** |
93c6a7423090
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff
changeset
|
5 |
93c6a7423090
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff
changeset
|
6 :: |
93c6a7423090
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff
changeset
|
7 |
93c6a7423090
"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. |
93c6a7423090
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff
changeset
|
9 ⬇ |
93c6a7423090
"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. |
93c6a7423090
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff
changeset
|
11 ⬇ |
93c6a7423090
"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. |
93c6a7423090
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff
changeset
|
13 ⬇ |
93c6a7423090
"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. |
93c6a7423090
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff
changeset
|
15 ⬇ |
93c6a7423090
"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. |
93c6a7423090
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff
changeset
|
17 |
93c6a7423090
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff
changeset
|
18 </token> |
93c6a7423090
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff
changeset
|
19 <xml name="edam_ontology"> |
93c6a7423090
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff
changeset
|
20 <edam_topics> |
93c6a7423090
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff
changeset
|
21 <edam_topic>topic_0196</edam_topic> |
93c6a7423090
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff
changeset
|
22 </edam_topics> |
93c6a7423090
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff
changeset
|
23 <edam_operations> |
93c6a7423090
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff
changeset
|
24 <edam_operation>operation_0525</edam_operation> |
93c6a7423090
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff
changeset
|
25 </edam_operations> |
93c6a7423090
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff
changeset
|
26 </xml> |
93c6a7423090
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff
changeset
|
27 <xml name="requirements"> |
93c6a7423090
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff
changeset
|
28 <requirements> |
93c6a7423090
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff
changeset
|
29 <requirement type="package" version="@TOOL_VERSION@">trycycler</requirement> |
93c6a7423090
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff
changeset
|
30 </requirements> |
93c6a7423090
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff
changeset
|
31 </xml> |
93c6a7423090
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff
changeset
|
32 <xml name="citations"> |
93c6a7423090
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff
changeset
|
33 <citations> |
93c6a7423090
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff
changeset
|
34 <citation type="bibtex"> |
93c6a7423090
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff
changeset
|
35 @misc{githubTrycycler, |
93c6a7423090
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff
changeset
|
36 author = {Ryan, Wick}, |
93c6a7423090
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff
changeset
|
37 year = {2020}, |
93c6a7423090
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff
changeset
|
38 title = {Trycycler}, |
93c6a7423090
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff
changeset
|
39 publisher = {GitHub}, |
93c6a7423090
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff
changeset
|
40 journal = {GitHub repository}, |
93c6a7423090
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff
changeset
|
41 url = {https://github.com/rrwick/Trycycler}, |
93c6a7423090
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff
changeset
|
42 } |
93c6a7423090
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff
changeset
|
43 </citation> |
93c6a7423090
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff
changeset
|
44 </citations> |
93c6a7423090
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff
changeset
|
45 </xml> |
93c6a7423090
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
iuc
parents:
diff
changeset
|
46 </macros> |