Mercurial > repos > bgruening > infernal

annotate macros.xml @ 7:477d829d3250 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 1527e05bcd748a2b3cef22e0e356697066a55635
author bgruening
date Sat, 11 Nov 2017 16:01:09 -0500
parents ee4be6eadd34
children c9e29ac5d099
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff changeset
1 <macros>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff changeset
2 <xml name="requirements">
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff changeset
3 <requirements>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff changeset
4 <requirement type="package">infernal</requirement>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff changeset
5 <requirement type="package" version="1.1.2">infernal</requirement>
6
ee4be6eadd34 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit ca2d37289d712b69ac15611bbf4961d083991bba
bgruening
parents: 5
diff changeset
6 <requirement type="package" version="8.25">coreutils</requirement>
5
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff changeset
7 </requirements>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff changeset
8 </xml>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff changeset
9 <token name="@VERSION@">1.1.2</token>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff changeset
10 <xml name="stdio">
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff changeset
11 <stdio>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff changeset
12 <exit_code range="1:" />
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff changeset
13 <exit_code range=":-1" />
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff changeset
14 <regex match="Error:" />
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff changeset
15 <regex match="Exception:" />
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff changeset
16 </stdio>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff changeset
17 </xml>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff changeset
18 <xml name="citations">
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff changeset
19 <citations>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff changeset
20 <citation type="bibtex">@article{Nawrocki15112013,
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff changeset
21 author = {Nawrocki, Eric P. and Eddy, Sean R.},
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff changeset
22 title = {Infernal 1.1: 100-fold faster RNA homology searches},
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff changeset
23 volume = {29},
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff changeset
24 number = {22},
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff changeset
25 pages = {2933-2935},
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff changeset
26 year = {2013},
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff changeset
27 doi = {10.1093/bioinformatics/btt509},
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff changeset
28 abstract ={Summary: Infernal builds probabilistic profiles of the sequence and secondary structure of an RNA family called covariance models (CMs) from structurally annotated multiple sequence alignments given as input. Infernal uses CMs to search for new family members in sequence databases and to create potentially large multiple sequence alignments. Version 1.1 of Infernal introduces a new filter pipeline for RNA homology search based on accelerated profile hidden Markov model (HMM) methods and HMM-banded CM alignment methods. This enables ∼100-fold acceleration over the previous version and ∼10 000-fold acceleration over exhaustive non-filtered CM searches.Availability: Source code, documentation and the benchmark are downloadable from http://infernal.janelia.org. Infernal is freely licensed under the GNU GPLv3 and should be portable to any POSIX-compliant operating system, including Linux and Mac OS/X. Documentation includes a user’s guide with a tutorial, a discussion of file formats and user options and additional details on methods implemented in the software.Contact: nawrockie@janelia.hhmi.org},
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff changeset
29 URL = {http://bioinformatics.oxfordjournals.org/content/29/22/2933.abstract},
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff changeset
30 eprint = {http://bioinformatics.oxfordjournals.org/content/29/22/2933.full.pdf+html},
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff changeset
31 journal = {Bioinformatics}
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff changeset
32 }</citation>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff changeset
33 </citations>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff changeset
34 </xml>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff changeset
35 </macros>