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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 9eeedfaf35c069d75014c5fb2e42046106bf813c-dirty
author bgruening
date Fri, 04 Mar 2016 07:24:17 -0500
parents ffa96097e5b2
children 0ac29b4bb1cb
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13:ffa96097e5b2 14:2f8a8962ae22
58 **What it does** 58 **What it does**
59 59
60 The cmstat utility prints out a tabular file of summary statistics for each given covariance model. 60 The cmstat utility prints out a tabular file of summary statistics for each given covariance model.
61 61
62 62
63 Output format 63 **Output format**
64 ------------- 64
65 65
66 By default, cmstat prints general statistics of the model and the alignment it was built from, one line per model in a 66 By default, cmstat prints general statistics of the model and the alignment it was built from, one line per model in a
67 tabular format. 67 tabular format.
68 68
69 The columns are: 69 The columns are:
84 target for entropy-weighting. If the ”model” field for this profile is ”hmm”, this field will be ”-”. 84 target for entropy-weighting. If the ”model” field for this profile is ”hmm”, this field will be ”-”.
85 (12) Mean relative entropy per match state, in bits, if the CM were transformed into an HMM (information from structure is ignored). The larger the difference between the CM and HMM 85 (12) Mean relative entropy per match state, in bits, if the CM were transformed into an HMM (information from structure is ignored). The larger the difference between the CM and HMM
86 relative entropy, the more the model will rely on structural conservation relative sequence conservation when identifying homologs. 86 relative entropy, the more the model will rely on structural conservation relative sequence conservation when identifying homologs.
87 87
88 88
89 For further questions please refere to the Infernal Userguide_. 89 For further questions please refere to the Infernal `Userguide <http://selab.janelia.org/software/infernal/Userguide.pdf>`_.
90
91 .. _Userguide: http://selab.janelia.org/software/infernal/Userguide.pdf
92
93
94 How do I cite Infernal?
95 -----------------------
96
97 The recommended citation for using Infernal 1.1 is E. P. Nawrocki and S. R. Eddy, Infernal 1.1: 100-fold faster RNA homology searches , Bioinformatics 29:2933-2935 (2013).
98
99 **Galaxy Wrapper Author**::
100
101 * Bjoern Gruening, University of Freiburg
102 90
103 ]]> 91 ]]>
104 </help> 92 </help>
93 <citations>
94 <citation type="doi">10.1093/bioinformatics/btt509</citation>
95 <citation type="bibtex">
96 @ARTICLE{bgruening_galaxytools,
97 Author = {Björn Grüning, Cameron Smith, Torsten Houwaart, Nicola Soranzo, Eric Rasche},
98 keywords = {bioinformatics, ngs, galaxy, cheminformatics, rna},
99 title = {{Galaxy Tools - A collection of bioinformatics and cheminformatics tools for the Galaxy environment}},
100 url = {https://github.com/bgruening/galaxytools}
101 }
102 </citation>
103 </citations>
104
105
105 </tool> 106 </tool>