Mercurial > repos > bgruening > infernal

comparison cmstat.xml @ 0:652f9d550531 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author bgruening
date Tue, 22 Apr 2014 13:56:22 -0400
parents
children fac157e22e1b
comparison
equal deleted inserted replaced
-1:000000000000 0:652f9d550531
1 <tool id="infernal_cmstat" name="Summary statistics" version="1.1.0.1">
2 <description>for covariance model (cmstat)</description>
3 <requirements>
4 <requirement type="package">infernal</requirement>
5 <requirement type="package" version="1.1">infernal</requirement>
6 <requirement type="package" version="8.21">gnu_coreutils</requirement>
7 </requirements>
8 <command>
9 ## a temp file is needed, because the standard tabular output from infernal is not usefull in Galaxy
10 ## it will be converted to a tab delimited file and piped to Galaxy
11 temp_tabular_output=\$(mktemp);
12
13 cmstat
14
15 #if str($cm_opts.cm_opts_selector) == "db":
16 $cm_opts.database.fields.path
17 #else:
18 $cm_opts.cmfile
19 #end if
20
21 > \$temp_tabular_output
22 ;
23
24 ## 1. replace all lines starting # (comment lines)
25 ## 2. replace the first 18 spaces with tabs, 18th field is a free text field (can contain spaces)
26 sed -e 's/#.*$//' -e '/^$/d' -e 's/ /\t/g' -e 's/\t/ /18g' \$temp_tabular_output > $outfile
27
28 </command>
29 <inputs>
30 <conditional name="cm_opts">
31 <param name="cm_opts_selector" type="select" label="Subject covariance models">
32 <option value="db" selected="True">Locally installed covariance models</option>
33 <option value="histdb">Covariance model from your history</option>
34 </param>
35 <when value="db">
36 <param name="database" type="select" label="Covariance models">
37 <options from_file="infernal.loc">
38 <column name="value" index="0"/>
39 <column name="name" index="1"/>
40 <column name="path" index="2"/>
41 </options>
42 </param>
43 </when>
44 <when value="histdb">
45 <param name="cmfile" type="data" format="cm" label="Covariance models file from the history."/>
46 </when>
47 </conditional>
48 </inputs>
49 <outputs>
50 <data format="tabular" name="outfile" label="cmstat on ${on_string}"/>
51 </outputs>
52 <help>
53
54
55 **What it does**
56
57 The cmstat utility prints out a tabular file of summary statistics for each given covariance model.
58
59
60 Output format
61 -------------
62
63 By default, cmstat prints general statistics of the model and the alignment it was built from, one line per model in a
64 tabular format.
65
66 The columns are:
67
68 (1) The index of this profile, numbering each on in the file starting from 1.
69 (2) The name of the profile.
70 (3) The optional accession of the profile, or ”-” if there is none.
71 (4) The number of sequences that the profile was estimated from.
72 (5) The effective number of sequences that the profile was estimated from, after Infernal applied an effective sequence number calculation such as the default entropy weighting.
73 (6) The length of the model in consensus residues (match states).
74 (7) The expected maximum length of a hit to the model.
75 (8) The number of basepairs in the model.
76 (9) The number of bifurcations in the model.
77 (10) What type of model will be used by default in cmsearch and cmscan for this profile, either ”cm” or ”hmm”. For profiles with 0 basepairs, this will be ”hmm” (unless the --nohmmonly option is used). For all other profiles, this will be ”cm”.
78 (11) Mean relative entropy per match state, in bits. This is the expected (mean) score per con-
79 sensus position. This is what the default entropy-weighting method for effective sequence
80 number estimation focuses on, so for default Infernal, this value will often reflect the default
81 target for entropy-weighting. If the ”model” field for this profile is ”hmm”, this field will be ”-”.
82 (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
83 relative entropy, the more the model will rely on structural conservation relative sequence conservation when identifying homologs.
84
85
86 For further questions please refere to the Infernal Userguide_.
87
88 .. _Userguide: http://selab.janelia.org/software/infernal/Userguide.pdf
89
90
91 How do I cite Infernal?
92 -----------------------
93
94 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).
95
96 **Galaxy Wrapper Author**::
97
98 * Bjoern Gruening, University of Freiburg
99
100 </help>
101 </tool>