Mercurial > repos > bgruening > infernal

annotate cmstat.xml @ 16:0ac29b4bb1cb 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 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
author bgruening
date Sat, 21 Jan 2017 17:34:00 -0500
parents 2f8a8962ae22
children 94cc7ef25867
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
16
0ac29b4bb1cb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents: 14
diff changeset
1 <tool id="infernal_cmstat" name="cmstat" version="@VERSION@.0">
0ac29b4bb1cb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents: 14
diff changeset
2 <description>Summary statistics for covariance model </description>
0ac29b4bb1cb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents: 14
diff changeset
3 <macros>
0ac29b4bb1cb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents: 14
diff changeset
4 <import>macros.xml</import>
0ac29b4bb1cb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents: 14
diff changeset
5 </macros>
0ac29b4bb1cb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents: 14
diff changeset
6 <expand macro="requirements"/>
0ac29b4bb1cb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents: 14
diff changeset
7 <expand macro="stdio" />
9
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
8 <command>
13
ffa96097e5b2 Uploaded
bgruening
parents: 12
diff changeset
9 <![CDATA[
9
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
10 ## a temp file is needed, because the standard tabular output from infernal is not usefull in Galaxy
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
11 ## it will be converted to a tab delimited file and piped to Galaxy
16
0ac29b4bb1cb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents: 14
diff changeset
12 ##temp_tabular_output=\$(mktemp);
9
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
13
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
14 cmstat
11
5c6344f67ad0 Uploaded
bgruening
parents: 9
diff changeset
15 #if str($cm_opts.cm_opts_selector) == "db":
9
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
16 $cm_opts.database.fields.path
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
17 #else:
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
18 $cm_opts.cmfile
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
19 #end if
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
20
16
0ac29b4bb1cb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents: 14
diff changeset
21 > $outfile
9
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
22
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
23
13
ffa96097e5b2 Uploaded
bgruening
parents: 12
diff changeset
24 ]]>
9
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
25 </command>
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
26 <inputs>
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
27 <conditional name="cm_opts">
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
28 <param name="cm_opts_selector" type="select" label="Subject covariance models">
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
29 <option value="db" selected="True">Locally installed covariance models</option>
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
30 <option value="histdb">Covariance model from your history</option>
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
31 </param>
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
32 <when value="db">
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
33 <param name="database" type="select" label="Covariance models">
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
34 <options from_file="infernal.loc">
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
35 <column name="value" index="0"/>
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
36 <column name="name" index="1"/>
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
37 <column name="path" index="2"/>
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
38 </options>
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
39 </param>
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
40 </when>
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
41 <when value="histdb">
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
42 <param name="cmfile" type="data" format="cm" label="Covariance models file from the history."/>
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
43 </when>
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
44 </conditional>
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
45 </inputs>
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
46 <outputs>
11
5c6344f67ad0 Uploaded
bgruening
parents: 9
diff changeset
47 <data format="tabular" name="outfile" label="cmstat on ${on_string}"/>
9
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
48 </outputs>
16
0ac29b4bb1cb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents: 14
diff changeset
49 <tests>
0ac29b4bb1cb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents: 14
diff changeset
50 <test>
0ac29b4bb1cb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents: 14
diff changeset
51 <conditional name="cm_opts">
0ac29b4bb1cb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents: 14
diff changeset
52 <param name="cm_opts_selector" value="histdb"/>
0ac29b4bb1cb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents: 14
diff changeset
53 <param name="cmfile" value="cmstat_input.cm"/>
0ac29b4bb1cb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents: 14
diff changeset
54 </conditional>
0ac29b4bb1cb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents: 14
diff changeset
55 <output name="outfile" >
0ac29b4bb1cb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents: 14
diff changeset
56 <assert_contents>
0ac29b4bb1cb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents: 14
diff changeset
57 <has_text text="idx"/>
0ac29b4bb1cb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents: 14
diff changeset
58 <has_text text="accession"/>
0ac29b4bb1cb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents: 14
diff changeset
59 <has_text text="nseq"/>
0ac29b4bb1cb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents: 14
diff changeset
60 </assert_contents>
0ac29b4bb1cb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents: 14
diff changeset
61 </output>
0ac29b4bb1cb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents: 14
diff changeset
62 </test>
0ac29b4bb1cb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents: 14
diff changeset
63 </tests>
9
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
64 <help>
13
ffa96097e5b2 Uploaded
bgruening
parents: 12
diff changeset
65 <![CDATA[
9
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
66
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
67
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
68 **What it does**
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
69
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
70 The cmstat utility prints out a tabular file of summary statistics for each given covariance model.
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
71
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
72
14
2f8a8962ae22 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 9eeedfaf35c069d75014c5fb2e42046106bf813c-dirty
bgruening
parents: 13
diff changeset
73 **Output format**
2f8a8962ae22 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 9eeedfaf35c069d75014c5fb2e42046106bf813c-dirty
bgruening
parents: 13
diff changeset
74
9
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
75
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
76 By default, cmstat prints general statistics of the model and the alignment it was built from, one line per model in a
13
ffa96097e5b2 Uploaded
bgruening
parents: 12
diff changeset
77 tabular format.
9
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
78
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
79 The columns are:
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
80
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
81 (1) The index of this profile, numbering each on in the file starting from 1.
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
82 (2) The name of the profile.
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
83 (3) The optional accession of the profile, or ”-” if there is none.
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
84 (4) The number of sequences that the profile was estimated from.
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
85 (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.
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
86 (6) The length of the model in consensus residues (match states).
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
87 (7) The expected maximum length of a hit to the model.
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
88 (8) The number of basepairs in the model.
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
89 (9) The number of bifurcations in the model.
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
90 (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”.
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
91 (11) Mean relative entropy per match state, in bits. This is the expected (mean) score per con-
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
92 sensus position. This is what the default entropy-weighting method for effective sequence
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
93 number estimation focuses on, so for default Infernal, this value will often reflect the default
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
94 target for entropy-weighting. If the ”model” field for this profile is ”hmm”, this field will be ”-”.
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
95 (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
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
96 relative entropy, the more the model will rely on structural conservation relative sequence conservation when identifying homologs.
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
97
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
98
16
0ac29b4bb1cb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents: 14
diff changeset
99 For further questions please refere to the Infernal `Userguide <http://eddylab.org/infernal/Userguide.pdf>`_.
9
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
100
13
ffa96097e5b2 Uploaded
bgruening
parents: 12
diff changeset
101 ]]>
9
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
102 </help>
16
0ac29b4bb1cb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents: 14
diff changeset
103 <expand macro="citations" />
0ac29b4bb1cb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents: 14
diff changeset
104
9
1aa4c036e41c Uploaded
bgruening
parents:
diff changeset
105 </tool>