Mercurial > repos > bgruening > infernal

annotate cmstat.xml @ 9:1d74ed49cf41 draft default tip

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 09c1d4ab75f5cd057ed57bf694217f0e355f785e
author bgruening
date Mon, 11 Nov 2024 10:27:19 +0000
parents c9e29ac5d099
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
8
c9e29ac5d099 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit a812ed8de433ac4e8b42afd636e70cfbb180d2b9"
bgruening
parents: 5
diff changeset
1 <tool id="infernal_cmstat" name="cmstat" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
5
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents: 3
diff changeset
2 <description>Summary statistics for covariance model </description>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents: 3
diff changeset
3 <macros>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents: 3
diff changeset
4 <import>macros.xml</import>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents: 3
diff changeset
5 </macros>
9
1d74ed49cf41 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 09c1d4ab75f5cd057ed57bf694217f0e355f785e
bgruening
parents: 8
diff changeset
6 <expand macro="xrefs"/>
5
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents: 3
diff changeset
7 <expand macro="requirements"/>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents: 3
diff changeset
8 <expand macro="stdio" />
0
652f9d550531 Uploaded
bgruening
parents:
diff changeset
9 <command>
2
fac157e22e1b Uploaded
bgruening
parents: 0
diff changeset
10 <![CDATA[
0
652f9d550531 Uploaded
bgruening
parents:
diff changeset
11 ## a temp file is needed, because the standard tabular output from infernal is not usefull in Galaxy
652f9d550531 Uploaded
bgruening
parents:
diff changeset
12 ## it will be converted to a tab delimited file and piped to Galaxy
5
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents: 3
diff changeset
13 ##temp_tabular_output=\$(mktemp);
0
652f9d550531 Uploaded
bgruening
parents:
diff changeset
14
652f9d550531 Uploaded
bgruening
parents:
diff changeset
15 cmstat
652f9d550531 Uploaded
bgruening
parents:
diff changeset
16 #if str($cm_opts.cm_opts_selector) == "db":
652f9d550531 Uploaded
bgruening
parents:
diff changeset
17 $cm_opts.database.fields.path
652f9d550531 Uploaded
bgruening
parents:
diff changeset
18 #else:
652f9d550531 Uploaded
bgruening
parents:
diff changeset
19 $cm_opts.cmfile
652f9d550531 Uploaded
bgruening
parents:
diff changeset
20 #end if
652f9d550531 Uploaded
bgruening
parents:
diff changeset
21
5
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents: 3
diff changeset
22 > $outfile
0
652f9d550531 Uploaded
bgruening
parents:
diff changeset
23
652f9d550531 Uploaded
bgruening
parents:
diff changeset
24
2
fac157e22e1b Uploaded
bgruening
parents: 0
diff changeset
25 ]]>
0
652f9d550531 Uploaded
bgruening
parents:
diff changeset
26 </command>
652f9d550531 Uploaded
bgruening
parents:
diff changeset
27 <inputs>
9
1d74ed49cf41 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 09c1d4ab75f5cd057ed57bf694217f0e355f785e
bgruening
parents: 8
diff changeset
28 <expand macro="DB" />
0
652f9d550531 Uploaded
bgruening
parents:
diff changeset
29 </inputs>
652f9d550531 Uploaded
bgruening
parents:
diff changeset
30 <outputs>
652f9d550531 Uploaded
bgruening
parents:
diff changeset
31 <data format="tabular" name="outfile" label="cmstat on ${on_string}"/>
652f9d550531 Uploaded
bgruening
parents:
diff changeset
32 </outputs>
5
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents: 3
diff changeset
33 <tests>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents: 3
diff changeset
34 <test>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents: 3
diff changeset
35 <conditional name="cm_opts">
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents: 3
diff changeset
36 <param name="cm_opts_selector" value="histdb"/>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents: 3
diff changeset
37 <param name="cmfile" value="cmstat_input.cm"/>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents: 3
diff changeset
38 </conditional>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents: 3
diff changeset
39 <output name="outfile" >
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents: 3
diff changeset
40 <assert_contents>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents: 3
diff changeset
41 <has_text text="idx"/>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents: 3
diff changeset
42 <has_text text="accession"/>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents: 3
diff changeset
43 <has_text text="nseq"/>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents: 3
diff changeset
44 </assert_contents>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents: 3
diff changeset
45 </output>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents: 3
diff changeset
46 </test>
9
1d74ed49cf41 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 09c1d4ab75f5cd057ed57bf694217f0e355f785e
bgruening
parents: 8
diff changeset
47 <test>
1d74ed49cf41 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 09c1d4ab75f5cd057ed57bf694217f0e355f785e
bgruening
parents: 8
diff changeset
48 <conditional name="cm_opts">
1d74ed49cf41 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 09c1d4ab75f5cd057ed57bf694217f0e355f785e
bgruening
parents: 8
diff changeset
49 <param name="cm_opts_selector" value="db"/>
1d74ed49cf41 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 09c1d4ab75f5cd057ed57bf694217f0e355f785e
bgruening
parents: 8
diff changeset
50 <param name="database" value="cmstat_input.cm"/>
1d74ed49cf41 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 09c1d4ab75f5cd057ed57bf694217f0e355f785e
bgruening
parents: 8
diff changeset
51 </conditional>
1d74ed49cf41 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 09c1d4ab75f5cd057ed57bf694217f0e355f785e
bgruening
parents: 8
diff changeset
52 <output name="outfile" >
1d74ed49cf41 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 09c1d4ab75f5cd057ed57bf694217f0e355f785e
bgruening
parents: 8
diff changeset
53 <assert_contents>
1d74ed49cf41 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 09c1d4ab75f5cd057ed57bf694217f0e355f785e
bgruening
parents: 8
diff changeset
54 <has_text text="idx"/>
1d74ed49cf41 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 09c1d4ab75f5cd057ed57bf694217f0e355f785e
bgruening
parents: 8
diff changeset
55 <has_text text="accession"/>
1d74ed49cf41 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 09c1d4ab75f5cd057ed57bf694217f0e355f785e
bgruening
parents: 8
diff changeset
56 <has_text text="nseq"/>
1d74ed49cf41 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 09c1d4ab75f5cd057ed57bf694217f0e355f785e
bgruening
parents: 8
diff changeset
57 </assert_contents>
1d74ed49cf41 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 09c1d4ab75f5cd057ed57bf694217f0e355f785e
bgruening
parents: 8
diff changeset
58 </output>
1d74ed49cf41 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 09c1d4ab75f5cd057ed57bf694217f0e355f785e
bgruening
parents: 8
diff changeset
59 </test>
5
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents: 3
diff changeset
60 </tests>
0
652f9d550531 Uploaded
bgruening
parents:
diff changeset
61 <help>
2
fac157e22e1b Uploaded
bgruening
parents: 0
diff changeset
62 <![CDATA[
0
652f9d550531 Uploaded
bgruening
parents:
diff changeset
63
652f9d550531 Uploaded
bgruening
parents:
diff changeset
64
652f9d550531 Uploaded
bgruening
parents:
diff changeset
65 **What it does**
652f9d550531 Uploaded
bgruening
parents:
diff changeset
66
652f9d550531 Uploaded
bgruening
parents:
diff changeset
67 The cmstat utility prints out a tabular file of summary statistics for each given covariance model.
652f9d550531 Uploaded
bgruening
parents:
diff changeset
68
652f9d550531 Uploaded
bgruening
parents:
diff changeset
69
3
2c2c5e5e495b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 9eeedfaf35c069d75014c5fb2e42046106bf813c-dirty
bgruening
parents: 2
diff changeset
70 **Output format**
2c2c5e5e495b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 9eeedfaf35c069d75014c5fb2e42046106bf813c-dirty
bgruening
parents: 2
diff changeset
71
0
652f9d550531 Uploaded
bgruening
parents:
diff changeset
72
652f9d550531 Uploaded
bgruening
parents:
diff changeset
73 By default, cmstat prints general statistics of the model and the alignment it was built from, one line per model in a
2
fac157e22e1b Uploaded
bgruening
parents: 0
diff changeset
74 tabular format.
0
652f9d550531 Uploaded
bgruening
parents:
diff changeset
75
652f9d550531 Uploaded
bgruening
parents:
diff changeset
76 The columns are:
652f9d550531 Uploaded
bgruening
parents:
diff changeset
77
652f9d550531 Uploaded
bgruening
parents:
diff changeset
78 (1) The index of this profile, numbering each on in the file starting from 1.
652f9d550531 Uploaded
bgruening
parents:
diff changeset
79 (2) The name of the profile.
652f9d550531 Uploaded
bgruening
parents:
diff changeset
80 (3) The optional accession of the profile, or ”-” if there is none.
652f9d550531 Uploaded
bgruening
parents:
diff changeset
81 (4) The number of sequences that the profile was estimated from.
652f9d550531 Uploaded
bgruening
parents:
diff changeset
82 (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.
652f9d550531 Uploaded
bgruening
parents:
diff changeset
83 (6) The length of the model in consensus residues (match states).
652f9d550531 Uploaded
bgruening
parents:
diff changeset
84 (7) The expected maximum length of a hit to the model.
652f9d550531 Uploaded
bgruening
parents:
diff changeset
85 (8) The number of basepairs in the model.
652f9d550531 Uploaded
bgruening
parents:
diff changeset
86 (9) The number of bifurcations in the model.
652f9d550531 Uploaded
bgruening
parents:
diff changeset
87 (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”.
652f9d550531 Uploaded
bgruening
parents:
diff changeset
88 (11) Mean relative entropy per match state, in bits. This is the expected (mean) score per con-
652f9d550531 Uploaded
bgruening
parents:
diff changeset
89 sensus position. This is what the default entropy-weighting method for effective sequence
652f9d550531 Uploaded
bgruening
parents:
diff changeset
90 number estimation focuses on, so for default Infernal, this value will often reflect the default
652f9d550531 Uploaded
bgruening
parents:
diff changeset
91 target for entropy-weighting. If the ”model” field for this profile is ”hmm”, this field will be ”-”.
652f9d550531 Uploaded
bgruening
parents:
diff changeset
92 (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
652f9d550531 Uploaded
bgruening
parents:
diff changeset
93 relative entropy, the more the model will rely on structural conservation relative sequence conservation when identifying homologs.
652f9d550531 Uploaded
bgruening
parents:
diff changeset
94
652f9d550531 Uploaded
bgruening
parents:
diff changeset
95
5
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents: 3
diff changeset
96 For further questions please refere to the Infernal `Userguide <http://eddylab.org/infernal/Userguide.pdf>`_.
0
652f9d550531 Uploaded
bgruening
parents:
diff changeset
97
2
fac157e22e1b Uploaded
bgruening
parents: 0
diff changeset
98 ]]>
0
652f9d550531 Uploaded
bgruening
parents:
diff changeset
99 </help>
5
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents: 3
diff changeset
100 <expand macro="citations" />
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents: 3
diff changeset
101
0
652f9d550531 Uploaded
bgruening
parents:
diff changeset
102 </tool>