Mercurial > repos > bgruening > rnaz

annotate rnaz.xml @ 3:3c43015da1d8 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/rnaz commit 2c2cc0e0638ebe372836509f5ff3d05a0bb34210-dirty
author bgruening
date Thu, 28 Sep 2017 11:57:06 -0400
parents 580ee1e91801
children 58fd61a8362e
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
580ee1e91801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e85474d72b07c70ca061f51b7165951038a06a6c
bgruening
parents: 1
diff changeset
1 <tool id="rnaz" name="RNAz" version="2.1.1">
0
8abf4c0a4af0 initial Uploaded
bgruening
parents:
diff changeset
2 <description>predicting structurally conserved and thermodynamically stable RNA secondary structures</description>
1
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
3
0
8abf4c0a4af0 initial Uploaded
bgruening
parents:
diff changeset
4 <requirements>
8abf4c0a4af0 initial Uploaded
bgruening
parents:
diff changeset
5 <requirement type="package" version="2.1">rnaz</requirement>
8abf4c0a4af0 initial Uploaded
bgruening
parents:
diff changeset
6 </requirements>
1
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
7
0
8abf4c0a4af0 initial Uploaded
bgruening
parents:
diff changeset
8 <stdio>
8abf4c0a4af0 initial Uploaded
bgruening
parents:
diff changeset
9 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
8abf4c0a4af0 initial Uploaded
bgruening
parents:
diff changeset
10 <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" />
8abf4c0a4af0 initial Uploaded
bgruening
parents:
diff changeset
11 </stdio>
1
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
12
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
13 <version_command>RNAz --version</version_command>
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
14 <command>
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
15 <![CDATA[
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
16 RNAz '$input'
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
17 --$forward_or_reverse
2
580ee1e91801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e85474d72b07c70ca061f51b7165951038a06a6c
bgruening
parents: 1
diff changeset
18 $zscore
1
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
19 $locarnate
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
20 $noshuffle
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
21 #if $cutoff != -1.0:
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
22 --cutoff=$cutoff
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
23 #end if
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
24 > temp.txt &&
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
25 grep -v -E "^ |^#|^$" temp.txt > '$outfile' &&
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
26 grep -E "^ |^#|^$" temp.txt
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
27 ]]>
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
28 </command>
0
8abf4c0a4af0 initial Uploaded
bgruening
parents:
diff changeset
29 <inputs>
8abf4c0a4af0 initial Uploaded
bgruening
parents:
diff changeset
30 <param format="txt" name="input" type="data" label="Input Alignment File" />
1
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
31 <param name="forward_or_reverse" type="select" label="Scored strand">
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
32 <option value="forward">Score forward strand (-f)</option>
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
33 <option value="reverse">Score reverse strand (-r)</option>
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
34 <option value="both-strands">Score both strands (-b)</option>
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
35 </param>
2
580ee1e91801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e85474d72b07c70ca061f51b7165951038a06a6c
bgruening
parents: 1
diff changeset
36 <param name="zscore" type="select" label="Which type of z-scores">
580ee1e91801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e85474d72b07c70ca061f51b7165951038a06a6c
bgruening
parents: 1
diff changeset
37 <option value="--mononucleotide">Use mononucleotide shuffled z-scores</option>
580ee1e91801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e85474d72b07c70ca061f51b7165951038a06a6c
bgruening
parents: 1
diff changeset
38 <option value="--dinucleotide" selected="true">Use dinucleotide shuffled z-scores</option>
580ee1e91801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e85474d72b07c70ca061f51b7165951038a06a6c
bgruening
parents: 1
diff changeset
39 </param>
1
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
40 <param argument="--cutoff" label="Probability cutoff" type="float" value="-1.0" help="-1.0 to deactivate"/>
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
41 <param argument="--locarnate" type="boolean" checked="false" truevalue="--locarnate" falsevalue="" label="Use decision model for structural alignments" />
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
42 <param argument="--no-shuffle" name="noshuffle" type="boolean" checked="false" truevalue="--no-shuffle" falsevalue="" label="Never fall back to shuffling" />
0
8abf4c0a4af0 initial Uploaded
bgruening
parents:
diff changeset
43 </inputs>
8abf4c0a4af0 initial Uploaded
bgruening
parents:
diff changeset
44 <outputs>
8abf4c0a4af0 initial Uploaded
bgruening
parents:
diff changeset
45 <data name="outfile" format="fasta" />
8abf4c0a4af0 initial Uploaded
bgruening
parents:
diff changeset
46 </outputs>
1
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
47 <tests>
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
48 <test>
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
49 <param name="input" value="rnaz_input_trna.aln"/>
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
50 <output name="outfile" file="rnaz_result_trna.fasta"/>
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
51 </test>
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
52 <test>
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
53 <param name="input" value="rnaz_test_input2.aln"/>
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
54 <output name="outfile" file="rnaz_result2.fasta"/>
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
55 </test>
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
56 </tests>
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
57 <help>
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
58 <![CDATA[
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
59
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
60 **What it does**
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
61
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
62 RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments. It can be used in genome wide screens to detect functional RNA structures, as found in noncoding RNAs and cis-acting regulatory elements of mRNAs.
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
63
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
64 **Input**
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
65
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
66 Input is a multiple sequence alignment file. Currently the the following alignment formats can be read: CLUSTALW, FASTA, PHYLIP,NEXUS, MAF, and XMFA. Alignments can be generated by any sequence based alignment program. Sequence alignment tools can be found in Galaxy too (e.g. ClustalW).
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
67
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
68 Example:
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
69
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
70 CLUSTAL 2.1 multiple sequence alignment
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
71
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
72
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
73 sacCer1 GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGTTAGGGGTTCGAGC
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
74
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
75 sacKlu GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGCTAGGGGTTCGAGC
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
76
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
77 sacBay GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGTTAGGGGTTCGAGC
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
78
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
79 sacCas GCTTCAGTAGCTCAGTCGGAAGAGCGTCAGTCTCATAATCTGAAGGTCGAGAGTTCGAAC
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
80
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
81 \** * * \** \** \**\** \** \**\** * *\** \**\**\* *\**\* * \**\**\** *
0
8abf4c0a4af0 initial Uploaded
bgruening
parents:
diff changeset
82
8abf4c0a4af0 initial Uploaded
bgruening
parents:
diff changeset
83
1
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
84 **Output**
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
85
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
86 In Galaxy RNAz gives you 2 output files: a summary file and a result file. For the example input they look like this:
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
87
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
88 Summary:
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
89
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
90 Sequences: 4
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
91 Columns: 60
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
92 Reading direction: forward
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
93 Mean pairwise identity: 82.50
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
94 Shannon entropy: 0.28395
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
95 G+C content: 0.51667
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
96 Mean single sequence MFE: -16.67
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
97 Consensus MFE: -15.59
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
98 Energy contribution: -15.53
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
99 Covariance contribution: -0.06
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
100 Combinations/Pair: 1.26
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
101 Mean z-score: -0.66
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
102 Structure conservation index: 0.93
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
103 Background model: mononucleotide
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
104 Decision model: sequence based alignment quality
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
105 SVM decision value: -0.64
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
106 SVM RNA-class probability: 0.238023
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
107 Prediction: OTHER
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
108
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
109
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
110 Result file:
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
111
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
112 >sacCer1
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
113
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
114 GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGC
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
115
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
116 ..((((...((((........))))....(((((((((((....))))))))))))))). ( -19.00, z-score = -1.44, R)
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
117
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
118 >sacKlu
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
119
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
120 GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGCUAGGGGUUCGAGC
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
121
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
122 ..((((...((((........))))....((((((((..(....)..)))))))))))). ( -16.00, z-score = -0.11, R)
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
123
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
124 >sacBay
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
125
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
126 GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGC
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
127
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
128 ..((((...((((........))))....(((((((((((....))))))))))))))). ( -19.00, z-score = -1.44, R)
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
129
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
130 >sacCas
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
131
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
132 GCUUCAGUAGCUCAGUCGGAAGAGCGUCAGUCUCAUAAUCUGAAGGUCGAGAGUUCGAAC
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
133
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
134 .((((((..((((........))))..............)))))).(((......))).. ( -12.69, z-score = 0.35, R)
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
135
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
136 >consensus
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
137
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
138 GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGC
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
139
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
140 ..((((...((((........))))....(((((((((((....))))))))))))))). (-15.59 = -15.53 + -0.06)
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
141
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
142
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
143
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
144
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
145
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
146
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
147 ]]>
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
148
0
8abf4c0a4af0 initial Uploaded
bgruening
parents:
diff changeset
149 </help>
1
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
150
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
151 <citations>
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
152 <citation type="doi">10.1142/9789814295291_0009</citation>
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
153 </citations>
e23c455f8335 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
bgruening
parents: 0
diff changeset
154
0
8abf4c0a4af0 initial Uploaded
bgruening
parents:
diff changeset
155 </tool>