Mercurial > repos > yating-l > multi_fasta_glimmer_hmm
comparison glimmerhmm.xml @ 0:b07a805758cc draft
planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 1245031a7d52c922c86f33ebfd0f20eb9ddf84ac-dirty
author | yating-l |
---|---|
date | Mon, 01 May 2017 15:29:33 -0400 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:b07a805758cc |
---|---|
1 <tool id="multi_fasta_glimmerhmm" name="Multi Fasta GlimmerHMM" version="4.0"> | |
2 <description>Predict ORFs in eukaryotic genomes for Multi Fasta file</description> | |
3 <requirements> | |
4 <requirement type="package" version="3.0.4">glimmerhmm</requirement> | |
5 </requirements> | |
6 <command detect_errors="aggressive"><![CDATA[ | |
7 python $__tool_directory__/multi_glimmer.py | |
8 --multi_fasta $input | |
9 --trained_dir $trained_specie.fields.path | |
10 --output $output | |
11 ]]></command> | |
12 <inputs> | |
13 <param name="input" type="data" format="fasta" label="Genome Sequence"/> | |
14 <param name="trained_specie" type="select" label="Select a specie"> | |
15 <options from_data_table="glimmer_hmm_trained_dir"> | |
16 <filter type="sort_by" column="2"/> | |
17 <validator type="no_options" message="No indexes are available"/> | |
18 </options> | |
19 </param> | |
20 </inputs> | |
21 <outputs> | |
22 <data format="gff3" name="output" /> | |
23 </outputs> | |
24 <help> | |
25 **What it does** | |
26 | |
27 GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM). | |
28 Although the gene finder conforms to the overall mathematical framework of a GHMM, | |
29 additionally it incorporates splice site models adapted from the GeneSplicer program and a | |
30 decision tree adapted from GlimmerM. It also utilizes Interpolated Markov Models for the | |
31 coding and noncoding models . Currently, GlimmerHMM's GHMM structure includes introns of each phase, | |
32 intergenic regions, and four types of exons (initial, internal, final, and single). | |
33 A basic user manual can be consulted here. | |
34 | |
35 **Example** | |
36 | |
37 Suppose you have the following DNA formatted sequences:: | |
38 | |
39 >SQ Sequence 8667507 BP; 1203558 A; 3121252 C; 3129638 G; 1213059 T; 0 other; | |
40 cccgcggagcgggtaccacatcgctgcgcgatgtgcgagcgaacacccgggctgcgcccg | |
41 ggtgttgcgctcccgctccgcgggagcgctggcgggacgctgcgcgtcccgctcaccaag | |
42 cccgcttcgcgggcttggtgacgctccgtccgctgcgcttccggagttgcggggcttcgc | |
43 cccgctaaccctgggcctcgcttcgctccgccttgggcctgcggcgggtccgctgcgctc | |
44 ccccgcctcaagggcccttccggctgcgcctccaggacccaaccgcttgcgcgggcctgg | |
45 | |
46 Running this tool will produce this:: | |
47 | |
48 ##gff-version 3 | |
49 ##sequence-region ConsensusfromCH236920mapping 1 4148552 | |
50 ConsensusfromCH236920mapping GlimmerHMM mRNA 1 122 . + . ID=ConsensusfromCH236920mapping.path1.gene1;Name=ConsensusfromCH236920mapping.path1.gene1 | |
51 ConsensusfromCH236920mapping GlimmerHMM CDS 1 122 . + 0 ID=ConsensusfromCH236920mapping.cds1.1; | |
52 ConsensusfromCH236920mapping GlimmerHMM mRNA 14066 15205 . - . ID=ConsensusfromCH236920mapping.path1.gene2;Name=ConsensusfromCH236920mapping.path1.gene2 | |
53 ConsensusfromCH236920mapping GlimmerHMM CDS 14066 15034 . - 0 ID=ConsensusfromCH236920mapping.cds2.1; | |
54 ConsensusfromCH236920mapping GlimmerHMM CDS 15137 15205 . - 0 ID=ConsensusfromCH236920mapping.cds2.2; | |
55 ConsensusfromCH236920mapping GlimmerHMM mRNA 19910 24210 . - . ID=ConsensusfromCH236920mapping.path1.gene3;Name=ConsensusfromCH236920mapping.path1.gene3 | |
56 </help> | |
57 | |
58 </tool> |