Mercurial > repos > bgruening > glimmer_hmm

annotate glimmerHMM/glimmerhmm_predict.xml @ 1:4da91bb244dc 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/glimmer_hmm commit 2effed877a778e455c63a76e994a0f2bb8f4dba0
author rmarenco
date Thu, 14 Jul 2016 15:11:33 -0400
parents c9699375fcf6
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
1 <tool id="glimmerhmm_predict" name="GlimmerHMM" version="2.0">
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
2 <description>Predict ORFs in eukaryotic genomes</description>
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
3 <command detect_errors="exit_code"><![CDATA[
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
4 glimmerhmm
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
5 $input $trained_specie.fields.path
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
6 -o $output
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
7 -g
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
8 $svm_splice_prediction
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
9 $partial_gene
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
10 #if str($top_n_predictions) != "-1":
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
11 -n $top_n_predictions
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
12 #end if
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
13 ]]></command>
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
14 <inputs>
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
15 <param name="input" type="data" format="fasta" label="Genome Sequence"/>
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
16 <param name="trained_specie" type="select" label="Select a specie">
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
17 <options from_data_table="glimmer_hmm_trained_dir">
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
18 <filter type="sort_by" column="2"/>
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
19 <validator type="no_options" message="No indexes are available"/>
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
20 </options>
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
21 </param>
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
22 <param name="partial_gene" type="boolean" label="Don't make partial gene predictions" truevalue="-f" falsevalue="" checked="false" />
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
23 <param name="svm_splice_prediction" type="boolean" label="Don't use svm splice site predictions" truevalue="-v" falsevalue="" checked="false" />
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
24 <param name="top_n_predictions" type="integer" label="top n best predictions, -1 means infinite" value="-1"/>
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
25 </inputs>
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
26 <outputs>
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
27 <data format="gff3" name="output" />
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
28 </outputs>
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
29 <help>
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
30
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
31 **What it does**
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
32
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
33 GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM).
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
34 Although the gene finder conforms to the overall mathematical framework of a GHMM,
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
35 additionally it incorporates splice site models adapted from the GeneSplicer program and a
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
36 decision tree adapted from GlimmerM. It also utilizes Interpolated Markov Models for the
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
37 coding and noncoding models . Currently, GlimmerHMM's GHMM structure includes introns of each phase,
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
38 intergenic regions, and four types of exons (initial, internal, final, and single).
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
39 A basic user manual can be consulted here.
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
40
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
41 -----
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
42
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
43 **Example**
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
44
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
45 Suppose you have the following DNA formatted sequences::
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
46
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
47 >SQ Sequence 8667507 BP; 1203558 A; 3121252 C; 3129638 G; 1213059 T; 0 other;
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
48 cccgcggagcgggtaccacatcgctgcgcgatgtgcgagcgaacacccgggctgcgcccg
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
49 ggtgttgcgctcccgctccgcgggagcgctggcgggacgctgcgcgtcccgctcaccaag
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
50 cccgcttcgcgggcttggtgacgctccgtccgctgcgcttccggagttgcggggcttcgc
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
51 cccgctaaccctgggcctcgcttcgctccgccttgggcctgcggcgggtccgctgcgctc
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
52 ccccgcctcaagggcccttccggctgcgcctccaggacccaaccgcttgcgcgggcctgg
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
53
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
54 Running this tool will produce this::
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
55
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
56 ##gff-version 3
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
57 ##sequence-region ConsensusfromCH236920mapping 1 4148552
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
58 ConsensusfromCH236920mapping GlimmerHMM mRNA 1 122 . + . ID=ConsensusfromCH236920mapping.path1.gene1;Name=ConsensusfromCH236920mapping.path1.gene1
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
59 ConsensusfromCH236920mapping GlimmerHMM CDS 1 122 . + 0 ID=ConsensusfromCH236920mapping.cds1.1;
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
60 ConsensusfromCH236920mapping GlimmerHMM mRNA 14066 15205 . - . ID=ConsensusfromCH236920mapping.path1.gene2;Name=ConsensusfromCH236920mapping.path1.gene2
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
61 ConsensusfromCH236920mapping GlimmerHMM CDS 14066 15034 . - 0 ID=ConsensusfromCH236920mapping.cds2.1;
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
62 ConsensusfromCH236920mapping GlimmerHMM CDS 15137 15205 . - 0 ID=ConsensusfromCH236920mapping.cds2.2;
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
63 ConsensusfromCH236920mapping GlimmerHMM mRNA 19910 24210 . - . ID=ConsensusfromCH236920mapping.path1.gene3;Name=ConsensusfromCH236920mapping.path1.gene3
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
64
1
4da91bb244dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 2effed877a778e455c63a76e994a0f2bb8f4dba0
rmarenco
parents: 0
diff changeset
65
4da91bb244dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 2effed877a778e455c63a76e994a0f2bb8f4dba0
rmarenco
parents: 0
diff changeset
66
0
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
67 </help>
c9699375fcf6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
bgruening
parents:
diff changeset
68 </tool>