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planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 28bd73b26b50165eded1d9ba995979acdf005ad1-dirty
author rmarenco
date Thu, 18 Aug 2016 18:50:00 -0400
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0ddb5ee32ff6 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 28bd73b26b50165eded1d9ba995979acdf005ad1-dirty
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1 <tool id="multi_fasta_glimmerhmm" name="Multi Fasta GlimmerHMM" version="4.0">
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2 <description>Predict ORFs in eukaryotic genomes for Multi Fasta file</description>
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3 <command detect_errors="aggressive"><![CDATA[
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4 python $__tool_directory__/multi_glimmer.py
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5 --multi_fasta $input
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6 --trained_dir $trained_specie.fields.path
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7 --output $output
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8 ]]></command>
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9 <inputs>
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10 <param name="input" type="data" format="fasta" label="Genome Sequence"/>
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11 <param name="trained_specie" type="select" label="Select a specie">
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12 <options from_data_table="glimmer_hmm_trained_dir">
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13 <filter type="sort_by" column="2"/>
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14 <validator type="no_options" message="No indexes are available"/>
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15 </options>
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16 </param>
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17 </inputs>
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18 <outputs>
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19 <data format="gff3" name="output" />
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20 </outputs>
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21 <help>
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22 **What it does**
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23
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24 GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM).
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25 Although the gene finder conforms to the overall mathematical framework of a GHMM,
0ddb5ee32ff6 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 28bd73b26b50165eded1d9ba995979acdf005ad1-dirty
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26 additionally it incorporates splice site models adapted from the GeneSplicer program and a
0ddb5ee32ff6 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 28bd73b26b50165eded1d9ba995979acdf005ad1-dirty
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27 decision tree adapted from GlimmerM. It also utilizes Interpolated Markov Models for the
0ddb5ee32ff6 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 28bd73b26b50165eded1d9ba995979acdf005ad1-dirty
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28 coding and noncoding models . Currently, GlimmerHMM's GHMM structure includes introns of each phase,
0ddb5ee32ff6 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 28bd73b26b50165eded1d9ba995979acdf005ad1-dirty
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29 intergenic regions, and four types of exons (initial, internal, final, and single).
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30 A basic user manual can be consulted here.
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31
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32 **Example**
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33
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34 Suppose you have the following DNA formatted sequences::
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35
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36 >SQ Sequence 8667507 BP; 1203558 A; 3121252 C; 3129638 G; 1213059 T; 0 other;
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37 cccgcggagcgggtaccacatcgctgcgcgatgtgcgagcgaacacccgggctgcgcccg
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38 ggtgttgcgctcccgctccgcgggagcgctggcgggacgctgcgcgtcccgctcaccaag
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39 cccgcttcgcgggcttggtgacgctccgtccgctgcgcttccggagttgcggggcttcgc
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40 cccgctaaccctgggcctcgcttcgctccgccttgggcctgcggcgggtccgctgcgctc
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41 ccccgcctcaagggcccttccggctgcgcctccaggacccaaccgcttgcgcgggcctgg
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42
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43 Running this tool will produce this::
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44
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45 ##gff-version 3
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46 ##sequence-region ConsensusfromCH236920mapping 1 4148552
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47 ConsensusfromCH236920mapping GlimmerHMM mRNA 1 122 . + . ID=ConsensusfromCH236920mapping.path1.gene1;Name=ConsensusfromCH236920mapping.path1.gene1
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48 ConsensusfromCH236920mapping GlimmerHMM CDS 1 122 . + 0 ID=ConsensusfromCH236920mapping.cds1.1;
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49 ConsensusfromCH236920mapping GlimmerHMM mRNA 14066 15205 . - . ID=ConsensusfromCH236920mapping.path1.gene2;Name=ConsensusfromCH236920mapping.path1.gene2
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50 ConsensusfromCH236920mapping GlimmerHMM CDS 14066 15034 . - 0 ID=ConsensusfromCH236920mapping.cds2.1;
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51 ConsensusfromCH236920mapping GlimmerHMM CDS 15137 15205 . - 0 ID=ConsensusfromCH236920mapping.cds2.2;
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52 ConsensusfromCH236920mapping GlimmerHMM mRNA 19910 24210 . - . ID=ConsensusfromCH236920mapping.path1.gene3;Name=ConsensusfromCH236920mapping.path1.gene3
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53 </help>
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54 </tool>