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comparison IMSAME.xml @ 3:09d02332c84c draft

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author bitlab
date Mon, 17 Dec 2018 12:19:58 -0500
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1 <tool id="IMSAME" name="IMSAME">
2 <description>A Pairwise Incremental Multi-Staged Alignment Method for Metagenomes Comparison</description>
3 <inputs>
4 <param name="query" type="data" format="fasta" label="Query metagenome" help="Query sequence file in fasta format" />
5 <param name="db" type="data" format="fasta" label="Reference metagenome" help="Reference sequence file in fasta format" />
6 <param name="evalue" type="text" size="30" value="10e-10" label="Evalue" help="Evalue for filtering HSPs" />
7 <param name="coverage" type="float" value="0.5" label="Coverage" help="Minimum coverage to accept an alignment" />
8 <param name="identity" type="float" value="0.5" label="Identity" help="Minimum identity to accept an alignment" />
9 <param name="kmer" type="integer" value="12" label="Word size" help="Word size for heuristicly exploring the search space" />
10 </inputs>
11 <command>/home/galaxy-bitlab/galaxy/tools/IMSAME/bin/IMSAME -query $query -db $db -evalue $evalue -coverage $coverage -identity $identity -kmer $kmer -out $output --full</command>
12 <outputs>
13 <data name="output" type="txt" label="Output alignments"/>
14 </outputs>
15
16 <help>
17
18 IMSAME (Incremental Multi-Stage Alignment of MEtagenomes) is a highly parallel, fine-grained software for the pairwise alignment of metagenomes specifically designed for accurately finding conserved homology signals across metagenomic sequences.
19
20 -----
21
22 **Manual**
23
24 To use IMSAME, simply upload two metagenomes in the fasta format and select these as Query and Reference metagenome. Once so, choose the parameters that suit best your comparison:
25
26 - Evalue: This parameter is the minimum expected value required for an alignment to be reported.
27
28 - Coverage: This parameter is the minimum coverage to report an alignment. Coverage is the length of the alignment divided by the length of the query read.
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30 - Identity: This parameter is the minimum identity to report an alignment.
31
32 - Word size: This parameter is the seed size used for heuristically exploring the search space.
33
34 </help>
35
36 <citations>
37 <citation type="doi">10.1089/cmb.2018.0081</citation>
38 </citations>
39 </tool>