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Commit message:
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IMSAME.xml |
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| diff -r 09d02332c84c -r 7430449b8814 IMSAME.xml --- a/IMSAME.xml Mon Dec 17 12:19:58 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,39 +0,0 @@ -<tool id="IMSAME" name="IMSAME"> - <description>A Pairwise Incremental Multi-Staged Alignment Method for Metagenomes Comparison</description> - <inputs> - <param name="query" type="data" format="fasta" label="Query metagenome" help="Query sequence file in fasta format" /> - <param name="db" type="data" format="fasta" label="Reference metagenome" help="Reference sequence file in fasta format" /> - <param name="evalue" type="text" size="30" value="10e-10" label="Evalue" help="Evalue for filtering HSPs" /> - <param name="coverage" type="float" value="0.5" label="Coverage" help="Minimum coverage to accept an alignment" /> - <param name="identity" type="float" value="0.5" label="Identity" help="Minimum identity to accept an alignment" /> - <param name="kmer" type="integer" value="12" label="Word size" help="Word size for heuristicly exploring the search space" /> - </inputs> - <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> - <outputs> - <data name="output" type="txt" label="Output alignments"/> - </outputs> - - <help> - -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. - ------ - -**Manual** - -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: - -- Evalue: This parameter is the minimum expected value required for an alignment to be reported. - -- 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. - -- Identity: This parameter is the minimum identity to report an alignment. - -- Word size: This parameter is the seed size used for heuristically exploring the search space. - - </help> - - <citations> - <citation type="doi">10.1089/cmb.2018.0081</citation> - </citations> -</tool> \ No newline at end of file |