| Previous changeset 4:7430449b8814 (2018-12-17) |
|
Commit message:
Uploaded |
|
added:
IMSAME/IMSAME.xml |
| b |
| diff -r 7430449b8814 -r 353e5673bcb8 IMSAME/IMSAME.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/IMSAME/IMSAME.xml Mon Dec 17 12:20:41 2018 -0500 |
| b |
| @@ -0,0 +1,39 @@ +<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 |