Mercurial > repos > matteoc > agame_custom_tools
diff fosm_cluster/clusterF.xml @ 0:68a3648c7d91 draft default tip
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author | matteoc |
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date | Thu, 22 Dec 2016 04:45:31 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fosm_cluster/clusterF.xml Thu Dec 22 04:45:31 2016 -0500 @@ -0,0 +1,19 @@ +<tool id="cluster" name="FosBin" version="0."> + <command> /home/inmare/galaxy/tools/fosm_cluster $f1 $l $o1 $o2 </command> + <description> k-means clustering of assembled fosmids.</description> + <help>The tool was designed to tentatively assign contigs from incomplete fosmid assemblies to clusters, ideally corresponding to single fosmids. Clustering is performed based on tetra-nucleotide frequencies of the contigs and coverage. The current version is only compatible with SPAdes output as coverage is recovered from the fasta headers. Future version migth require a different set of input files. Full details are in Chiara et al. #paper id. Clustering of contigs is performed by a custom script based on the R implementation of the K-means algorithm, using 1500 starting positions for the centroids. The clustering is performed on metrics based on coverage, GC composition and tetra-nucleotide composition of each contig, which are computed directly from the fasta file. The user must input the desired number of clusters, contigs are partitioned accordingly." </help> + <inputs> + <param name="f1" type="data" format="fasta" label="fasta file with contigs" help="currently need to be in SPAdes format"/> + <param name="l" type="integer" label="number of clusters" value="5" help="should correspond to the number of fosmids"/> + </inputs> + <outputs> + <data name="o1" ftype="tabular" format="txt" label="fosmids to cluster table"/> + <data name="o2" ftype="fasta" format="fasta" label="modified fasta file, containing cluster identifiers in the header"/> + </outputs> + <test> + <param name="f1" value="sim1_galaxy.fasta"/> + <param name="l" value="9" /> + <o1 name="outfile1" value="res"/> + <o2 name="outfile2" value="fasta.fas"/> + </test> +</tool>