annotate README @ 2:ab37eb09b4ca draft default tip

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/oases commit d5a2de4b4c556e028fc5ef7ffcc7c2d0cf31c5ec

# 13/02/2024
The version 1.4.0+galaxy0 of the tool uses bioconda dependencies
        <requirement type="package" version="0.2.09">oases</requirement>
        <requirement type="package" version="1.2.10">velvet</requirement>
        <requirement type="package" version="3.12.1">python</requirement>


# 15/04/2017
The tool now uses bioconda dependencies
        <requirement type="package" version="0.2.09">oases</requirement>
        <requirement type="package" version="1.2.10">velvet</requirement>
As the output is not deterministic, test search for line matching oases locus ranging in 1-25

#Created 28/11/2014
#Christophe Antoniewski, CNRS/University Pierre et Marie Curie, [e-mail]
# inspired from the oases wrapper developped by Konrad Paszkiewicz, Exeter Sequencing Service, University of Exeter 

Oases optimiser

This Galaxy tool is intended to provide a crude but effective method of producing semi-optimised transcriptome assemblies.
It operates by performing a number of user defined Velvet assemblies upon which Oases is then run.
The results of all of these runs are then put through a final Oases step where they act as scaffolds for the main assembly.
Note that this wrapper is designed to focused on small RNA reads from small RNA sequencings and will run velvetg with kmers ranging from 11 to 35 
Prerequisites:

1. Enclosed scripts
2. package_ged_velvet and package_ged_oases dependency packages

Limitations:

This is a crude optimisation step which DOES NOT try to evaluate the quality of each assembly or map to any reference cDNA.