<macros>
    <token name="@TOOL_VERSION@">0.5.1</token>
    <token name="@PIPELINE@">                                                                                
**Trycycler pipeline**                                                                                  
                                                                                                        
    ::                                                                                                  
                                                                                                        
        Trycycler subsample: make maximally-independent read subsets of an appropriate depth.           
                ⬇                                                                                       
        Trycycler cluster: carries out complete-linkage clustering of all contig sequences.             
                ⬇                                                                                       
        Trycycler reconcile/msa: reconcile the contigs within each cluster and perform a multiple sequence alignment.
                ⬇                                                                                       
        Trycycler partition: split the reads between the different clusters.                            
                ⬇                                                                                       
        Trycycler consensus: generate a consensus contig sequence for each cluster.                     
          
    </token>
    <xml name="edam_ontology">
        <edam_topics>                                                                                       
            <edam_topic>topic_0196</edam_topic>
        </edam_topics>
        <edam_operations>
            <edam_operation>operation_0525</edam_operation>
        </edam_operations>
    </xml>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">trycycler</requirement>
        </requirements>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="bibtex">                                                                   
                @misc{githubTrycycler,                                                                   
                author = {Ryan, Wick},                                                    
                year = {2020},                                                                 
                title = {Trycycler},                                                        
                publisher = {GitHub},
                journal = {GitHub repository},                                               
                url = {https://github.com/rrwick/Trycycler},                        
                }                                                                    
            </citation>
        </citations>
    </xml>
</macros>
