comparison mothur/tools/mothur/cluster.classic.xml @ 35:95d75b35e4d2

Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)

34:1be61ceb20d7

<tool id="mothur_cluster_classic" name="Cluster.classic" version="1.27.0">
 <description>Assign sequences to OTUs (Dotur implementation)</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='cluster.classic'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.[fna]n\.sabund$:'$sabund,'^\S+\.[fna]n\.rabund$:'$rabund,'^\S+\.[fna]n\.list$:'$otulist

  <data format="rabund" name="rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"/>
  <data format="sabund" name="sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/>
  <data format="list" name="otulist" label="${tool.name} on ${on_string}: list (OTU List)"/>
 </outputs>
 <requirements>
  <requirement type="package" version="1.27">mothur</requirement>
 </requirements>
 <tests>
 </tests>
 <help>
**Mothur Overview**

35:95d75b35e4d2

<tool id="mothur_cluster_classic" name="Cluster.classic" version="1.88.0">
 <description>Assign sequences to OTUs (Dotur implementation)</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='cluster.classic'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.[fna]n\.sabund$:'$sabund,'^\S+\.[fna]n\.rabund$:'$rabund,'^\S+\.[fna]n\.list$:'$otulist

  <data format="rabund" name="rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"/>
  <data format="sabund" name="sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/>
  <data format="list" name="otulist" label="${tool.name} on ${on_string}: list (OTU List)"/>
 </outputs>
 <requirements>
  <requirement type="package" version="1.33">mothur</requirement>
 </requirements>
 <tests>
 </tests>
 <help>
**Mothur Overview**