view mothur/tools/mothur/cluster.fragments.xml @ 7:7bfe1f843858

Support Mothur v1.20 trim.seqs - added name parameter and optional trim.names output phylo.diversity - group optional, put group and groups in conditional - breaks get.lineage remove.lineage - allow multiple taxons dist.shared - added processors consensus.seqs - add cutoff parameter trim.seqs,phylo.diversity,get.lineage,remove.lineage,dist.shared,consensus.seqs new tools - chimera.uchime deunique.tree count.seqs shared/relabund files - Column headings refactor lib/galaxy/datatypes/metagenomics.py add filters to label and group selects in tool configs mothur_wrapper.py updated with new tools params

<tool id="mothur_cluster_fragments" name="Cluster.fragments" version="1.20.0">
 <description> Group sequences that are part of a larger sequence</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='cluster.fragments'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.fragclust\.\w+$:'$out_fasta,'^\S+\.names$:'$out_names
  --outputdir='$logfile.extra_files_path'
  --fasta=$fasta
  --name=$names
  #if int($diffs.__str__) > 0:
   --diffs=$diffs
  #end if
  #if 100 >= int($percent.__str__) > 0:
   --percent=$percent
  #end if
 </command>
 <inputs>
  <param name="fasta" type="data" format="fasta" label="fasta - Sequences to filter"/>
  <param name="names" type="data" format="names" optional="true" label="name - Sequences Name reference"/>
  <param name="diffs" type="integer" value="0" label="diffs - Number of mismatched bases to allow between sequences in a group (default 0)"/>
  <param name="percent" type="integer" value="0" label="percent - percentage of differences allowed ( between 1 and 100, default 0)" 
    help="The percent parameter allows you to set percentage of differences allowed, default=0. percent=2 means if the number of difference is less than or equal to two percent of the length of the fragment, then cluster. You may use diffs and percent at the same time to say something like: If the number or differences is greater than 1 or more than 2% of the fragment length, don't merge.">
   <validator type="in_range" message="percentage differences allowed  must be between 0 and 100" min="0" max="100"/>
  </param>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format_source="fasta" name="out_fasta" label="${tool.name} on ${on_string}: fasta" />
  <data format="names" name="out_names" label="${tool.name} on ${on_string}: names" />
 </outputs>
 <requirements>
  <requirement type="binary">mothur</requirement>
 </requirements>
 <tests>
 </tests>
 <help>
**Mothur Overview**

Mothur_, initiated by Dr. Patrick Schloss and his software development team
in the Department of Microbiology and Immunology at The University of Michigan,
provides bioinformatics for the microbial ecology community.

.. _Mothur: http://www.mothur.org/wiki/Main_Page

**Command Documenation**

The cluster.fragments_ command groups sequences that are part of a larger sequence.

.. _cluster.fragments: http://www.mothur.org/wiki/Cluster.fragments


 </help>
</tool>