view mothur/tools/mothur/degap.seqs.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_degap_seqs" name="Degap.seqs" version="1.20.0">
 <description>Remove gap characters from sequences</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='degap.seqs'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+.ng\.\w+$:'$out_fasta
  --outputdir='$logfile.extra_files_path'
  --fasta=$fasta
 </command>
 <inputs>
  <param name="fasta" type="data" format="fasta" label="fasta - Dataset"/>
 </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" />
 </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 degap.seqs_ command reads a fasta file and outputs a fasta containing the sequences after all gap characters are removed.

.. _degap.seqs: http://www.mothur.org/wiki/Degap.seqs


 </help>
</tool>