annotate mothur/tools/mothur/pairwise.seqs.xml @ 35:95d75b35e4d2

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

<tool id="mothur_pairwise_seqs" name="Pairwise.seqs" version="1.20.0">
 <description>calculate uncorrected pairwise distances between sequences</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='pairwise.seqs'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.dist$:'$out_dist
  --outputdir='$logfile.extra_files_path'
  --fasta=$fasta
  --align=$align
  #if len($calc.__str__) > 0:
   --calc=$calc
  #end if
  $countends
  #if float($cutoff.__str__) > 0.0:
   --cutoff=$cutoff
  #end if
  #if $scoring.setby == 'user':
   --match=$scoring.match
   --mismatch=$scoring.mismatch
   --gapopen=$scoring.gapopen
   --gapextend=$scoring.gapextend
  #end if
  #if len($output.__str__) > 0:
   --output=$output
  #end if
  --processors=8
 </command>
 <inputs>
  <param name="fasta" type="data" format="fasta" label="fasta - Fasta"/>
  <param name="align" type="select" label="align - Select a pairwise alignment method" help="">
   <option value="needleman">needleman (default)</option>
   <option value="gotoh">gotoh</option>
   <option value="blast">blast</option>
  </param>
  <param name="calc" type="select" label="calc - Calc Method - Gap Penality" help="">
   <option value="">use default</option>
   <option value="onegap">onegap - counts a string of gaps as a single gap</option>
   <option value="nogaps">nogaps - ignores gaps</option>
   <option value="eachgap ">eachgap - penalize each gap</option>
  </param>
  <param name="countends" type="boolean" checked="true" truevalue="" falsevalue="--countends=false" label="countends - Countends" 
                 help="Penalize terminal gaps"/>
  <param name="cutoff" type="float" value="0.0" label="cutoff - Distance Cutoff threshold - ignored if not > 0" 
                 help="Do not save any distances larger than this, a common value would be 0.10"/>
  
  <conditional name="scoring">
   <param name="setby" type="select" label="Scoring match, mismatch, gapopen, and gapextend" help="">
    <option value="default">Use default settings</option>
    <option value="user">Manually set scoring values</option>
   </param>
   <when value="default"/>
   <when value="user">
    <param name="match" type="integer" value="1" label="match - Pairwise alignment reward for a match"/>
    <param name="mismatch" type="integer" value="-1" label="mismatch - Pairwise alignment penalty for a mismatch"/>
    <param name="gapopen" type="integer" value="-2" label="gapopen - Pairwise alignment penalty for opening a gap"/>
    <param name="gapextend" type="integer" value="-1" label="gapextend - Pairwise alignment penalty for extending a gap"/>
   </when>
  </conditional>


  <param name="output" type="select" label="output - Distance Matrix Output Format" help="">
   <option value="">Default Column-Formatted Matrix</option>
   <option value="lt">Phylip formatted Lower Triangle Matrix</option>
   <option value="square">Phylip formatted Square Matrix</option>
  </param>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="pair.dist" name="out_dist" label="${tool.name} on ${on_string}: dist">
   <change_format>
    <when input="output" value="lt" format="lower.dist" />
    <when input="output" value="square" format="square.dist" />
   </change_format>
  </data>
 </outputs>
 <requirements>
  <requirement type="package" version="1.33">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 pairwise.seqs_ command will calculate uncorrected pairwise distances between sequencesi as a column-formatted_distance_matrix_ or  phylip-formatted_distance_matrix_.

.. _column-formatted_distance_matrix: http://www.mothur.org/wiki/Column-formatted_distance_matrix
.. _phylip-formatted_distance_matrix: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix
.. _pairwise.seqs: http://www.mothur.org/wiki/Pairwise.seqs


 </help>
</tool>