annotate mothur/tools/mothur/align.seqs.xml @ 1:fcc0778f6987

Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository

<tool id="mothur_align_seqs" name="Align.seqs" version="1.16.0">
 <description>Align sequences to a template alignment</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='align.seqs'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.align$:'$out_file,'^\S+\.align\.report$:'$report
  --outputdir='$logfile.extra_files_path'
  --candidate=$candidate
  --template=$alignment.template
  #if $search.method == 'kmer': 
   --ksize=$search.ksize
  #else: 
   --search=$search.method
  #end if
  --align=$align
  #if $scoring.adjust == 'yes': 
   --match=$scoring.match
   --mismatch=$scoring.mismatch
   --gapopen=$scoring.gapopen
   --gapextend=$scoring.gapextend
  #end if
  #if $reverse.flip == 'yes': 
   --flip=true
   --threshold=$reverse.threshold
  #end if
  --processors=2
 </command>
 <inputs>
  <param name="candidate" type="data" format="fasta" label="candidate - Candiate Sequences"/>
  <conditional name="alignment">
   <param name="source" type="select" label="Select Template from" help="">
    <option value="hist">History</option>
    <option value="ref">Cached Reference</option>
   </param>
   <when value="ref">
    <param name="template" type="select" label="template - Select an alignment database " help="">
     <options from_file="mothur_aligndb.loc">
      <column name="name" index="0" />
      <column name="value" index="1" />
     </options>
    </param>
   </when>
   <when value="hist">
    <param name="template" type="data" format="fasta" label="template - Template to align with" help=""/>
   </when>
  </conditional>
  <conditional name="search">
   <param name="method" type="select" label="Select a search method" help="">
    <option value="kmer">kmer (default)</option>
    <option value="suffix">suffix tree</option>
    <option value="blast">blast</option>
   </param>
   <when value="kmer">
    <param name="ksize" type="integer" value="8" label="ksize - kmer length between 5 and 12">
      <validator type="in_range" message="ksize - kmer length between 5 and 12" min="5" max="12"/>
    </param>
   </when>
   <when value="suffix"/>
   <when value="blast"/>
  </conditional>
  <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>

  <conditional name="scoring">
   <param name="adjust" type="select" label="Alignment scoring values" help="">
    <option value="no">use defaults</option>
    <option value="yes">adjust values</option>
   </param>
   <when value="no"/>
   <when value="yes">
    <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>

  <conditional name="reverse">
   <param name="flip" type="select" label="flip - Try to align against the reverse complement" help="">
    <option value="no">No</option>
    <option value="yes">Yes values</option>
   </param>
   <when value="no"/>
   <when value="yes">
    <param name="threshold" type="float" value=".5" label="threshold - Cutoff (0. - 1.) at which an alignment is deemed 'bad' and the reverse complement may be tried."/>
   </when>
  </conditional>

 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="align" name="out_file" label="${tool.name} on ${on_string}: align" />
  <data format="align.report" name="report" label="${tool.name} on ${on_string}: align.report" />
 </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 align.seqs_ command aligns a user-supplied fasta-formatted candidate sequence file to a user-supplied fasta-formatted template alignment.

.. _align.seqs: http://www.mothur.org/wiki/Align.seqs


 </help>
</tool>