view mothur/tools/mothur/chimera.slayer.xml @ 1:fcc0778f6987

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

<tool id="mothur_chimera_slayer" name="Chimera.slayer" version="1.16.0">
 <description>Find putative chimeras using slayer</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='chimera.slayer'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.slayer\.chimeras$:'$out_file,'^\S+\.slayer\.accnos$:'$out_accnos
  --outputdir='$logfile.extra_files_path'
  --tmpdir='${logfile.extra_files_path}/input'
  --fasta=$fasta
  #if $alignment.source == 'self':
   --template='self'
   #if $alignment.name.__str__ != "None" and len($alignment.name.__str__) > 0:
    --name=$alignment.name
   #end if
  #else:
   --template=$alignment.template
  #end if
  #if $options.setby == 'user':
   --search=$options.search
   --window=$options.window
   --increment=$options.increment
   --match=$options.match
   --mismatch=$options.mismatch
   --numwanted=$options.numwanted
   --parents=$options.parents
   --minsim=$options.minsim
   --mincov=$options.mincov
   --iters=$options.iters
   --minbs=$options.minbs
   --minsnp=$options.minsnp
   --divergence=$options.divergence
   $options.trim
  #end if
  --processors=2
 </command>
 <inputs>
  <param name="fasta" type="data" format="fasta" label="fasta - 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>
    <option value="self">Self - Use abundant sequences from the input Candiate Sequences fasta </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>
   <when value="self">
    <param name="name" type="data" format="names" optional="true" label="names - Sequences Names"/>
   </when>
  </conditional>
  <conditional name="options">
   <param name="setby" type="select" label="Slayer Options" help="">
    <option value="default">Use default settings</option>
    <option value="user">Manually set options</option>
   </param>
   <when value="default"/>
   <when value="user">
    <param name="search" type="select" label="search - Search method for finding the closest parent" help="">
     <option value="distance" selected="true">distance</option>
     <option value="kmer">kmer</option>
     <option value="blast">blast</option>
    </param>
    <param name="window" type="integer" value="50" label="window - Window size for searching for chimeras (default 50)" />
    <param name="increment" type="integer" value="5" label="increment - Increment for window slide on each iteration (default 5)" />
    <param name="match" type="integer" value="5" label="match - Reward matched bases (default 5)"/>
    <param name="mismatch" type="integer" value="-4" label="mismatch - Penalty for mismatched bases (default -4)"/>
    <param name="numwanted" type="integer" value="15" label="numwanted - Number of potential parents to to compare with query sequence (default 15)"/>
    <param name="parents" type="integer" value="3" label="parents - Number of potential parents to investigate from the numwanted best matches"/>
    <param name="minsim" type="integer" value="90" label="minsim - Minimum similarity % between the query and parent (default 90)"/>
    <param name="mincov" type="integer" value="70" label="mincov - Minimum coverage % of closest matches in template and the query (default 70)"/>
    <param name="iters" type="integer" value="100" label="iters - Number of bootstrap iterations to try (default 100)"/>
    <param name="minbs" type="integer" value="90" label="minbs - Minimum bootstrap support % for calling a sequence chimeric (default 90)"/>
    <param name="minsnp" type="integer" value="100" label="minsnp - Percent of SNPs to sample on each side of breakpoint for computing bootstrap support (default 100)"/>
    <param name="divergence" type="float" value="1.007" label="divergence - Divergence cutoff for chimera determination (default 1.007)"/>
    <param name="trim" type="boolean" truevalue="--trim=True" falsevalue="" checked="false" label="trim - include chimeric sequences trimmed to their longest peice" />
   </when>
  </conditional>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="txt" name="out_file" label="${tool.name} on ${on_string}: slayer.chimeras" />
  <data format="accnos" name="out_accnos" label="${tool.name} on ${on_string}: slayer.accnos" />
 </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 chimera.slayer_ command identifies putative chimeras using the slayer approach.

.. _chimera.slayer: http://www.mothur.org/wiki/Chimera.slayer


 </help>
</tool>