annotate mothur/tools/mothur/chimera.uchime.xml @ 33:d53b9eb16c2d

mothur_wrapper.py - convert_value needs to return a String

<tool id="mothur_chimera_uchime" name="Chimera.uchime" version="1.22.0">
 <description>Find putative chimeras using uchime</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='chimera.uchime'
  ##  stool.trim.unique.good.fasta
  ##  stool.trim.unique.good.uchime.chimera
  ##  stool.trim.unique.good.uchime.accnos
  ##  stool.trim.unique.good.uchime.alns
  #if $chimealns:
   --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.uchime\.chimeras?$:'$out_file,'^\S+\.uchime\.accnos$:'$out_accnos,'^\S+\.uchime\.alns$:'$out_alns
  #else:
   --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.uchime\.chimeras?$:'$out_file,'^\S+\.uchime\.accnos$:'$out_accnos
  #end if
  --outputdir='$logfile.extra_files_path'
  --fasta=$fasta
  #if $template.source == 'ref':
   --reference=$template.reference
  #elif $template.source == 'hist':
   --reference=$template.reference
  #elif $template.source == 'self':
   --reference='self'
   #if float($template.abskew.__str__) > 0:
    --abskew=$template.abskew
   #end if
   #if $template.group.__str__ != '':
    --group=$template.group
   #end if
  #elif $template.source == 'names':
   --name=$template.name
  #end if
  #if float($minh.__str__) > 0:
   --minh=$minh
  #end if
  #if float($mindiv.__str__) > 0:
   --mindiv=$mindiv
  #end if
  #if float($xn.__str__) > 0:
   --xn=$xn
  #end if
  #if float($dn.__str__) > 0:
   --dn=$dn
  #end if
  #if float($xa.__str__) > 0:
   --xa=$xa
  #end if
  #if int($chunks.__str__) > 0:
   --chunks=$chunks
  #end if
  #if int($minchunk.__str__) > 0:
   --minchunk=$minchunk
  #end if
  #if len($idsmoothwindow.__str__) > 0 and int($idsmoothwindow.__str__) > 0:
   --idsmoothwindow=$idsmoothwindow
  #end if
  ## #if len($minsmoothid.__str__) > 0 and float($minsmoothid.__str__) > 0:
  ##  --minsmoothid=$minsmoothid
  ## #end if
  #if int($maxp.__str__) > 0:
   --maxp=$maxp
  #end if
  #if int($minlen.__str__) > 0:
   --minlen=$minlen
  #end if
  #if int($maxlen.__str__) > 0:
   --maxlen=$maxlen
  #end if
  $skipgaps
  $skipgaps2
  #if $alignment.ucl:
    --ucl=true
   #if $alignment.queryfract != None and len($alignment.queryfract) > 0 and 1.0 >= float($alignment.queryfract) > 0: 
    --queryfract=$alignment.queryfract
   #end if
  #end if
  $chimealns
  --processors=8
 </command>
 <inputs>
  <param name="fasta" type="data" format="align" label="fasta - Candiate Aligned Sequences"/>
  <conditional name="template">
   <param name="source" type="select" label="Select Reference Template from" help="">
    <option value="hist">History</option>
    <option value="ref">Cached Reference</option>
    <option value="self">Self</option>
    <option value="names">Use a names file</option>
   </param>
   <when value="ref">
    <param name="reference" type="select" label="reference - 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="reference" type="data" format="fasta" label="reference - Reference to align with" help=""/>
   </when>
   <when value="self">
    <param name="abskew" type="float" value="1.9" label="abskew - Abundance skew (default 1.9)" help="Abundance skew is: min [ abund(parent1), abund(parent2) ] / abund(query)"/>
    <param name="group" type="data" format="groups" optional="true" label="group - Sequences Name reference"
           help="use the more abundant sequences from the same sample to check the query sequence"/>

   </when>
   <when value="names">
    <param name="name" type="data" format="names" label="name - Sequence names"/>
   </when>
  </conditional>

  <param name="minh" type="float" value="0.3" label="minh - mininum score to report chimera. Default 0.3" help="Values from 0.1 to 5 might be reasonable. Lower values increase sensitivity but may report more false positives."/>
  <param name="mindiv" type="float" value="0.5" label="mindiv - minimum divergence ratio, default 0.5" help="to ignore very close chimeras, increase mindiv to 1.0 or 2.0, to increase sensitivity decrease minh to 0.1"/>

  <param name="xn" type="float" value="8.0" label="xn - weight of a no vote. Default 8.0" help="Decreasing this weight to around 3 or 4 may give better performance on denoised data"/>
  <param name="dn" type="float" value="1.4" label="dn - pseudo-count prior on number of no votes. Default 1.4" help="Reasonable values are probably in the range from 0.2 to 2.0"/>
  <param name="xa" type="float" value="1.0" label="xa - eight of an abstain vote. Default 1.0" help="Reasonable values might range from 0.1 to 2.0"/>


  <param name="chunks" type="integer" value="4" label="chunks - number of chunks. Default 4." help="number of chunks to extract from the query sequence when searching for parents."/>
  <param name="minchunk" type="integer" value="64" label="minchunk - minimum length of a chunk. Default 64." help=""/>
  <param name="idsmoothwindow" type="integer" value="32" optional="True" label="idsmoothwindow - the length of id smoothing window. Default 32" help=""/>
  <!-- not supported in uchime 
  <param name="minsmoothid" type="float" value="0.95" optional="True" label="minsmoothid - minimum factional identity over smoothed window of candidate parent. Default 0.95" help=""/>
  -->
  <param name="maxp" type="integer" value="2" label="maxp - maximum number of candidate parents to consider. Default 2" help="increasing maxp gives only a very small improvement in sensivity but tends to increase the error rate quite a bit"/>
  <param name="minlen" type="integer" value="0" label="minlen - minimum unaligned sequence length. Default 10" help="Applies to both query and reference sequences."/>
  <param name="maxlen" type="integer" value="0" label="maxlen - maximum unaligned sequence length. Defaults 10000" help="Applies to both query and reference sequences."/>

   <param name="skipgaps" type="boolean" falsevalue="--skipgaps=false" truevalue="" checked="true" label="skipgaps - columns containing gaps do not count as diffs. Default=T" help="controls how gapped columns affect counting of diffs"/>
   <param name="skipgaps2" type="boolean" falsevalue="--skipgaps2=false" truevalue="" checked="true" label="skipgaps2 - column is immediately adjacent to a column containing a gap, it is not counted as a diff. Default=T" help="controls how gapped columns affect counting of diffs"/>

  <param name="chimealns" type="boolean" falsevalue="" truevalue="--chimealns=true" checked="false" label="chimealns - Produce a file containing multiple alignments of query sequences to parents in human readable format. " help="Alignments show columns with differences that support or contradict a chimeric model."/>


  <conditional name="alignment">
   <param name="ucl" type="boolean" falsevalue="global" truevalue="local" checked="false" label="ucl - Use local-X alignments." help="global-X is the default"/>
   <when value="global"/>
   <when value="local">
    <param name="queryfract" type="float" value="0.5" label="queryfract - minimum fraction of the query sequence that must be covered by a local-X alignment. Default 0.5." help=""/>
   </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 ${on_string}: uchime.chimeras" />
  <data format="accnos" name="out_accnos" label="${tool.name} on ${on_string}: uchime.accnos" />
  <data format="txt" name="out_alns" label="${tool.name} on ${on_string}: uchime.alns" >
   <filter>chimealns == True</filter>
  </data>
 </outputs>
 <requirements>
  <requirement type="package" version="1.27">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.uchime_ command reads a fasta file and reference file and outputs potentially chimeric sequences. The original uchime program was written by Robert C. Edgar and donated to the public domain, http://drive5.com/uchime

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


 </help>
</tool>