view mothur/tools/mothur/seq.error.xml @ 15:a6189f58fedb

Mothur - updated for Mothur version 1.22.0

<tool id="mothur_seq_error" name="Seq.error" version="1.22.0">
 <description>assess error rates in sequencing data</description>
 <command interpreter="python">
  mothur_wrapper.py 
  #import re, os.path
  #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__]
  #if 'summary' in $output_sel.__str__.split(','):
    #set results = $results + ["'^\S+.error.summary$:'" + $summary_out.__str__]
  #end if
  #if 'seq' in $output_sel.__str__.split(','):
    #set results = $results + ["'^\S+.error.seq$:'" + $seq_out.__str__]
  #end if
  #if 'seq_forward' in $output_sel.__str__.split(','):
    #set results = $results + ["'^\S+.error.seq.forward$:'" + $seq_forward_out.__str__]
  #end if
  #if 'seq_reverse' in $output_sel.__str__.split(','):
    #set results = $results + ["'^\S+.error.seq.reverse$:'" + $seq_reverse_out.__str__]
  #end if
  #if 'chimera' in $output_sel.__str__.split(','):
    #set results = $results + ["'^\S+.error.chimera$:'" + $chimera_out.__str__]
  #end if
  #if 'count' in $output_sel.__str__.split(','):
    #set results = $results + ["'^\S+.error.count$:'" + $count_out.__str__]
  #end if
  #if 'matrix' in $output_sel.__str__.split(','):
    #set results = $results + ["'^\S+.error.matrix$:'" + $matrix_out.__str__]
  #end if
  #if 'ref_query' in $output_sel.__str__.split(','):
    #set results = $results + ["'^\S+.error.ref-query$:'" + $ref_query_out.__str__]
  #end if
  --cmd='seq.error'
  --outputdir='$logfile.extra_files_path'
  --fasta=$fasta_in
  --reference=$alignment.template
  #if $name_in.__str__ != "None" and len($name_in.__str__) > 0:
   --name=$name_in
  #end if
  #if $qual.use.__str__ == 'yes':
   --qfile=$qfile_in
   --alignreport=$alignreport_in
   #if 'quality' in $output_sel.__str__.split(','):
    #set results = $results + ["'^\S+.error.quality$:'" + $quality_out.__str__]
   #end if
   #if 'qual_forward' in $output_sel.__str__.split(','):
    #set results = $results + ["'^\S+.error.qual.forward$:'" + $qual_forward_out.__str__]
   #end if
   #if 'qual_reverse' in $output_sel.__str__.split(','):
    #set results = $results + ["'^\S+.error.qual.reverse$:'" + $qual_reverse_out.__str__]
   #end if
  #end if
  #if $threshold.__str__ != '':
   --threshold=$threshold
  #end if
  $ignorechimeras
  --result=#echo ','.join($results)
  --processors=8
 </command>
 <inputs>
  <param name="fasta_in" type="data" format="align" label="fasta - Candiate Sequences"/>
  <conditional name="alignment">
   <param name="source" type="select" label="Select Reference Template from" help="">
    <option value="ref">Cached Reference</option>
    <option value="history">Your History</option>
   </param>
   <when value="ref">
    <param name="template" 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="history">
    <param name="template" type="data" format="align" label="reference - Reference to align with" help=""/>
   </when>
  </conditional>

  <param name="name_in" type="data" format="names" optional="true" label="name - Sequences Name reference"/>

  <conditional name="qual">
   <param name="use" type="select" label="Include a quality file and an alignment report as inputs" help="">
    <option value="no">No</option>
    <option value="yes">Yes</option>
   </param>
   <when value="yes"> 
    <param name="qfile_in" type="data" format="qual" label="qfile - Fasta Quality"/>
    <param name="alignreport_in" type="data" format="align.report" label="alignreport - Align Report"/>
   </when>
   <when value="no"/> 
  </conditional>

  <param name="threshold" type="float" value="" optional="true" label="threshold - error rate at which to report (default 1.)"
         help="">
   <validator type="in_range" message="error rate threshold between 0. and 1." min="0.0" max="1.0"/>
  </param>
  <param name="ignorechimeras" type="boolean" truevalue="" falsevalue="--ignorechimeras=false" checked="true" label="ignorechimeras - " />

  <param name="output_sel" type="select" multiple="true" display="checkboxes" label="Outputs as history datasets" >
    <option value="summary">error.summary</option>
    <option value="seq">error.seq</option>
    <option value="seq_forward">error.seq.forward</option>
    <option value="seq_reverse">error.seq.reverse</option>
    <option value="chimera">error.chimera</option>
    <option value="count">error.count</option>
    <option value="matrix">error.matrix</option>
    <option value="quality">error.quality</option>
    <option value="qual_forward">error.qual.forward</option>
    <option value="qual_reverse">error.qual.reverse</option>
    <option value="ref_query">error.ref-query</option>
  </param>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="tabular" name="summary_out" label="${tool.name} on ${on_string}: error.summary" >
   <filter>('summary' in output_sel)</filter>
  </data>
  <data format="fasta" name="seq_out" label="${tool.name} on ${on_string}: error.seq" >
   <filter>('seq' in output_sel)</filter>
  </data>
  <data format="tabular" name="seq_forward_out" label="${tool.name} on ${on_string}: error.seq.forward" >
   <filter>('seq_forward' in output_sel)</filter>
  </data>
  <data format="tabular" name="seq_reverse_out" label="${tool.name} on ${on_string}: error.seq.reverse" >
   <filter>('seq_reverse' in output_sel)</filter>
  </data>
  <data format="tabular" name="chimera_out" label="${tool.name} on ${on_string}: error.chimera" >
   <filter>('chimera' in output_sel)</filter>
  </data>
  <data format="tabular" name="count_out" label="${tool.name} on ${on_string}: error.count" >
   <filter>('count' in output_sel)</filter>
  </data>
  <data format="tabular" name="matrix_out" label="${tool.name} on ${on_string}: error.matrix" >
   <filter>('matrix' in output_sel)</filter>
  </data>
  <data format="tabular" name="quality_out" label="${tool.name} on ${on_string}: error.quality" >
   <filter>('quality' in output_sel)</filter>
  </data>
  <data format="tabular" name="qual_forward_out" label="${tool.name} on ${on_string}: error.qual.forward" >
   <filter>('qual_forward' in output_sel)</filter>
  </data>
  <data format="tabular" name="qual_reverse_out" label="${tool.name} on ${on_string}: error.qual.reverse" >
   <filter>('qual_reverse' in output_sel)</filter>
  </data>
  <data format="align" name="ref_query_out" label="${tool.name} on ${on_string}: error.ref-query" >
   <filter>('ref_query' in output_sel)</filter>
  </data>
 </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 seq.error_ command evaluates error rate for sequences by comparing to the fasta-formatted template_alignment_.
This is demonstrated in http://www.mothur.org/wiki/Schloss_SOP#Error_analysis

.. _template_alignment: http://www.mothur.org/wiki/Alignment_database
.. _seq.error: http://www.mothur.org/wiki/Seq.error


 </help>
</tool>