annotate mothur/tools/mothur/chimera.perseus.xml @ 32:ec8df51e841a

Fixes courtesy of Peter Briggs: metagenomics.py: - Groups class: Fix for when second column not present - Axes class: make 'sniff' method more sensitive to try and restrict arbitrary tabular data uploads being sniffed as this type mothur_wrapper.py: - update cmd_dict['chimera.perseus'], to use correct inputs - add --beta option (needed for chimera.perseus tool) - add function for converting input floats from scientific notation (e.g. 1e-6, which mothur can't handle) to decimal format (e.g. 0.00001, which it can) chimera.perseus.xml: - add output data item for the "accnos" file (not previous captured in the history) trim.flows.xml: - cosmetic change: base name for additional output data items is now "trim.flows", rather than "logfile" (clarifies history items) shhh.flows.xml: - cosmetic change: update default value specified in help for mindiff to be consistent with that given in the mothur documentation

<tool id="mothur_chimera_perseus" name="Chimera.perseus" version="1.23.0" >
 <description>Find putative chimeras using chimeraCheck</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='chimera.perseus'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.perseus\.chimeras?$:'$out_file
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.perseus\.chimeras?$:'$out_file,'^\S+\.perseus\.accnos$:'$out_accnos
  --outputdir='$logfile.extra_files_path'
  --fasta=$fasta
  --name=$name
  #if $group.__str__ != "None" and len($group.__str__) > 0:
   --group='$group'
  #end if
  #if $alpha.__str__ != '':
   --alpha=$alpha
  #end if
  #if $beta.__str__ != '':
   --beta=$beta
  #end if
  #if $cutoff.__str__ != '':
   --cutoff=$cutoff
  #end if
  --processors=8
 </command>
 <inputs>
  <param name="fasta" type="data" format="align" label="fasta - Candiate Aligned Sequences"/>
  <param name="name" type="data" format="names" label="name - Names "/>
  <param name="group" type="data" format="group" optional="true" label="group - Sequences Name reference"/>
  <param name="alpha" type="float" value="-5.54" optional="true" label="alpha" help="The default is -5.54"/>
  <param name="beta" type="float" value="0.33" optional="true" label="beta" help="The default is 0.33"/>
  <param name="cutoff" type="float" value="0.50" optional="true" label="cutoff" help="The default is 0.50"/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="tabular" name="out_file" label="${tool.name} on ${on_string}: perseus.chimeras" />
  <data format="accnos" name="out_accnos" label="${tool.name} on ${on_string}: perseus.accnos" />
 </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.perseus_ command reads a fasta and name file, and outputs potentially chimeric sequences.

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


 </help>
</tool>