annotate mothur/tools/mothur/align.check.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_align_check" name="Align.check" version="1.19.0">
 <description>Calculate the number of potentially misaligned bases</description>
 <command interpreter="python">
  mothur_wrapper.py 
   --cmd='align.check'
   --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.align\.check$:'$out_file
   --outputdir='$logfile.extra_files_path'
   --fasta=$fasta
   --map=$ss.map
 </command>
  <inputs>
   <param name="fasta" type="data" format="align" label="fasta - Aligned Sequences"/>
   <conditional name="ss">
    <param name="source" label="Select Secondary Structure Map from" type="select">
     <option value="cached">Cached Secondary Structure Maps</option>
     <option value="history">Your History</option>
    </param>
    <when value="cached">
     <param name="map" type="select" label="map - Select a secondary structure map" help="Contact Galaxy team for additions">
      <options from_file="mothur_map.loc">
       <column name="name" index="0" />
       <column name="value" index="1" />
      </options>
     </param>
    </when>
    <when value="history">
     <param name="map" format="map" type="data" label="Secondary Structure Map" />
    </when>
   </conditional>
  </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="align.check" name="out_file" label="${tool.name} on ${on_string}: align.check"/>
 </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 align.check_ command allows you to calculate the number of potentially misaligned bases in a 16S rRNA gene sequence alignment using a secondary_structure_map_.  If you are familiar with the editor window in ARB, this is the same as counting the number of ~, #, -, and = signs.  

.. _secondary_structure_map: http://www.mothur.org/wiki/Secondary_structure_map
.. _align.check: http://www.mothur.org/wiki/Align.check

 </help>
</tool>