annotate mothur/tools/mothur/merge.files.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_merge_files" name="Merge.files" version="1.19.0">
 <description>Merge data</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='merge.files'
  --result='^mothur.\S+\.logfile$:'$logfile,'mergefile:'$output
  --outputdir='$logfile.extra_files_path'
  --input=${merge.input}#for i in $merge.inputs#,${i.input}#end for#
  --output='mergefile'
 </command>
 <inputs>
  <conditional name="merge">
   <param name="type" type="select" format="fasta,qual,groups,names,accnos" label="Merge">
    <option value="fasta">fasta</option>
    <option value="qual">qual</option>
    <option value="groups">groups</option>
    <option value="names">names</option>
    <option value="accnos">accnos</option>
   </param>
   <when value="fasta">
    <param name="input" type="data" format="fasta" label="input - fasta"/>
    <repeat name="inputs" title="And fasta"> 
     <param name="input" type="data" format="fasta" label="input - fasta"/>
    </repeat>
   </when> <!-- fasta --> 
   <when value="qual">
    <param name="input" type="data" format="qual" label="input - qual"/>
    <repeat name="inputs" title="And qual"> 
     <param name="input" type="data" format="qual" label="input - qual"/>
    </repeat>
   </when> <!-- qual --> 
   <when value="groups">
    <param name="input" type="data" format="groups" label="input - groups"/>
    <repeat name="inputs" title="And group"> 
     <param name="input" type="data" format="groups" label="input - groups"/>
    </repeat>
   </when> <!-- groups --> 
   <when value="names">
    <param name="input" type="data" format="names" label="input - names"/>
    <repeat name="inputs" title="And name"> 
     <param name="input" type="data" format="names" label="input - names"/>
    </repeat>
   </when> <!-- names --> 
   <when value="accnos">
    <param name="input" type="data" format="accnos" label="input - accnos"/>
    <repeat name="inputs" title="And accno"> 
     <param name="input" type="data" format="accnos" label="input - accnos"/>
    </repeat>
   </when> <!-- fasta --> 
  </conditional> <!-- merge -->
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="input" name="output" label="${tool.name} on ${on_string}: ${merge.type}"/>
 </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 merge.files_ command merge inputs into a single output.

.. _merge.files: http://www.mothur.org/wiki/Merge.files


 </help>
</tool>