comparison mothur/tools/mothur/consensus.seqs.xml @ 4:5265aa9067e0

set output formats to match input formats

3:b849cd7e132a

   #if $otu.label.__str__ != "None" and len($otu.label.__str__) > 0:
    --label='$otu.label'
   #end if
   --result='^mothur.\S+\.logfile$:'$logfile
   --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
   --new_datasets='^\S+?\.(((unique|[0-9.]*)\.)?cons\.fasta)$:fasta','^\S+?\.(((unique|[0-9.]*)\.)?cons\.names)$:names','^\S+?\.(((unique|[0-9.]*)\.)?cons\.summary)$:tabular'
  #else
   --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.cons\.summary$:'$summary,'^\S+\.cons\.fasta$:'$cons_fasta
  #end if
 </command>
 <inputs>
  <param name="fasta" type="data" format="fasta" label="fasta - Sequences to Bin" help="Sequences must be the same length"/>
  <param name="name" type="data" format="names" optional="true" label="name - Sequences Name reference"/>
  <conditional name="otu">
   <param name="use" type="select" label="Consensus sequence">
    <option value="no">Single consensus sequence</option>
    <option value="yes">Consensus sequence for each OTU in list</option>

 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="tabular" name="summary" label="${tool.name} on ${on_string}: cons.summary">
   <filter>otu['use'] == 'no'</filter>
  </data>
  <data format="fasta" name="cons_fasta" label="${tool.name} on ${on_string}: cons.fasta">
   <filter>otu['use'] == 'no'</filter>
  </data>
 </outputs>
 <requirements>
  <requirement type="binary">mothur</requirement>

4:5265aa9067e0

   #if $otu.label.__str__ != "None" and len($otu.label.__str__) > 0:
    --label='$otu.label'
   #end if
   --result='^mothur.\S+\.logfile$:'$logfile
   --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
   --new_datasets='^\S+?\.(((unique|[0-9.]*)\.)?cons\.fasta)$:${fasta.ext}','^\S+?\.(((unique|[0-9.]*)\.)?cons\.names)$:names','^\S+?\.(((unique|[0-9.]*)\.)?cons\.summary)$:tabular'
  #else
   --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.cons\.summary$:'$summary,'^\S+\.cons\.fasta$:'$cons_fasta
  #end if
 </command>
 <inputs>
  <param name="fasta" type="data" format="align" label="fasta - Sequences to Bin" help="Sequences must be the same length"/>
  <param name="name" type="data" format="names" optional="true" label="name - Sequences Name reference"/>
  <conditional name="otu">
   <param name="use" type="select" label="Consensus sequence">
    <option value="no">Single consensus sequence</option>
    <option value="yes">Consensus sequence for each OTU in list</option>

 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="tabular" name="summary" label="${tool.name} on ${on_string}: cons.summary">
   <filter>otu['use'] == 'no'</filter>
  </data>
  <data format_source="fasta" name="cons_fasta" label="${tool.name} on ${on_string}: cons.fasta">
   <filter>otu['use'] == 'no'</filter>
  </data>
 </outputs>
 <requirements>
  <requirement type="binary">mothur</requirement>