comparison mothur/tools/mothur/classify.otu.xml @ 7:7bfe1f843858

Support Mothur v1.20 trim.seqs - added name parameter and optional trim.names output phylo.diversity - group optional, put group and groups in conditional - breaks get.lineage remove.lineage - allow multiple taxons dist.shared - added processors consensus.seqs - add cutoff parameter trim.seqs,phylo.diversity,get.lineage,remove.lineage,dist.shared,consensus.seqs new tools - chimera.uchime deunique.tree count.seqs shared/relabund files - Column headings refactor lib/galaxy/datatypes/metagenomics.py add filters to label and group selects in tool configs mothur_wrapper.py updated with new tools params

6:ce6e81622c6a

<tool id="mothur_classify_otu" name="Classify.otu" version="1.19.0" force_history_refresh="True">
 <description>Assign sequences to taxonomy</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='classify.otu'
  --result='^mothur.\S+\.logfile$:'$logfile

  #end if
  --basis=$basis
  $probs
 </command>
 <inputs>
  <param name="otu" type="data" format="list" label="read.otu(list=) - OTU List "/>
  <conditional name="tax">
   <param name="source" type="select" label="Select Taxonomy from" help="">
    <option value="hist">History</option>
    <option value="ref">Cached Reference</option>
   </param>

   <when value="hist">
    <param name="taxonomy" type="data" format="seq.taxonomy" label="taxonomy - Taxonomy Reference"/>
   </when>
  </conditional>
  <conditional name="reftax">
   <param name="source" type="select" label="Select Taxonomy from" help="">
    <option value="none">None</option>
    <option value="hist">History</option>
    <option value="ref">Cached Reference</option>
   </param>
   <when value="none"/>
   <when value="ref">

7:7bfe1f843858

<tool id="mothur_classify_otu" name="Classify.otu" version="1.20.0" force_history_refresh="True">
 <description>Assign sequences to taxonomy</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='classify.otu'
  --result='^mothur.\S+\.logfile$:'$logfile

  #end if
  --basis=$basis
  $probs
 </command>
 <inputs>
  <param name="otu" type="data" format="list" label="list - OTU List "/>
  <conditional name="tax">
   <param name="source" type="select" label="Select Taxonomy from" help="">
    <option value="hist">History</option>
    <option value="ref">Cached Reference</option>
   </param>

   <when value="hist">
    <param name="taxonomy" type="data" format="seq.taxonomy" label="taxonomy - Taxonomy Reference"/>
   </when>
  </conditional>
  <conditional name="reftax">
   <param name="source" type="select" label="Select Reference Taxonomy used in Classify.seqs from" help="Including the reference taxonomy file used when you classified your sequences keep the rankIDs in the summary file static.">
    <option value="none">Selection is Optional</option>
    <option value="hist">History</option>
    <option value="ref">Cached Reference</option>
   </param>
   <when value="none"/>
   <when value="ref">