annotate mothur/tools/mothur/merge.groups.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

<tool id="mothur_merge_groups" name="Merge.groups" version="1.20.0" >
 <description>Merge groups in a shared file</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='merge.groups'
  ## 98_sq_phylip_amazon.fn.merge.shared
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.merge\.\S+$:'$shared
  --outputdir='$logfile.extra_files_path'
  --shared=$otu
  #if $design.source == 'hist':
   --design=$design_dataset
  #else:
   --design=$generated_design
  #end if
  #if $groups.__str__ != "None" and len($groups.__str__) > 0:
   --groups=$groups
  #end if
  #if $label.__str__ != "None" and len($label.__str__) > 0:
   --label='$label'
  #end if
 </command>
 <inputs>
  <param name="otu" type="data" format="shared" label="shared - OTU Shared Dataset"/>
  <param name="groups" type="select" optional="true" label="groups - Pick groups to include" multiple="true">
   <options from_dataset="otu">
    <column name="name" index="1"/>
    <column name="value" index="1"/>
    <filter type="static_value" name="ignore_header" keep="False" column="1" value = "Group"/>
    <filter type="unique_value" name="unq_grp" column="1" />
   </options>
  </param>
  <param name="label" type="select" label="label - Pick OTU Labels to include" optional="true" multiple="true">
   <options from_dataset="otu">
    <column name="name" index="0"/>
    <column name="value" index="0"/>
    <filter type="static_value" name="ignore_header" keep="False" column="0" value = "label"/>
    <filter type="unique_value" name="unq_lbl" column="0" />
   </options>
  </param>
  <conditional name="design">
   <param name="source" type="select" label="Grouping Design from" help="">
    <option value="hist">Your History</option>
    <option value="build">Build a grouping design</option>
   </param>
   <when value="hist">
    <param name="design_dataset" type="data" format="tabular" label="design - assign groups to new grouping"
           help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character)"/>
   </when>
   <when value="build">
    <repeat name="groupings" title="Grouping">
     <param name="name" type="text" label="Name for a new combined grouping"/>
     <param name="groups" type="select" multiple="true" label="Select groups for to include in this grouping">
      <options from_dataset="otu">
       <column name="name" index="1"/>
       <column name="value" index="1"/>
       <filter type="static_value" name="ignore_header" keep="False" column="1" value = "Group"/>
       <filter type="unique_value" name="unq_grp" column="1" />
      </options>
     </param>
    </repeat>
   </when>
  </conditional> <!-- design -->
 </inputs>
 <configfiles>
  <configfile name="generated_design">
#if $design.source == 'build':
#for $grouping in $design.groupings:
#set grp_str = $grouping.groups.__str__
#if grp_str != None and len(grp_str) > 0:
#for $grp in grp_str.split(','):
$grp	$grouping.name
#end for
#end if
#end for
#end if
  </configfile>
 </configfiles>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="shared" name="shared" label="${tool.name} on ${on_string}: merge.shared" />
 </outputs>
 <requirements>
  <requirement type="binary">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.groups_ command reads a shared_ file and a design file and merges the groups in the shared file that are in the same grouping in the design file.

A design file partitions a list of names into groups.  It is a tab-delimited file with 2 columns: name and group, e.g. :
        ======= =======
        duck    bird
        cow     mammal
        pig     mammal
        goose   bird
        cobra   reptile
        ======= =======

The Make_Design tool can construct a design file from a Mothur dataset that contains group names.

.. _shared: http://www.mothur.org/wiki/Shared_file
.. _merge.groups: http://www.mothur.org/wiki/Merge.groups

 </help>
</tool>