view mothur/tools/mothur/remove.rare.xml @ 1:fcc0778f6987

Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository

<tool id="mothur_remove_rare" name="Remove.rare" version="1.16.0">
 <description>Remove rare OTUs</description>
 <command interpreter="python">
  mothur_wrapper.py 
  ## output {group_file_name}.pick.{label}.groups   {list_file_name}.pick.{label}.list 
  #import re, os.path
  #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__]
  --cmd='remove.rare'
  --outputdir='$logfile.extra_files_path'
  #if isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('shared').__class__):
   --shared=$otu
   #if $group_in.__str__ != "None" and len($group_in.__str__) > 0:
    --group=$group_in
   #end if
   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($input.otu_in.__str__)) + ":'" + $pick_shared.__str__]
  #elif isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('rabund').__class__):
   --rabund=$otu
   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($input.otu_in.__str__)) + ":'" + $pick_rabund.__str__]
  #elif isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('sabund').__class__):
   --sabund=$otu
   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($input.otu_in.__str__)) + ":'" + $pick_sabund.__str__]
  #elif isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('list').__class__):
   --list=$otu
   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($input.otu_in.__str__)) + ":'" + $pick_list.__str__]
   $bygroup
  #end if
  #if $label.__str__ != "None" and len($label.__str__) > 0:
   --label=$label
  #end if
  #if $groups.__str__ != "None" and len($groups.__str__) > 0:
   --groups=$groups
  #end if
  --nseqs=$nseqs
  --result=#echo ','.join($results)
 </command>
 <inputs>
  <param name="otu" type="data" format="list,rabund,sabund,shared" label="shared/relabund - Otu dataset"/>
  <param name="group_in" type="data" format="groups" label="group - Groups" optional="true"/>
  <param name="label" type="select" optional="true" label="label - OTU Labels" >
   <options from_dataset="otu">
    <column name="name" index="0"/>
    <column name="value" index="0"/>
    <filter type="unique_value" name="unq_lbl" column="0" />
   </options>
  </param>
  <param name="groups" type="select" optional="true" label="groups - Pick groups to annalyze" multiple="true">
   <options from_dataset="otu">
    <column name="name" index="1"/>
    <column name="value" index="1"/>
    <filter type="unique_value" name="unq_grp" column="1" />
   </options>
  </param>
  <param name="nseqs" type="integer" value="1" label="nseqs - iNumber of sequences cutoff for an otu to be deemed rare"/> 
  <param name="bygroup" type="boolean" truevalue="--bygroup=true" falsevalue="" checked="false" label="bygroup - Remove any OTU that has nseqs or fewer sequences across all groups"/> 
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="list" name="pick_list" label="${tool.name} on ${on_string}: pick.list">
   <filter>otu.datatype == 'list'</filter>
  </data>
  <data format="rabund" name="pick_rabund" label="${tool.name} on ${on_string}: pick.rabund">
   <filter>otu.datatype == 'rabund'</filter>
  </data>
  <data format="sabund" name="pick_sabund" label="${tool.name} on ${on_string}: pick.sabund">
   <filter>otu.datatype == 'sabund'</filter>
  </data>
  <data format="shared" name="pick_shared" label="${tool.name} on ${on_string}: pick.shared">
   <filter>otu.datatype == 'shared'</filter>
  </data>
 </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 remove.rare_ command reads one of the following file types: list, rabund, sabund or shared file. It outputs a new file after removing the rare otus.

.. _remove.rare: http://www.mothur.org/wiki/Remove.rare


 </help>
</tool>