annotate mothur/tools/mothur/remove.rare.xml @ 2:e990ac8a0f58

Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository

<tool id="mothur_remove_rare" name="Remove.rare" version="1.19.0">
 <description>Remove rare OTUs</description>
 <command interpreter="python">
  mothur_wrapper.py 
  ## output {group_file_name}.pick.groups   {list_file_name}.pick.{format} 
  #import re, os.path
  #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__]
  --cmd='remove.rare'
  --outputdir='$logfile.extra_files_path'
  #if isinstance($input.otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('shared').__class__):
   --shared=$input.otu
   $input.bygroup
   #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0:
    --groups=$input.groups
   #end if
   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($input.otu.__str__)) + ":'" + $pick_otu.__str__]
  #elif isinstance($input.otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('rabund').__class__):
   --rabund=$input.otu
   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($input.otu.__str__)) + ":'" + $pick_otu.__str__]
  #elif isinstance($input.otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('sabund').__class__):
   --sabund=$input.otu
   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($input.otu.__str__)) + ":'" + $pick_otu.__str__]
  #elif isinstance($input.otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('list').__class__):
   --list=$input.otu
   #if $input.group.__str__ != "None" and len($input.group.__str__) > 0:
    --group=$input.group
    #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($input.group.__str__)) + ":'" + $pick_group.__str__]
   #end if
   #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0:
    --groups=$input.groups
   #end if
   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($input.otu.__str__)) + ":'" + $pick_otu.__str__]
  #end if
  #if $input.label.__str__ != "None" and len($input.label.__str__) > 0:
   --label=$input.label
  #end if
  --nseqs=$nseqs
  --result=#echo ','.join($results)
 </command>
 <inputs>
  <conditional name="input">
   <param name="source" type="select" label="Select Input Format">
    <option value="shared">shared</option>
    <option value="list">list and groups</option>
    <option value="default">rabund, sabund, or list</option>
   </param>
   <when value="shared">
    <param name="otu" type="data" format="shared" label="shared - Otu dataset"/>
    <param name="groups" type="select" optional="true" label="groups - Pick groups to analyze" 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="bygroup" type="boolean" truevalue="--bygroup=true" falsevalue="" checked="false" label="bygroup - Remove any OTU that has nseqs or fewer sequences across all groups"/> 
    <param name="label" type="select" multiple="true" 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>
   </when>
   <when value="list">
    <param name="otu" type="data" format="list" label="list - Otu dataset"/>
    <param name="group" type="data" format="groups" label="group - Groups" />
    <param name="groups" type="select" optional="true" label="groups - Pick groups to analyze" multiple="true">
     <options from_dataset="group">
      <column name="name" index="1"/>
      <column name="value" index="1"/>
      <filter type="unique_value" name="unq_grp" column="1" />
     </options>
    </param>
    <param name="label" type="select" multiple="false" 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>
   </when>
   <when value="default">
    <param name="otu" type="data" format="shared,list,rabund,sabund" label="shared,list,rabund,sabund - Otu dataset"/>
    <param name="label" type="select" multiple="true" 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>
   </when>
  </conditional>
  <param name="nseqs" type="integer" value="1" label="nseqs - Number of sequences cutoff for an otu to be deemed rare"/> 
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format_source="otu" name="pick_otu" label="${tool.name} on ${on_string}: pick.${input.otu.ext}"/>
  <data format="groups" name="pick_group" label="${tool.name} on ${on_string}: pick.groups">
   <filter>input['source'] == 'list'</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.

.. _list: http://www.mothur.org/wiki/List_file
.. _sabund: http://www.mothur.org/wiki/Sabund_file
.. _rabund: http://www.mothur.org/wiki/Rabund_file
.. _shared: http://www.mothur.org/wiki/Shared_file
.. _remove.rare: http://www.mothur.org/wiki/Remove.rare


 </help>
</tool>