annotate mothur/tools/mothur/split.abund.xml @ 0:3202a38e44d9

Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository

<tool id="mothur_split_abund" name="Split.abund" version="1.15.0" force_history_refresh="True">
 <description>Separate sequences into rare and abundant groups</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='split.abund'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.abund\.list$:'$abund_list,'^\S+\.rare\.list$:'$rare_list,'^\S+\.rare\.accnos$:'$rare_accnos,'^\S+\.abund\.accnos$:'$abund_accnos
  --outputdir='$logfile.extra_files_path'
  --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
  --new_datasets='^\S+?\.((unique|[0-9.]+)\.(rare|abund)\.fasta)$:fasta','^\S+?\.((unique|[0-9.]+)\.(rare|abund)\.groups)$:groups','^\S+?\.((unique|[0-9.]+)\.(rare|abund)\.accnos)$:accnos'
  --fasta=$fasta
  #if $search.type == "list":
   --list=$search.input
   #if $search.label.__str__ != "None" and len($search.label.__str__) > 0:
    --label=$search.label
   #end if
  #elif $search.type == "name":
   --name=$search.input
  #end if
  --cutoff=$cutoff
  #if $group.__str__ != "None" and len($group.__str__) > 0:
   --group=$group
  #end if
  #if $groups.__str__ != "None" and len($groups.__str__) > 0:
   --groups=$groups
  #end if
  $accnos
 </command>
 <inputs>
  <param name="fasta" type="data" format="fasta" label="fasta - Fasta"/>
  <conditional name="search">
   <param name="type" type="select" label="Type to screen" help="">
    <option value="list">OTU List</option>
    <option value="name">Name reference</option>
   </param>
   <when value="name">
    <param name="input" type="data" format="names" label="name - Name reference"/>
   </when>
   <when value="list">
    <param name="input" type="data" format="list" label="list - OTU List"/>
    <param name="label" type="select" label="label - OTU Labels" multiple="true">
     <options from_dataset="input">
      <column name="name" index="0"/>
      <column name="value" index="0"/>
     </options>
    </param>
   </when>
  </conditional>
  <param name="cutoff" type="integer" value="10" label="cutoff - Cutoff parameter is used to qualify what is abundant and rare."/>
  <param name="group" type="data" format="groups" optional="true" label="group - Group dataset"/>
  <param name="groups" type="select" label="groups - Group Selection (all used if none are selected)" multiple="true">
   <options from_dataset="group">
    <column name="name" index="1"/>
    <column name="value" index="1"/>
    <filter type="unique_value" name="unq_grp" column="1" />
   </options>
  </param>
  <param name="accnos" type="boolean" truevalue="--accnos=true" falsevalue="" checked="false" label="accnos - Produce rare and abundant Accession outputs"/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="list" name="abund_list" label="${tool.name} on ${on_string}: abund.list" />
  <data format="list" name="rare_list" label="${tool.name} on ${on_string}: rare.list" />
  <data format="accnos" name="rare_accnos" label="${tool.name} on ${on_string}: rare.accnos">
   <filter>accnos == True</filter>
  </data>
  <data format="accnos" name="abund_accnos" label="${tool.name} on ${on_string}: abund.accnos">
   <filter>accnos == True</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 split.abund_ command reads a fasta file and a list or a names file and splits the sequences into rare and abundant groups.

.. _split.abund: http://www.mothur.org/wiki/Split.abund

 </help>
</tool>