annotate mothur/tools/mothur/collect.shared.xml @ 1:fcc0778f6987

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

<tool id="mothur_collect_shared" name="Collect.shared" version="1.16.0" force_history_refresh="True">
 <description>Generate collector's curves for calculators on OTUs</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='collect.shared'
  --result='^mothur.\S+\.logfile$:'$logfile
  --outputdir='$logfile.extra_files_path'
  --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
  --new_datasets='^\S+?\.(anderberg|braycurtis|jabund|jclass|jest|kstest|kulczynski|kulczynskicody|lennon|morisitahorn|ochiai|shared\.ace|shared\.chao|shared\.nseqs|shared\.sobs|sorabund|sorclass|sorest|thetan|thetayc|whittaker)$:tabular'
  --READ_cmd='read.otu'
  #if $input.source == 'similarity':
   --READ_list=$input.otu
   #if $otu_group.__str__ != "None" and len($otu_group.__str__) > 0:
    --READ_group='$otu_group'
   #end if
   #if $input.label.__str__ != "None" and len($input.label.__str__) > 0:
    --READ_label='$input.label'
   #end if
  #elif $input.source == 'shared':
   --READ_shared=$input.otu
   #if $input.label.__str__ != "None" and len($input.label.__str__) > 0:
    --READ_label='$input.label'
   #end if
  #end if
  #if $calc.__str__ != "None" and len($calc.__str__) > 0:
    --calc='$calc'
  #end if
  $all
  #if float($freq.__str__) > 0:
   --freq=$freq
  #end if
  #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0:
   --groups=$input.groups
  #end if
 </command>
 <inputs>
  <conditional name="input">
   <param name="source" type="select" label="Generate Collector Curvers for">
    <option value="similarity">OTU list</option>
    <option value="shared">OTU Shared</option>
   </param>
   <when value="similarity">
     <param name="otu" type="data" format="list" label="read.otu(list=) - OTU List"/>
     <param name="otu_group" type="data" format="groups" label="read.otu(group) - Group file for the OTU List"/>
     <param name="label" type="select" label="label - OTU Labels" multiple="true">
      <options from_dataset="otu">
       <column name="name" index="0"/>
       <column name="value" index="0"/>
      </options>
     </param>
     <param name="groups" type="select" label="groups - Groups to consider" multiple="true">
      <options from_dataset="otu_group">
       <column name="name" index="1"/>
       <column name="value" index="1"/>
       <filter type="unique_value" name="unq_grp" column="1" />
      </options>
     </param>
   </when>
   <when value="shared">
     <param name="otu" type="data" format="shared" label="read.otu(shared=) - OTU Shared"/>
     <param name="label" type="select" label="label - OTU Labels" multiple="true">
      <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" label="groups - Groups to condider" 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>
   </when>
  </conditional>
  <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
   <options from_file="mothur_calculators.loc">
     <column name="mult" index="1"/>
     <column name="name" index="0"/>
     <column name="value" index="0"/>
     <filter type="static_value" name="mult" column="1" value="shared" />
   </options>
  </param>
  <param name="freq" type="float" value="0.0" label="freq - "/>

  <param name="all" type="boolean" truevalue="--all=true" falsevalue="" checked="false" label="all - Include RAM intensive sharedsobs and sharedchao calculations"/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
 </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 collect.shared_ command generates collector's curves for calculators, which describe the similarity between communities or their shared richness. Collector's curves describe how richness or diversity change as you sample additional individuals. If a collector's curve becomes parallel to the x-axis, you can be reasonably confident that you have done a good job of sampling and can trust the last value in the curve.

.. _collect.shared: http://www.mothur.org/wiki/Collect.shared

 </help>
</tool>