annotate mothur/tools/mothur/summary.shared.xml @ 0:3202a38e44d9

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

<tool id="mothur_summary_shared" name="Summary.shared" version="1.15.0"  force_history_refresh="True">
 <description>Summary of calculator values for OTUs</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='summary.shared'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.summary$:'$summary
  --outputdir='$logfile.extra_files_path'
  --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
  --new_datasets='^\S+?\.((\S+)\.(unique|[0-9.]*)\.dist)$:lower.dist'
  --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 $input.groups.__str__ != "None" and len($input.groups.__str__) > 0:
   --groups=$input.groups
  #end if
  #*
  --READ_list=$otu
  #if $otu_group.__str__ != "None" and len($otu_group.__str__) > 0:
   --READ_group='$otu_group'
  #end if
  #if $label.__str__ != "None" and len($label.__str__) > 0:
   --label='$label'
  #end if
  *#
  #if $calc.__str__ != "None" and len($calc.__str__) > 0:
   --calc='$calc'
  #end if
  $all
 </command>
 <inputs>
  <!-- list,group  or shared -->
  <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"/>
       <filter type="unique_value" name="unq_lbl" column="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 - Pairwise comparision groups" 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_calulators.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="all" type="boolean" truevalue="--all=true" falsevalue="" checked="false" label="all - Include RAM intensive sharedsobs and sharedchao calculations"/>
  <param name="distance" type="boolean" truevalue="--distance=true" falsevalue="" checked="false" label="distance - Output a distance file for each calculator at each label"/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="tabular" name="summary" label="${tool.name} on ${on_string}: shared.summary" />
 </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 summary.shared_ command produce a summary file that has the calculator value for each line in the OTU data and for all possible comparisons between the different groups in the group file.

.. _summary.shared: http://www.mothur.org/wiki/Summary.shared

 </help>
</tool>