annotate mothur/tools/mothur/summary.single.xml @ 1:fcc0778f6987

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

<tool id="mothur_summary_single" name="Summary.single" version="1.16.0" force_history_refresh="True">
 <description>Summary of calculator values for OTUs</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='summary.single'
  --result='^mothur.\S+\.logfile$:'$logfile
  --outputdir='$logfile.extra_files_path'
  --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
  --new_datasets='^\S+\.((\S+?)\.summary)$:tabular'
  --READ_cmd='read.otu'
  --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='$calc'
  #end if
  #if int($abund.__str__) > 0:
   --abund=$abund
  #end if
  #if int($size.__str__) > 0:
   --size=$size
  #end if
  $groupmode
  --processors=2
 </command>
 <inputs>
  <param name="otu" type="data" format="list" label="read.otu(list=) - OTU List"/>
  <param name="otu_group" type="data" format="groups" optional="true" label="read.otu(group=) - Group file for the OTU List"/>
  <param name="label" type="select" label="label - OTU Labels" multiple="true">
   <options from_dataset="otu">
    <column name="name" index="0"/>
    <column name="value" index="0"/>
   </options>
  </param>
  <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
   <options from_file="mothur_calculators.loc">
     <column name="mult" index="1"/>
     <column name="name" index="0"/>
     <column name="value" index="0"/>
     <filter type="static_value" name="mult" column="1" value="single" />
   </options>
  </param>
  <param name="abund" type="integer" value="10" label="abund - ACE Estimator threshold for abundant versus rare OTUs"/>
  <param name="size" type="integer" value="0" label="size - "/>
  <param name="groupmode" type="boolean" truevalue="--groupmode=true" falsevalue="--groupmode=false" checked="true" label="groupmode - Collate shared summary results in one file"/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${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 summary.single_ 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.single: http://www.mothur.org/wiki/Summary.single

 </help>
</tool>