comparison mothur/tools/mothur/summary.single.xml @ 2:e990ac8a0f58

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

1:fcc0778f6987

<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:

   --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"/>

     <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>

.. _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>

2:e990ac8a0f58

<tool id="mothur_summary_single" name="Summary.single" version="1.19.0" force_history_refresh="True">
 <description>Summary of calculator values for OTUs</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='summary.single'
  #if isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('shared').__class__) and not $groupmode.__str__ == '--groupmode=true': 
   --result='^mothur.\S+\.logfile$:'$logfile
   --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
   --new_datasets='^\S+\.((\S+?)\.summary)$:tabular'
  #else:
   --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.summary$:'$summary
  #end if
  --outputdir='$logfile.extra_files_path'
  #if isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('shared').__class__):
   --shared=$otu
   $groupmode
  #elif isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('rabund').__class__):
   --rabund=$otu
  #elif isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('sabund').__class__):
   --sabund=$otu
  #elif isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('list').__class__):
   --list=$otu
  #end if
  #if $label.__str__ != "None" and len($label.__str__) > 0:
   --label='$label'
  #end if
  #if $calc.__str__ != "None" and len($calc.__str__) > 0:

   --abund=$abund
  #end if
  #if int($size.__str__) > 0:
   --size=$size
  #end if
 </command>
 <inputs>
  <param name="otu" type="data" format="list,rabund,sabund,shared" label="list,rabund,sabund,shared - 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="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
   <options from_file="mothur_calculators.loc">
     <column name="mult" index="1"/>

     <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"
    help="If false, create a summary file per group."/>
 </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}: summary" >
   <filter>(otu.file_ext == 'shared' and groupmode == True)</filter>
  </data>
 </outputs>
 <requirements>
  <requirement type="binary">mothur</requirement>
 </requirements>
 <tests>

.. _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.  This can be useful if you aren't interested in generating collector's or rarefaction curves for your multi-sample data analysis. It would be worth your while, however, to look at the collector's curves for the calculators you are interested in to determine how sensitive the values are to sampling. If the values are not sensitive to sampling, then you can trust the values. Otherwise, you need to keep sampling.  For calc parameter choices see: http://www.mothur.org/wiki/Calculators

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

 </help>
</tool>