diff mothur/tools/mothur/rarefaction.shared.xml @ 0:3202a38e44d9

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mothur/tools/mothur/rarefaction.shared.xml	Tue Jun 07 17:32:23 2011 -0400
@@ -0,0 +1,110 @@
+<tool id="mothur_rarefaction_shared" name="Rarefaction.shared" version="1.15.0">
+ <description>Generate inter-sample rarefaction curves for OTUs</description>
+ <command interpreter="python">
+  mothur_wrapper.py 
+  --cmd='rarefaction.shared'
+  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.rarefaction$:'$rarefaction
+  --outputdir='$logfile.extra_files_path'
+  --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=$input.groups
+  #end if
+  #if int($iters.__str__) > 0:
+   --iters=$iters
+  #end if
+  $jumble
+  #if $calc.__str__ != "None" and len($calc.__str__) > 0:
+    --calc='$calc'
+  #end if
+ </command>
+ <inputs>
+  <conditional name="input">
+   <param name="source" type="select" label="Generate Heatmap 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"/>
+      </options>
+     </param>
+     <param name="groups" type="select" label="groups - Groups to consider" 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="iters" type="integer" value="0" label="iters - Number of randomizations"/>
+  <param name="jumble" type="boolean" truevalue="" falsevalue="--jumble=false" checked="true" label="jumble"/>
+  <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
+   <options from_file="mothur_calulators.loc">
+     <column name="mult2" index="2"/>
+     <column name="name" index="0"/>
+     <column name="value" index="0"/>
+     <filter type="static_value" name="mult2" column="2" value="rare" />
+   </options>
+  </param>
+ </inputs>
+ <outputs>
+  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
+  <data format="tabular" name="rarefaction" label="${tool.name} on ${on_string}: shared.rarefaction" />
+ </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 rarefaction.shared_ command generates inter-sample rarefaction curves using a re-sampling without replacement approach. The traditional way that ecologists use rarefaction is not to randomize the sampling order within a sample, rather between samples. For instance, if we wanted to know the number of OTUs in the human colon, we might sample from various sites within the colon, and sequence a bunch of 16S rRNA genes. By determining the number of OTUs in each sample and comparing the composition of those samples it is possible to determine how well you have sampled the biodiversity within the individual.
+
+.. _rarefaction.shared: http://www.mothur.org/wiki/Rarefaction.shared
+
+ </help>
+</tool>