diff mothur/tools/mothur/summary.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/summary.shared.xml	Tue Jun 07 17:32:23 2011 -0400
@@ -0,0 +1,121 @@
+<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>