diff mothur/tools/mothur/venn.xml @ 2:e990ac8a0f58

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

--- a/mothur/tools/mothur/venn.xml	Tue Jun 07 17:35:35 2011 -0400
+++ b/mothur/tools/mothur/venn.xml	Tue Jun 07 17:39:06 2011 -0400
@@ -1,72 +1,51 @@
-<tool id="mothur_venn" name="Venn" version="1.16.0"  force_history_refresh="True">
- <description>Generate Venn diagrams gor groups </description>
+<tool id="mothur_venn" name="Venn" version="1.19.0"  force_history_refresh="True">
+ <description>Generate Venn diagrams for groups </description>
  <command interpreter="python">
   mothur_wrapper.py 
   --cmd='venn'
   --result='^mothur.\S+\.logfile$:'$logfile
   --outputdir='$logfile.extra_files_path'
-  --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
-  --new_datasets='^\S+?\.(\S+\.svg)$:svg'
-  --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 $as_datasets.__str__ == "yes":
+   --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
+   --new_datasets='^\S+?\.(\S+\.svg)$:svg'
+  #end if
+  #if $input.source == 'shared':
+   --shared=$input.otu
    #if $input.label.__str__ != "None" and len($input.label.__str__) > 0:
     --label='$input.label'
    #end if
    #if $input.calc.__str__ != "None" and len($input.calc.__str__) > 0:
      --calc='$input.calc'
    #end if
-  #elif $input.source == 'shared':
-   --READ_shared=$input.otu
+   $nseqs
+   $permute
+   #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0:
+    --groups=$input.groups
+   #end if
+  #elif $input.source == 'similarity':
+   --list=$input.otu
    #if $input.label.__str__ != "None" and len($input.label.__str__) > 0:
     --label='$input.label'
    #end if
-   #if $calc.__str__ != "None" and len($calc.__str__) > 0:
-     --calc='$calc'
+   #if $input.calc.__str__ != "None" and len($input.calc.__str__) > 0:
+     --calc='$input.calc'
    #end if
-   $nseqs
-   $permute
-  #end if
-  #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0:
-   --groups=$input.groups
+   #if $input.abund >= 5:
+     --abund='$input.abund'
+   #end if
+
   #end if
  </command>
  <inputs>
-  <!-- get.relabund  relabund type should also work -->
   <conditional name="input">
    <param name="source" type="select" label="Generate Heatmap for">
+    <option value="shared">OTU Shared</option>
     <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"/>
+   <when value="shared">
+     <param name="otu" type="data" format="shared" label="shared - OTU Shared"/>
      <param name="calc" type="select" multiple="true" label="calc - Calculators (Uses defaults if none selected)">
-      <option value="sob">Chao</option>
-      <option value="chao">Chao</option>
-      <option value="ace">Ace</option>
-     </param>
-     <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="calc" type="select" multiple="true" label="calc - Calculators (Uses defaults if none selected)">
-      <option value="sharedsobs">Shared Chao</option>
+      <option value="sharedsobs">Shared Sobs</option>
       <option value="sharedchao">Shared Chao</option>
       <option value="sharedace">Shared Ace</option>
      </param>
@@ -85,9 +64,27 @@
       </options>
      </param>
    </when>
+   <when value="similarity">
+     <param name="otu" type="data" format="list" label="list - OTU List"/>
+     <param name="calc" type="select" multiple="true" label="calc - Calculators (Uses defaults if none selected)">
+      <option value="sobs">Sobs</option>
+      <option value="chao">Chao</option>
+      <option value="ace">Ace</option>
+     </param>
+     <param name="abund" type="integer" value="10" label="abund - Abundance when using the ace calculator ( >= 5 )">
+      <validator type="in_range" min="5" />
+     </param>
+     <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>
+   </when>
   </conditional>
   <param name="nseqs" type="boolean" truevalue="--nseqs=true" falsevalue="" checked="false" label="nseqs - Output the number of sequences represented by the otus in the picture"/>
   <param name="permute" type="boolean" truevalue="--permute=true" falsevalue="" checked="false" label="permute - Create pictures with all possible 4-way permutations of groups"/>
+  <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Create a new history dataset for each image"/>
  </inputs>
  <outputs>
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
@@ -108,7 +105,7 @@
 
 **Command Documenation**
 
-The venn_ command generates Venn diagrams to compare the richness shared among 2, 3, or 4 groups. 
+The venn_ command generates Venn diagrams to compare the richness shared among 2, 3, or 4 groups.  For calc parameter choices see: http://www.mothur.org/wiki/Calculators
 
 .. _venn: http://www.mothur.org/wiki/Venn