diff mothur/tools/mothur/tree.shared.xml @ 2:e990ac8a0f58

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

--- a/mothur/tools/mothur/tree.shared.xml	Tue Jun 07 17:35:35 2011 -0400
+++ b/mothur/tools/mothur/tree.shared.xml	Tue Jun 07 17:39:06 2011 -0400
@@ -1,69 +1,66 @@
-<tool id="mothur_tree_shared" name="Tree.shared" version="1.16.0" force_history_refresh="True">
+<tool id="mothur_tree_shared" name="Tree.shared" version="1.19.0" force_history_refresh="True">
  <description>Generate a newick tree for dissimilarity among groups</description>
  <command interpreter="python">
   mothur_wrapper.py 
   --cmd='tree.shared'
-  --result='^mothur.\S+\.logfile$:'$logfile
-  --outputdir='$logfile.extra_files_path'
-  --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
-  --new_datasets='^\S+?([a-z]+\.(unique|[0-9.]*)\.tre)$:tre'
-  --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'
+  #if $input.source == 'shared':
+   --result='^mothur.\S+\.logfile$:'$logfile
+   #if $input.as_datasets.__str__ == "yes":
+    --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
+    --new_datasets='^\S+?([a-z]+\.(unique|[0-9.]*)\.tre)$:tre'
+   #end if
+   --shared=$input.dist
+   #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0:
+    --groups=$input.groups
    #end if
    #if $input.label.__str__ != "None" and len($input.label.__str__) > 0:
-    --READ_label='$input.label'
+    --label='$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='$input.label'
+  #else: 
+   --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.tre$:'$tre
+   --outputdir='$logfile.extra_files_path'
+   #if $input.source == 'column':
+    --column=$input.dist
+    --name=$input.name
+   #elif $input.source == 'phylip':
+    --phylip=$input.dist
+    #if $input.name.__str__ != "None" and len($input.name.__str__) > 0:
+     --name=$input.name
+    #end if
    #end if
   #end if
-  #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0:
-   --groups=$input.groups
-  #end if
   #if $calc.__str__ != "None" and len($calc.__str__) > 0:
    --calc=$calc
   #end if
  </command>
  <inputs>
-  <!-- list,group  or shared -->
+  <!-- column,name  phylip  or shared -->
   <conditional name="input">
-   <param name="source" type="select" label="Generate Heatmap for">
-    <option value="similarity">OTU list</option>
+   <param name="source" type="select" label="Select input format">
     <option value="shared">OTU Shared</option>
+    <option value="column">Pairwise Column Distance Matrix</option>
+    <option value="phylip">Phylip Distance Matrix</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 value="column">
+    <param name="dist" type="data" format="pair.dist" label="column - Distance Matrix"/>
+    <param name="name" type="data" format="names" label="name - Sequences Name reference"/>
+   </when>
+   <when value="phylip">
+    <param name="dist" type="data" format="lower.dist,square.dist" label="phylip - Distance Matrix"/>
+    <param name="name" type="data" format="names" optional="true" label="name - Names"/>
    </when>
    <when value="shared">
-     <param name="otu" type="data" format="shared" label="read.otu(shared=) - OTU Shared"/>
+     <param name="dist" type="data" format="shared" label="shared - OTU Shared"/>
+     <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Create a new history dataset for each label and calculator"/>
      <param name="label" type="select" label="label - OTU Labels" multiple="true">
-      <options from_dataset="otu">
+      <options from_dataset="dist">
        <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">
+      <options from_dataset="dist">
        <column name="name" index="1"/>
        <column name="value" index="1"/>
        <filter type="unique_value" name="unq_grp" column="1" />
@@ -82,6 +79,9 @@
  </inputs>
  <outputs>
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
+  <data format="tre" name="tre" label="${tool.name} on ${on_string}: tre">
+   <filter>input['source'] != 'shared'</filter>
+  </data>
  </outputs>
  <requirements>
   <requirement type="binary">mothur</requirement>
@@ -99,7 +99,7 @@
 
 **Command Documenation**
 
-The tree.shared_ command will generate a newick-formatted tree file that describes the dissimilarity (1-similarity) among multiple groups.
+The tree.shared_ command will generate a newick-formatted tree file that describes the dissimilarity (1-similarity) among multiple groups.  For calc parameter choices see: http://www.mothur.org/wiki/Calculators
 
 .. _tree.shared: http://www.mothur.org/wiki/Tree.shared