diff mothur/tools/mothur/heatmap.sim.xml @ 2:e990ac8a0f58

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

--- a/mothur/tools/mothur/heatmap.sim.xml	Tue Jun 07 17:35:35 2011 -0400
+++ b/mothur/tools/mothur/heatmap.sim.xml	Tue Jun 07 17:39:06 2011 -0400
@@ -1,30 +1,22 @@
-<tool id="mothur_heatmap_sim" name="Heatmap.sim" version="1.16.0"  force_history_refresh="True">
+<tool id="mothur_heatmap_sim" name="Heatmap.sim" version="1.19.0"  force_history_refresh="True">
  <description>Generate a heatmap for pariwise similarity</description>
  <command interpreter="python">
   mothur_wrapper.py 
   --cmd='heatmap.sim'
-  --result='^mothur.\S+\.logfile$:'$logfile
   --outputdir='$logfile.extra_files_path'
-  --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
-  --new_datasets='^\S+?\.((unique|[0-9.]*)(\S+)\.heatmap\.sim\.svg)$:svg'
-  #if $input.source == 'similarity':
-   --READ_cmd='read.otu'
-   --READ_list=$input.otu
-   #if $otu_group.__str__ != "None" and len($otu_group.__str__) > 0:
-    --READ_group='$otu_group'
+  #if $as_datasets.__str__ == "yes":
+   #if $input.source == 'shared':
+    --result='^mothur.\S+\.logfile$:'$logfile
+    --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
+    --new_datasets='^\S+?\.((unique|[0-9.]*)(\S+)\.heatmap\.sim\.svg)$:svg'
+   #else:
+    --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.heatmap\.sim\.svg$:'$heatmap
    #end if
-   #if $input.label.__str__ != "None" and len($input.label.__str__) > 0:
-    --label='$input.label'
-   #end if
-   #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0:
-    --groups=$input.groups
-   #end if
-   #if $input.calc.__str__ != "None" and len($input.calc.__str__) > 0:
-     --calc='$input.calc'
-   #end if
-  #elif $input.source == 'shared':
-   --READ_cmd='read.otu'
-   --READ_shared=$input.otu
+  #else:
+   --result='^mothur.\S+\.logfile$:'$logfile
+  #end if
+  #if $input.source == 'shared':
+   --shared=$input.otu
    #if $input.label.__str__ != "None" and len($input.label.__str__) > 0:
     --label='$input.label'
    #end if
@@ -39,45 +31,15 @@
    --name=$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
  </command>
  <inputs>
-  <!-- get.relabund  relabund type should also work -->
   <conditional name="input">
    <param name="source" type="select" label="Generate Heatmap for">
-    <option value="similarity">OTU list</option>
-    <option value="shared">OTU Shared</option>
-    <option value="column">Pairwise Column Distance Matrix</option>
-    <option value="phylip">Phylip Distance Matrix</option>
+    <option value="shared">shared - Sample Similarity - OTU Shared</option>
+    <option value="phylip">phylip - Phylip Distance Matrix</option>
+    <option value="column">colomn - Pairwise Column 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 include" 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>
-     <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
-      <options from_file="mothur_calculators.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="shar" />
-      </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">
@@ -94,6 +56,14 @@
        <filter type="unique_value" name="unq_grp" column="1" />
       </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="mult2" index="2"/>
+        <column name="name" index="0"/>
+        <column name="value" index="0"/>
+        <filter type="static_value" name="mult2" column="2" value="shar" />
+      </options>
+     </param>
    </when>
    <when value="column">
        <param name="dist" type="data" format="pair.dist" label="column - Distance Matrix"/>
@@ -101,12 +71,15 @@
    </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>
   </conditional>
+  <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 ${on_string}: logfile" />
+  <data format="svg" name="heatmap" label="${tool.name} on ${on_string}: heatmap.sim.svg">
+    <filter>as_datasets != 'true' and input['source'] != 'shared'</filter>
+  </data>
  </outputs>
  <requirements>
   <requirement type="binary">mothur</requirement>
@@ -124,8 +97,12 @@
 
 **Command Documenation**
 
-The heatmap.sim_ command generates a heat map from data provided in either a .list or a .shared file.
+The heatmap.sim_ command generates a heat map from data provided in either a shared_ file, a phylip_ distance matrix, or a column_ distance matrix and a name_ file.  For calc parameter choices see: http://www.mothur.org/wiki/Calculators
 
+.. _shared: http://www.mothur.org/wiki/Shared_file
+.. _phylip: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix
+.. _column: http://www.mothur.org/wiki/Column-formatted_distance_matrix
+.. _name: http://www.mothur.org/wiki/Name_file
 .. _heatmap.sim: http://www.mothur.org/wiki/Heatmap.sim
 
  </help>