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

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

--- a/mothur/tools/mothur/heatmap.bin.xml	Tue Jun 07 17:35:35 2011 -0400
+++ b/mothur/tools/mothur/heatmap.bin.xml	Tue Jun 07 17:39:06 2011 -0400
@@ -1,30 +1,31 @@
-<tool id="mothur_heatmap_bin" name="Heatmap.bin" version="1.16.0"  force_history_refresh="True">
+<tool id="mothur_heatmap_bin" name="Heatmap.bin" version="1.19.0"  force_history_refresh="True">
  <description>Generate a heatmap for OTUs</description>
  <command interpreter="python">
   mothur_wrapper.py 
   --cmd='heatmap.bin'
   --result='^mothur.\S+\.logfile$:'$logfile
   --outputdir='$logfile.extra_files_path'
-  --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
-  --new_datasets='^\S+?\.((\S+)\.(unique|[0-9.]*)\.heatmap\.bin\.svg)$: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 $input.label.__str__ != "None" and len($input.label.__str__) > 0:
-    --READ_label='$input.label'
-   #end if
-  #elif $input.source == 'shared':
-   --READ_relabund=$input.otu
-   #if $input.label.__str__ != "None" and len($input.label.__str__) > 0:
-    --READ_label='$input.label'
-   #end if
+  #if $as_datasets.__str__ == "yes":
+   --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
+   --new_datasets='^\S+?\.((\S+)\.(unique|[0-9.]*)\.heatmap\.bin\.svg)$:svg'
   #end if
-  #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0:
+  #if isinstance($input.otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('shared').__class__):
+   --shared=$input.otu
+  #elif isinstance($input.otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('rabund').__class__):
+   --rabund=$input.otu
+  #elif isinstance($input.otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('sabund').__class__):
+   --sabund=$input.otu
+  #elif isinstance($input.otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('list').__class__):
+   --list=$input.otu
+  #elif isinstance($input.otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('relabund').__class__):
+   --relabund=$input.otu
+  #end if
+  #if $input.has_groups != 'no' and $input.groups.__str__ != "None" and len($input.groups.__str__) > 0:
    --groups=$input.groups
   #end if
+  #if $input.label.__str__ != "None" and len($input.label.__str__) > 0:
+   --label='$input.label'
+  #end if
   #if $scale.__str__ != "None" and len($scale.__str__) > 0:
    --scale='$scale'
   #end if
@@ -39,42 +40,54 @@
   #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="relabund">OTU Relative Abundance</option>
+  <conditional name="input">
+   <param name="has_groups" type="select" label="Generate Heatmap for">
+    <option value="default">shared  or relabund</option>
+    <option value="no">list, rabund, sabund</option>
+    <option value="yes">list, rabund, sabund with groups</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="default">
+     <param name="otu" type="data" format="shared,relabund" label="shared,relabund - OTU List"/>
+     <param name="groups" type="select" label="groups - Groups to condider" 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>
      <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">
+   </when>
+   <when value="no">
+     <param name="otu" type="data" format="list,rabund,sabund" label="list,rabund,sabund - 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>
+   </when>
+   <when value="yes">
+     <param name="otu" type="data" format="list,rabund,sabund" label="list,rabund,sabund - OTU List"/>
+     <param name="otu_group" type="data" format="groups" label="read.otu(group) - Group file for the OTU List"/>
+     <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>
-   </when>
-   <when value="relabund">
-     <param name="otu" type="data" format="relabund" label="read.otu(relabund=) - OTU Relative Abundance"/>
      <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" />
+       <filter type="unique_value" name="unq_lbl" column="0" />
       </options>
      </param>
    </when>
@@ -88,11 +101,12 @@
   <param name="sorted" type="select" label="sorted - Sort heatmap">
    <option value="">By shared</option>
    <option value="none">Don't sort</option>
-   <option value="totalotu">By Total OTUs</option>
-   <option value="totalgroup">By Total Groups</option>
+   <option value="topotu">By Total OTUs</option>
+   <option value="topgroup">By Total Groups</option>
   </param>
   <param name="numotu" type="integer" value="0" label="numotu - Limit the number of OTUs displayed (ignored if 0)"/>
   <param name="fontsize" type="integer" value="24" label="fontsize - Fontsize (default is 24)"/>
+  <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" />
@@ -113,8 +127,10 @@
 
 **Command Documenation**
 
-The heatmap.bin_ command generates a heat map from data provided in either a .list or a .shared file.
+The heatmap.bin_ command generates a heat map from data provided in either a list_ or a shared_ file.
 
+.. _list: http://www.mothur.org/wiki/List_file
+.. _shared: http://www.mothur.org/wiki/Shared_file
 .. _heatmap.bin: http://www.mothur.org/wiki/Heatmap.bin
 
  </help>