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

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

--- a/mothur/tools/mothur/pca.xml	Tue Jun 07 17:35:35 2011 -0400
+++ b/mothur/tools/mothur/pca.xml	Tue Jun 07 17:39:06 2011 -0400
@@ -1,5 +1,5 @@
-<tool id="mothur_pca" name="Pca" version="1.16.0">
- <description>generate principle components plot data</description>
+<tool id="mothur_pca" name="Pca" version="1.19.0">
+ <description>Principal Coordinate Analysis for a shared file</description>
  <command interpreter="python">
   mothur_wrapper.py 
   ## 98_sq_phylip_amazon.fn.unique.pca.axes
@@ -7,71 +7,36 @@
   --cmd='pca'
   --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.pca.axes$:'$pca_axes,'^\S+\.pca.loadings$:'$pca_loadings
   --outputdir='$logfile.extra_files_path'
-  --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 $input.groups.__str__ != "None" and len($input.groups.__str__) > 0:
-    --READ_groups='$input.groups'
-   #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
-   #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0:
-    --READ_groups='$input.groups'
-   #end if
+  #if isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('shared').__class__):
+   --shared=$otu
+  #elif isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('relabund').__class__):
+   --relabund=$otu
+  #end if
+  #if $label.__str__ != "None" and len($label.__str__) > 0:
+   --label='$label'
+  #end if
+  #if $groups.__str__ != "None" and len($groups.__str__) > 0:
+   --groups='$groups'
   #end if
   $metric
  </command>
  <inputs>
-  <conditional name="input">
-   <param name="source" type="select" label="Generate principle components 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"/>
-      </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 - 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" />
-      </options>
-     </param>
-   </when>
-  </conditional>
-  <param name="metric" type="boolean" truevalue="" falsevalue="--Metric=False" checked="true" label="metric - Calculate pearson correlation coefficient" />
+  <param name="otu" type="data" format="shared,relabund" label="shared,relabund - OTU Shared or Relabund file"/>
+  <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">
+    <column name="name" index="1"/>
+    <column name="value" index="1"/>
+    <filter type="unique_value" name="unq_grp" column="1" />
+   </options>
+  </param>
+  <param name="metric" type="boolean" truevalue="" falsevalue="--metric=False" checked="true" label="metric - Calculate pearson correlation coefficient" />
  </inputs>
  <outputs>
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
@@ -94,8 +59,10 @@
 
 **Command Documenation**
 
-The pca_ command generate principle components plot data.
+The pca_ command generate principle components plot data for a shared_ or relabund_ file.
 
+.. _shared: http://www.mothur.org/wiki/Shared_file
+.. _relabund: http://www.mothur.org/wiki/Get.relabund
 .. _pca: http://www.mothur.org/wiki/Pca
 
  </help>