diff mothur/tools/mothur/rarefaction.single.xml @ 2:e990ac8a0f58

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

--- a/mothur/tools/mothur/rarefaction.single.xml	Tue Jun 07 17:35:35 2011 -0400
+++ b/mothur/tools/mothur/rarefaction.single.xml	Tue Jun 07 17:39:06 2011 -0400
@@ -1,4 +1,4 @@
-<tool id="mothur_rarefaction_single" name="Rarefaction.single" version="1.16.0" force_history_refresh="True">
+<tool id="mothur_rarefaction_single" name="Rarefaction.single" version="1.19.0" force_history_refresh="True">
  <description>Generate intra-sample rarefaction curves for OTUs</description>
  <command interpreter="python">
   mothur_wrapper.py 
@@ -6,11 +6,15 @@
   --result='^mothur.\S+\.logfile$:'$logfile
   --outputdir='$logfile.extra_files_path'
   --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
-  --new_datasets='^\S+?\.(((\S+)\.)?rarefaction)$:tabular'
-  --READ_cmd='read.otu'
-  --READ_list=$otu
-  #if $otu_group.__str__ != "None" and len($otu_group.__str__) > 0:
-   --READ_group='$otu_group'
+  --new_datasets='^\S+?\.(((\S+)\.)?(rarefaction|r_\w*))$:tabular'
+  #if isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('shared').__class__):
+   --shared=$otu
+  #elif isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('rabund').__class__):
+   --rabund=$otu
+  #elif isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('sabund').__class__):
+   --sabund=$otu
+  #elif isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('list').__class__):
+   --list=$otu
   #end if
   #if $label.__str__ != "None" and len($label.__str__) > 0:
    --label='$label'
@@ -30,8 +34,7 @@
   --processors=2
  </command>
  <inputs>
-  <param name="otu" type="data" format="list,shared" label="read.otu(list=) - OTU List"/>
-  <param name="otu_group" type="data" format="groups" optional="true" label="read.otu(lis =) - Group file for the OTU List"/>
+  <param name="otu" type="data" format="list,rabund,sabund,shared" label="list,rabund,sabund,shared - OTU List"/>
   <param name="label" type="select" label="label - OTU Labels" multiple="true">
    <options from_dataset="otu">
     <column name="name" index="0"/>
@@ -71,7 +74,7 @@
 
 **Command Documenation**
 
-The rarefaction.single_ command generates intra-sample rarefaction curves using a re-sampling without replacement approach. Rarefaction curves provide a way of comparing the richness observed in different samples.
+The rarefaction.single_ command generates intra-sample rarefaction curves using a re-sampling without replacement approach. Rarefaction curves provide a way of comparing the richness observed in different samples.  For calc parameter choices see: http://www.mothur.org/wiki/Calculators
 
 .. _rarefaction.single: http://www.mothur.org/wiki/Rarefaction.single