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

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

--- a/mothur/tools/mothur/collect.single.xml	Tue Jun 07 17:35:35 2011 -0400
+++ b/mothur/tools/mothur/collect.single.xml	Tue Jun 07 17:39:06 2011 -0400
@@ -1,16 +1,20 @@
-<tool id="mothur_collect_single" name="Collect.single" version="1.16.0" force_history_refresh="True">
- <description>Summary of calculator values for OTUs</description>
+<tool id="mothur_collect_single" name="Collect.single" version="1.19.0" force_history_refresh="True">
+ <description>Generate collector's curves for OTUs</description>
  <command interpreter="python">
   mothur_wrapper.py 
   --cmd='collect.single'
   --result='^mothur.\S+\.logfile$:'$logfile
   --outputdir='$logfile.extra_files_path'
   --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
-  --new_datasets='^\S+\.(\S+)$:tabular'
-  --READ_cmd='read.otu'
-  --READ_list=$otu
-  #if $otu_group.__str__ != "None" and len($otu_group.__str__) > 0:
-   --READ_group='$otu_group'
+  --new_datasets='^\S+?\.(\S+)$: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='$label'
@@ -24,13 +28,12 @@
   #if int($size.__str__) > 0:
    --size=$size
   #end if
- </command>
   #if float($freq.__str__) > 0:
    --freq=$freq
   #end if
+ </command>
  <inputs>
-  <param name="otu" type="data" format="list,shared" label="read.otu(list=) - OTU List"/>
-  <param name="otu_group" type="data" format="groups" optional="true" label="read.otu(group=) - Group file for the OTU List"/>
+  <param name="otu" type="data" format="list,rabund,sabund,shared" label="list,rabund,sabund,shared - OTU List"/>
   <param name="label" type="select" label="label - OTU Labels" multiple="true">
    <options from_dataset="otu">
     <column name="name" index="0"/>
@@ -46,9 +49,11 @@
      <filter type="static_value" name="mult" column="1" value="single" />
    </options>
   </param>
-  <param name="abund" type="integer" value="10" label="abund - ACE Estimator threshold for abundant versus rare OTUs"/>
-  <param name="size" type="integer" value="0" label="size - "/>
-  <param name="freq" type="float" value="0.0" label="freq - "/>
+  <param name="abund" type="integer" value="10" label="abund - ACE Estimator threshold for abundant versus rare OTUs (default 10)"/>
+  <param name="size" type="integer" value="0" label="size - sample size for OTU prediction (ignored if &lt; 1)" 
+    help="By default these calculators will base the prediction on a sample that is the same size as the initial sampling"/>
+  <param name="freq" type="float" value="0.0" label="freq - frequency for output (default is every 100 sequences)" 
+    help="Use a decimal between 0 and 1 to set the frequency as a percentage of the number of sequences"/>
  </inputs>
  <outputs>
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
@@ -69,8 +74,9 @@
 
 **Command Documenation**
 
-The collect.single_ command generates collector's curves using calculators, that describe the richness, diversity, and other features of individual samples. Collector's curves describe how richness or diversity change as you sample additional individuals. If a collector's curve becomes parallel to the x-axis, you can be reasonably confident that you have done a good job of sampling and can trust the last value in the curve. Otherwise, you need to keep sampling.
+The collect.single_ command generates collector's curves using calculators_, that describe the richness, diversity, and other features of individual samples. Collector's curves describe how richness or diversity change as you sample additional individuals. If a collector's curve becomes parallel to the x-axis, you can be reasonably confident that you have done a good job of sampling and can trust the last value in the curve. Otherwise, you need to keep sampling.  For calc parameter choices see: http://www.mothur.org/wiki/Calculators
 
+.. _calculators: http://www.mothur.org/wiki/Calculators
 .. _collect.single: http://www.mothur.org/wiki/Collect.single
 
  </help>