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

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

--- a/mothur/tools/mothur/collect.shared.xml	Tue Jun 07 17:35:35 2011 -0400
+++ b/mothur/tools/mothur/collect.shared.xml	Tue Jun 07 17:39:06 2011 -0400
@@ -1,4 +1,4 @@
-<tool id="mothur_collect_shared" name="Collect.shared" version="1.16.0" force_history_refresh="True">
+<tool id="mothur_collect_shared" name="Collect.shared" version="1.19.0" force_history_refresh="True">
  <description>Generate collector's curves for calculators on OTUs</description>
  <command interpreter="python">
   mothur_wrapper.py 
@@ -7,74 +7,40 @@
   --outputdir='$logfile.extra_files_path'
   --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
   --new_datasets='^\S+?\.(anderberg|braycurtis|jabund|jclass|jest|kstest|kulczynski|kulczynskicody|lennon|morisitahorn|ochiai|shared\.ace|shared\.chao|shared\.nseqs|shared\.sobs|sorabund|sorclass|sorest|thetan|thetayc|whittaker)$:tabular'
-  --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 $input.source == 'shared':
-   --READ_shared=$input.otu
-   #if $input.label.__str__ != "None" and len($input.label.__str__) > 0:
-    --READ_label='$input.label'
-   #end if
+  --shared=$otu
+  #if $label.__str__ != "None" and len($label.__str__) > 0:
+   --label='$label'
   #end if
   #if $calc.__str__ != "None" and len($calc.__str__) > 0:
-    --calc='$calc'
+   --calc='$calc'
   #end if
   $all
   #if float($freq.__str__) > 0:
    --freq=$freq
   #end if
-  #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0:
-   --groups=$input.groups
+  #if $groups.__str__ != "None" and len($groups.__str__) > 0:
+   --groups=$groups
   #end if
  </command>
  <inputs>
-  <conditional name="input">
-   <param name="source" type="select" label="Generate Collector Curvers 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 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>
-   </when>
-  </conditional>
-  <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
+  <param name="otu" type="data" format="shared" label="shared - OTU Shared"/>
+  <param name="label" type="select" label="label - OTU Label filter" multiple="true">
+   <help>To filter: select labels to include</help>
+   <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 filter (uses all groups if none are selected)" multiple="true">
+   <help>To filter: select select at least 2 groups</help>
+   <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="calc" type="select" label="calc - Calculators (Uses defaults if none are selected)" multiple="true">
    <options from_file="mothur_calculators.loc">
      <column name="mult" index="1"/>
      <column name="name" index="0"/>
@@ -105,8 +71,9 @@
 
 **Command Documenation**
 
-The collect.shared_ command generates collector's curves for calculators, which describe the similarity between communities or their shared richness. 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.
+The collect.shared_ command generates collector's curves for calculators_, which describe the similarity between communities or their shared richness. 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.  For calc parameter choices see: http://www.mothur.org/wiki/Calculators
 
+.. _calculators: http://www.mothur.org/wiki/Calculators
 .. _collect.shared: http://www.mothur.org/wiki/Collect.shared
 
  </help>