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

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

--- a/mothur/tools/mothur/dist.shared.xml	Tue Jun 07 17:35:35 2011 -0400
+++ b/mothur/tools/mothur/dist.shared.xml	Tue Jun 07 17:39:06 2011 -0400
@@ -1,37 +1,28 @@
-<tool id="mothur_dist_shared" name="Dist.shared" version="1.16.0" force_history_refresh="True">
+<tool id="mothur_dist_shared" name="Dist.shared" version="1.19.0" force_history_refresh="True">
  <description>Generate a phylip-formatted dissimilarity distance matrix among multiple groups</description>
  <command interpreter="python">
   mothur_wrapper.py 
   --cmd='dist.shared'
   --result='^mothur.\S+\.logfile$:'$logfile
   --outputdir='$logfile.extra_files_path'
-  --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
-  #if len($output.__str__) > 0:
-   #if $output.__str__ == 'square':
-    --new_datasets='^\S+?\.([a-z]+\.(unique|[0-9.]*)\.(square|lt))\.dist$:square.dist'
-   #elif $output.__str__ == 'lt':
+  #if $as_datasets.__str__ == "yes":
+   --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
+   #if len($output.__str__) > 0:
+    #if $output.__str__ == 'square':
+     --new_datasets='^\S+?\.([a-z]+\.(unique|[0-9.]*)\.(square|lt))\.dist$:square.dist'
+    #elif $output.__str__ == 'lt':
+     --new_datasets='^\S+?\.([a-z]+\.(unique|[0-9.]*)\.(square|lt))\.dist$:lower.dist'
+    #end if
+   #else:
     --new_datasets='^\S+?\.([a-z]+\.(unique|[0-9.]*)\.(square|lt))\.dist$:lower.dist'
    #end if
-  #else:
-   --new_datasets='^\S+?\.([a-z]+\.(unique|[0-9.]*)\.(square|lt))\.dist$:lower.dist'
   #end if
-  --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 $input.groups.__str__ != "None" and len($input.groups.__str__) > 0:
-   --groups=$input.groups
+  #if $groups.__str__ != "None" and len($groups.__str__) > 0:
+   --groups=$groups
   #end if
   #if $calc.__str__ != "None" and len($calc.__str__) > 0:
    --calc=$calc
@@ -42,47 +33,21 @@
  </command>
  <inputs>
   <!-- list,group  or shared -->
-  <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"/>
-       <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_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="otu" type="data" format="shared" label="shared - OTU Shared"/>
+  <param name="label" type="select" label="label - OTU Labels to calculate" 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 analyze" 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="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
    <options from_file="mothur_calculators.loc">
      <column name="mult2" index="2"/>
@@ -91,10 +56,11 @@
      <filter type="static_value" name="mult2" column="2" value="shar" />
    </options>
   </param>
-  <param name="output" type="select" label="output - Distance Matrix Output Format" help="">
+  <param name="output" type="select" label="output - Distance Matrix Output Format" help="A Distance Matrix will be generated for each calculator label pair">
    <option value="lt">Phylip formatted Lower Triangle Matrix</option>
    <option value="square">Phylip formatted Square Matrix</option>
   </param>
+  <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Create a new history dataset for each distance matrix"/>
  </inputs>
  <outputs>
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
@@ -115,8 +81,10 @@
 
 **Command Documenation**
 
-The dist.shared_ command will generate a phylip-formatted distance matrix that describes the dissimilarity (1-similarity) among multiple groups.
+The dist.shared_ command will generate a phylip-formatted_distance_matrix_ that describes the dissimilarity (1-similarity) among multiple groups from a shared_ file. For calc parameter choices see: http://www.mothur.org/wiki/Calculators
 
+.. _phylip-formatted_distance_matrix: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix
+.. _shared: http://www.mothur.org/wiki/Shared_file
 .. _dist.shared: http://www.mothur.org/wiki/Dist.shared