diff mothur/tools/mothur/get.oturep.xml @ 2:e990ac8a0f58

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

--- a/mothur/tools/mothur/get.oturep.xml	Tue Jun 07 17:35:35 2011 -0400
+++ b/mothur/tools/mothur/get.oturep.xml	Tue Jun 07 17:39:06 2011 -0400
@@ -1,12 +1,14 @@
-<tool id="mothur_get_oturep" name="Get.oturep" version="1.16.0"  force_history_refresh="True">
+<tool id="mothur_get_oturep" name="Get.oturep" version="1.19.0"  force_history_refresh="True">
  <description>Generate a fasta with a representative sequence for each OTU</description>
  <command interpreter="python">
   mothur_wrapper.py 
   --cmd='get.oturep'
   --result='^mothur.\S+\.logfile$:'$logfile
   --outputdir='$logfile.extra_files_path'
-  --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
-  --new_datasets='^\S+?\.((unique|[0-9.]*)(\S+)\.rep\.fasta)$:fasta','^\S+?\.((unique|[0-9.]*)(\S+)\.rep\.names)$:names'
+  #if $as_datasets.__str__ == "yes":
+   --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
+   --new_datasets='^\S+?\.((unique|[0-9.]*)(\S+)\.rep\.fasta)$:fasta','^\S+?\.((unique|[0-9.]*)(\S+)\.rep\.names)$:names'
+  #end if
   --fasta=$fasta
   --list=$otu_list
   #if $input.source == 'column':
@@ -21,8 +23,13 @@
   #if $label.__str__ != "None" and len($label.__str__) > 0:
    --label='$label'
   #end if
-  #if $groups.__str__ != "None" and len($groups.__str__) > 0:
-   --groups=$groups
+  #if $pick.type == 'yes':
+   #if $pick.group.__str__ != "None" and len($pick.group.__str__) > 0:
+    --group=$pick.group
+   #end if
+   #if $pick.groups.__str__ != "None" and len($pick.groups.__str__) > 0:
+    --groups=$pick.groups
+   #end if
   #end if
   #if $sorted.__str__ != "None" and len($sorted.__str__) > 0:
    --sorted=$sorted
@@ -34,26 +41,36 @@
   <param name="fasta" type="data" format="fasta" label="fasta - Fasta"/>
   <param name="otu_list" type="data" format="list" label="list - OTU List"/>
   <conditional name="input">
-   <param name="source" type="select" label="Distance Matrix">
+   <param name="source" type="select" label="Distance Matrix Format">
     <option value="column">Pairwise Column Distance Matrix</option>
     <option value="phylip">Phylip Distance Matrix</option>
    </param>
    <when value="column">
-       <param name="dist" type="data" format="pair.dist" label="column - Distance Matrix"/>
-       <param name="name" type="data" format="names" label="name - Sequences Name reference"/>
+    <param name="dist" type="data" format="pair.dist" label="column - Distance Matrix"/>
+    <param name="name" type="data" format="names" label="name - Sequences Name reference"/>
    </when>
    <when value="phylip">
-       <param name="dist" type="data" format="lower.dist,square.dist" label="phylip - Distance Matrix"/>
-       <param name="name" type="data" format="names" optional="true" label="name - Names"/>
+    <param name="dist" type="data" format="lower.dist,square.dist" label="phylip - Distance Matrix"/>
+    <param name="name" type="data" format="names" optional="true" label="name - Names"/>
    </when>
   </conditional>
-  <param name="group" type="data" format="groups" optional="true" label="group - Group file for the OTU List"/>
-  <param name="groups" type="select" label="groups - Groups to consider" multiple="true">
-   <options from_dataset="group">
-    <column name="name" index="1"/>
-    <column name="value" index="1"/>
-   </options>
-  </param>
+  <conditional name="pick">
+   <param name="type" type="select" label="Parse a group file into abundant and rare groups?" help="">
+    <option value="no" selected="true">No</option>
+    <option value="yes">Yes</option>
+   </param>
+   <when value="no"/>
+   <when value="yes">
+    <param name="group" type="data" format="groups" label="group - Group file for the OTU List"/>
+    <param name="groups" type="select" label="groups - Group Selection (all used if none are selected)" multiple="true">
+     <options from_dataset="group">
+      <column name="name" index="1"/>
+      <column name="value" index="1"/>
+      <filter type="unique_value" name="unq_grp" column="1" />
+     </options>
+    </param>
+   </when>
+  </conditional> <!-- pick -->
   <param name="label" type="select" label="label - OTU Labels" multiple="true">
    <options from_dataset="otu_list">
     <column name="name" index="0"/>
@@ -67,8 +84,8 @@
    <option value="size">Bin Size</option>
    <option value="group">Group</option>
   </param>
-
   <param name="large" type="boolean" checked="false" truevalue="--large=true" falsevalue="" label="large - Distance Matrix is very Large"/>
+  <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Create a new history dataset for each label"/>
  </inputs>
  <outputs>
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />