diff mothur/tools/mothur/consensus.seqs.xml @ 0:3202a38e44d9

Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mothur/tools/mothur/consensus.seqs.xml	Tue Jun 07 17:32:23 2011 -0400
@@ -0,0 +1,73 @@
+<tool id="mothur_consensus_seqs" name="Consensus.seqs" version="1.15.0" force_history_refresh="True">
+ <description>Find a consensus sequence for each OTU or phylotype</description>
+ <command interpreter="python">
+  mothur_wrapper.py 
+  --cmd='consensus.seqs'
+  --outputdir='$logfile.extra_files_path'
+  --fasta=$fasta
+  #if $name.__str__ != "None" and len($name.__str__) > 0:
+   --name=$name
+  #end if
+  #if $otu.use == 'yes':
+   --list=$otu.list
+   #if $otu.label.__str__ != "None" and len($otu.label.__str__) > 0:
+    --label='$otu.label'
+   #end if
+   --result='^mothur.\S+\.logfile$:'$logfile
+   --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
+   --new_datasets='^\S+?\.(((unique|[0-9.]*)\.)?cons\.fasta)$:fasta','^\S+?\.(((unique|[0-9.]*)\.)?cons\.names)$:names','^\S+?\.(((unique|[0-9.]*)\.)?cons\.summary)$:tabular'
+  #else
+   --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.cons\.summary$:'$summary,'^\S+\.cons\.fasta$:'$cons_fasta
+  #end if
+ </command>
+ <inputs>
+  <param name="fasta" type="data" format="fasta" label="fasta - Sequences to Bin" help="Sequences must be the same length"/>
+  <param name="name" type="data" format="names" optional="true" label="name - Sequences Name reference"/>
+  <conditional name="otu">
+   <param name="use" type="select" label="Consensus sequence">
+    <option value="no">Single consensus sequence</option>
+    <option value="yes">Consensus sequence for each OTU in list</option>
+   </param>
+   <when value="no"/>
+   <when value="yes">
+    <param name="list" type="data" format="list" label="list - OTU List"/>
+    <param name="label" type="select" optional="true" label="label - OTU Labels" multiple="true">
+     <options from_dataset="list">
+      <column name="name" index="0"/>
+      <column name="value" index="0"/>
+     </options>
+    </param>
+   </when>
+  </conditional> <!-- -->
+ </inputs>
+ <outputs>
+  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
+  <data format="tabular" name="summary" label="${tool.name} on ${on_string}: cons.summary">
+   <filter>otu['use'] == 'no'</filter>
+  </data>
+  <data format="fasta" name="cons_fasta" label="${tool.name} on ${on_string}: cons.fasta">
+   <filter>otu['use'] == 'no'</filter>
+  </data>
+ </outputs>
+ <requirements>
+  <requirement type="binary">mothur</requirement>
+ </requirements>
+ <tests>
+ </tests>
+ <help>
+**Mothur Overview**
+
+Mothur_, initiated by Dr. Patrick Schloss and his software development team
+in the Department of Microbiology and Immunology at The University of Michigan,
+provides bioinformatics for the microbial ecology community.
+
+.. _Mothur: http://www.mothur.org/wiki/Main_Page
+
+**Command Documenation**
+
+The consensus.seqs_ command can be used in 2 ways: create a consensus sequence from a fastafile, or with a listfile create a consensus sequence for each otu. Sequences must be aligned.
+
+.. _consensus.seqs: http://www.mothur.org/wiki/Consensus.seqs
+
+ </help>
+</tool>