diff mothur/tools/mothur/shhh.seqs.xml @ 18:697156806162

Mothur - update for Mothur version 1.23.0

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mothur/tools/mothur/shhh.seqs.xml	Tue Jan 17 11:22:44 2012 -0600
@@ -0,0 +1,56 @@
+<tool id="mothur_shhh_seqs" name="Shhh.seqs" version="1.23.0">
+ <description>Denoise program (Quince SeqNoise)</description>
+ <command interpreter="python">
+  mothur_wrapper.py 
+  #import re, os.path
+  --cmd='shhh.seqs'
+  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.shhh\.fasta$:'$shhh_fasta,'^\S+\.shhh\.names$:'$shhh_names,'^\S+\.shhh\.map$:'$shhh_map
+  --outputdir='$logfile.extra_files_path'
+  --fasta=$fasta
+  --name=$name
+  #if $group.__str__ != "None" and len($group.__str__) > 0:
+   --group=$group
+  #end if
+  #if $sigma.__str__ != '':
+   --sigma=$sigma 
+  #end if
+  --processors=8
+ </command>
+ <inputs>
+  <param name="fasta" type="data" format="fasta" label="fasta - Sequences" help=""/>
+  <param name="name" type="data" format="names" label="name - Sequences Name reference"/>
+  <param name="group" type="data" format="groups" optional="true" label="group - Sequences Name reference"/>
+  <param name="sigma" type="float" value="" optional="true" label="sigma" 
+         help="default .01">
+   <validator type="in_range" message="sigma between 0. and 1." min="0.0" max="1.0"/>
+  </param>
+ </inputs>
+ <outputs>
+  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
+  <data format_source="fasta" name="shhh_fasta" label="${tool.name} on ${on_string}: shhh.fasta"/>
+  <data format_source="names" name="shhh_names" label="${tool.name} on ${on_string}: shhh.names"/>
+  <data format_source="txt" name="shhh_map" label="${tool.name} on ${on_string}: shhh.map"/>
+ </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 shhh.seqs_ command is a mothur-based rewrite of Chris Quince's sequence denoting program, SeqNoise.  Schloss prefers pre.cluster for this operation.
+
+.. _shhh.seqs: http://www.mothur.org/wiki/Shhh.seqs
+
+
+ </help>
+</tool>