diff mothur/tools/mothur/chimera.perseus.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/chimera.perseus.xml	Tue Jan 17 11:22:44 2012 -0600
@@ -0,0 +1,58 @@
+<tool id="mothur_chimera_perseus" name="Chimera.perseus" version="1.23.0" >
+ <description>Find putative chimeras using chimeraCheck</description>
+ <command interpreter="python">
+  mothur_wrapper.py 
+  --cmd='chimera.perseus'
+  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.perseus\.chimeras?$:'$out_file
+  --outputdir='$logfile.extra_files_path'
+  --fasta=$fasta
+  --name=$name
+  #if $group.__str__ != "None" and len($group.__str__) > 0:
+   --group='$group'
+  #end if
+  #if $alpha.__str__ != '':
+   --alpha=$alpha
+  #end if
+  #if $beta.__str__ != '':
+   --beta=$beta
+  #end if
+  #if $cutoff.__str__ != '':
+   --cutoff=$cutoff
+  #end if
+  --processors=8
+ </command>
+ <inputs>
+  <param name="fasta" type="data" format="align" label="fasta - Candiate Aligned Sequences"/>
+  <param name="name" type="data" format="names" label="name - Names "/>
+  <param name="group" type="data" format="group" optional="true" label="group - Sequences Name reference"/>
+  <param name="alpha" type="float" value="-5.54" optional="true" label="alpha" help="The default is -5.54"/>
+  <param name="beta" type="float" value="0.33" optional="true" label="beta" help="The default is 0.33"/>
+  <param name="cutoff" type="float" value="0.50" optional="true" label="cutoff" help="The default is 0.50"/>
+ </inputs>
+ <outputs>
+  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
+  <data format="tabular" name="out_file" label="${tool.name} on ${on_string}: perseus.chimeras" />
+ </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 chimera.perseus_ command reads a fasta and name file, and outputs potentially chimeric sequences.
+
+.. _chimera.perseus: http://www.mothur.org/wiki/Chimera.perseus
+
+
+ </help>
+</tool>