diff mothur/tools/mothur/chimera.check.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/chimera.check.xml	Tue Jun 07 17:32:23 2011 -0400
@@ -0,0 +1,84 @@
+<tool id="mothur_chimera_check" name="Chimera.check" version="1.15.0" force_history_refresh="True">
+ <description>Find putative chimeras using chimeraCheck</description>
+ <command interpreter="python">
+  mothur_wrapper.py 
+  --cmd='chimera.check'
+  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.chimeracheck\.chimeras$:'$out_file
+  --outputdir='$logfile.extra_files_path'
+  --fasta=$fasta
+  --template=$alignment.template
+  #if int($ksize.__str__) > 0:
+   --ksize=$ksize
+  #end if
+  #if int($increment.__str__) > 0:
+   --increment=$increment
+  #end if
+  #if $svg.gen == 'yes':
+   --svg=true
+   --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
+   --new_datasets='^(\S+)\.chimeracheck\.svg$:svg'
+   #if $name.__str__ != "None" and len($name.__str__) > 0:
+    --name='$name'
+   #end if
+  #end if
+ </command>
+ <inputs>
+  <param name="fasta" type="data" format="fasta" label="fasta - Candiate Sequences"/>
+  <conditional name="alignment">
+   <param name="source" type="select" label="Select Template from" help="">
+    <option value="hist">History</option>
+    <option value="ref">Cached Reference</option>
+   </param>
+   <when value="ref">
+    <param name="template" type="select" label="template - Select an alignment database " help="">
+     <options from_file="mothur_aligndb.loc">
+      <column name="name" index="0" />
+      <column name="value" index="1" />
+     </options>
+    </param>
+   </when>
+   <when value="hist">
+    <param name="template" type="data" format="fasta" label="template - Template to align with" help=""/>
+   </when>
+  </conditional>
+  <param name="ksize" type="integer" value="7" label="ksize - kmer length to determine differences between sequence fragments (uses default if &lt; 1)"/>
+  <param name="increment" type="integer" value="10" label="increment - Increment for window slide on each iteration (uses default if &lt; 1)"
+         help="Default is 10, but you may set it up to sequence length minus twice the window."/>
+  <conditional name="svg">
+   <param name="gen" type="select" label="svg - Generate a SVG plot for each query sequence" help="">
+    <option value="no" selected="true">No</option>
+    <option value="yes">Yes</option>
+   </param>
+   <when value="no"/>
+   <when value="yes">
+    <param name="name" type="data" format="names" optional="true" label="name - Names of queries for which to generate SVG plot"/>
+   </when>
+  </conditional>
+ </inputs>
+ <outputs>
+  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
+  <data format="txt" name="out_file" label="${tool.name} on ${on_string}: chimeracheck.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.check_ command identifies putative chimeras using the chimeraCheck approach. Note: following the RDP model this method does not determine whether or not a sequence is chimeric, but allows you to determine that based on the IS values produced.
+
+.. _chimera.check: http://www.mothur.org/wiki/Chimera.check
+
+
+ </help>
+</tool>