diff mothur/tools/mothur/chimera.slayer.xml @ 2:e990ac8a0f58

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

--- a/mothur/tools/mothur/chimera.slayer.xml	Tue Jun 07 17:35:35 2011 -0400
+++ b/mothur/tools/mothur/chimera.slayer.xml	Tue Jun 07 17:39:06 2011 -0400
@@ -1,4 +1,4 @@
-<tool id="mothur_chimera_slayer" name="Chimera.slayer" version="1.16.0">
+<tool id="mothur_chimera_slayer" name="Chimera.slayer" version="1.19.0">
  <description>Find putative chimeras using slayer</description>
  <command interpreter="python">
   mothur_wrapper.py 
@@ -8,12 +8,12 @@
   --tmpdir='${logfile.extra_files_path}/input'
   --fasta=$fasta
   #if $alignment.source == 'self':
-   --template='self'
+   --reference='self'
    #if $alignment.name.__str__ != "None" and len($alignment.name.__str__) > 0:
     --name=$alignment.name
    #end if
   #else:
-   --template=$alignment.template
+   --reference=$alignment.template
   #end if
   #if $options.setby == 'user':
    --search=$options.search
@@ -30,19 +30,20 @@
    --minsnp=$options.minsnp
    --divergence=$options.divergence
    $options.trim
+   $options.split
   #end if
   --processors=2
  </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="">
+   <param name="source" type="select" label="Select Reference Template from" help="">
     <option value="hist">History</option>
     <option value="ref">Cached Reference</option>
     <option value="self">Self - Use abundant sequences from the input Candiate Sequences fasta </option>
    </param>
    <when value="ref">
-    <param name="template" type="select" label="template - Select an alignment database " help="">
+    <param name="template" type="select" label="reference - Select an alignment database " help="">
      <options from_file="mothur_aligndb.loc">
       <column name="name" index="0" />
       <column name="value" index="1" />
@@ -50,7 +51,7 @@
     </param>
    </when>
    <when value="hist">
-    <param name="template" type="data" format="fasta" label="template - Template to align with" help=""/>
+    <param name="template" type="data" format="fasta" label="reference - Reference to align with" help=""/>
    </when>
    <when value="self">
     <param name="name" type="data" format="names" optional="true" label="names - Sequences Names"/>
@@ -75,12 +76,13 @@
     <param name="numwanted" type="integer" value="15" label="numwanted - Number of potential parents to to compare with query sequence (default 15)"/>
     <param name="parents" type="integer" value="3" label="parents - Number of potential parents to investigate from the numwanted best matches"/>
     <param name="minsim" type="integer" value="90" label="minsim - Minimum similarity % between the query and parent (default 90)"/>
-    <param name="mincov" type="integer" value="70" label="mincov - Minimum coverage % of closest matches in template and the query (default 70)"/>
+    <param name="mincov" type="integer" value="70" label="mincov - Minimum coverage % of closest matches in reference and the query (default 70)"/>
     <param name="iters" type="integer" value="100" label="iters - Number of bootstrap iterations to try (default 100)"/>
     <param name="minbs" type="integer" value="90" label="minbs - Minimum bootstrap support % for calling a sequence chimeric (default 90)"/>
     <param name="minsnp" type="integer" value="100" label="minsnp - Percent of SNPs to sample on each side of breakpoint for computing bootstrap support (default 100)"/>
     <param name="divergence" type="float" value="1.007" label="divergence - Divergence cutoff for chimera determination (default 1.007)"/>
     <param name="trim" type="boolean" truevalue="--trim=True" falsevalue="" checked="false" label="trim - include chimeric sequences trimmed to their longest peice" />
+    <param name="split" type="boolean" truevalue="--split=True" falsevalue="" checked="false" label="split - detect tri- and quadmeras" help="if a sequence comes back as non-chimeric, mothur will test the two sides to see if they are chimeric."/>
    </when>
   </conditional>
  </inputs>
@@ -107,6 +109,20 @@
 
 The chimera.slayer_ command identifies putative chimeras using the slayer approach.
 
+ChimeraSlayer_ is a chimeric sequence detection utility, compatible with near-full length Sanger sequences and shorter 454-FLX sequences (~500 bp).
+
+Chimera Slayer involves the following series of steps that operate to flag chimeric 16S rRNA sequences: 
+
+ (A) the ends of a query sequence are searched against an included database of reference chimera-free 16S sequences to identify potential parents of a chimera; 
+ (B) candidate parents of a chimera are selected as those that form a branched best scoring alignment to the NAST-formatted query sequence; 
+ (C) the NAST alignment of the query sequence is improved in a `chimera-aware' profile-based NAST realignment to the selected reference parent sequences; and 
+ (D) an evolutionary framework is used to flag query sequences found to exhibit greater sequence homology to an in silico chimera formed between any two of the selected reference parent sequences.
+
+Note: 
+It is not recommended to blindly discard all sequences flagged as chimeras. Some may represent naturally formed chimeras that do not represent PCR artifacts. Sequences flagged may warrant further investigation.
+
+
+.. _ChimeraSlayer: http://microbiomeutil.sourceforge.net/
 .. _chimera.slayer: http://www.mothur.org/wiki/Chimera.slayer