diff mothur/tools/mothur/chimera.slayer.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.slayer.xml	Tue Jun 07 17:32:23 2011 -0400
@@ -0,0 +1,100 @@
+<tool id="mothur_chimera_slayer" name="Chimera.slayer" version="1.15.0">
+ <description>Find putative chimeras using slayer</description>
+ <command interpreter="python">
+  mothur_wrapper.py 
+  --cmd='chimera.slayer'
+  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.slayer\.chimeras$:'$out_file,'^\S+\.slayer\.accnos$:'$out_accnos
+  --outputdir='$logfile.extra_files_path'
+  --tmpdir='${logfile.extra_files_path}/input'
+  --fasta=$fasta
+  --template=$alignment.template
+  #if $options.setby == 'user':
+   --search=$options.search
+   --window=$options.window
+   --increment=$options.increment
+   --match=$options.match
+   --mismatch=$options.mismatch
+   --numwanted=$options.numwanted
+   --parents=$options.parents
+   --minsim=$options.minsim
+   --mincov=$options.mincov
+   --iters=$options.iters
+   --minbs=$options.minbs
+   --minsnp=$options.minsnp
+   --divergence=$options.divergence
+  #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>
+  <conditional name="options">
+   <param name="setby" type="select" label="Slayer Options" help="">
+    <option value="default">Use default settings</option>
+    <option value="user">Manually set options</option>
+   </param>
+   <when value="default"/>
+   <when value="user">
+    <param name="search" type="select" label="search - Search method for finding the closest parent" help="">
+     <option value="distance" selected="true">distance</option>
+     <option value="kmer">kmer</option>
+     <option value="blast">blast</option>
+    </param>
+    <param name="window" type="integer" value="50" label="window - Window size for searching for chimeras (default 50)" />
+    <param name="increment" type="integer" value="5" label="increment - Increment for window slide on each iteration (default 5)" />
+    <param name="match" type="integer" value="5" label="match - Reward matched bases (default 5)"/>
+    <param name="mismatch" type="integer" value="-4" label="mismatch - Penalty for mismatched bases (default -4)"/>
+    <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="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)"/>
+   </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 ${on_string}: slayer.chimeras" />
+  <data format="accnos" name="out_accnos" label="${tool.name} on ${on_string}: slayer.accnos" />
+ </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.slayer_ command identifies putative chimeras using the slayer approach.
+
+.. _chimera.slayer: http://www.mothur.org/wiki/Chimera.slayer
+
+
+ </help>
+</tool>