diff mothur/tools/mothur/classify.seqs.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/classify.seqs.xml	Tue Jun 07 17:32:23 2011 -0400
@@ -0,0 +1,138 @@
+<tool id="mothur_classify_seqs" name="Classify.seqs" version="1.15.0">
+ <description>Assign sequences to taxonomy</description>
+ <command interpreter="python">
+  mothur_wrapper.py 
+  --cmd='classify.seqs'
+  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.taxonomy$:'$taxonomy_out,'^\S+\.tax\.summary$:'$tax_summary
+  --outputdir='$logfile.extra_files_path'
+  --fasta=$fasta
+  --template=$alignment.template
+  --taxonomy=$tax.taxonomy
+  #if $classify.method == 'bayesian': 
+   --method=$classify.method
+   #if 15 >= int($classify.ksize.__str__) >= 4:
+    --ksize=$classify.ksize
+   #end if
+   #if int($classify.iters.__str__) > 0:
+    --iters=$classify.iters
+   #end if
+   #if 100 >= int($classify.cutoff.__str__) > 0:
+    --cutoff=$classify.cutoff
+   #end if
+   $classify.probs
+  #elif $classify.method == 'knn': 
+   --method=$classify.method
+   --numwanted=$classify.search.numwanted
+   #if $classify.search.algorithm == 'kmer':
+    --search=$classify.search.algorithm
+    --ksize=$classify.search.ksize
+   #elif $classify.search.algorithm == 'blast':
+    --search=$classify.search.algorithm
+    --match=$classify.search.match
+    --mismatch=$classify.search.mismatch
+    --gapopen=$classify.search.gapopen
+    --gapextend=$classify.search.gapextend
+   #elif $classify.knn.search == 'suffix':
+    --search=$classify.search.algorithm
+   #elif $classify.search.algorithm == 'distance':
+    --search=$classify.search.algorithm
+   #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>
+  <conditional name="tax">
+   <param name="source" type="select" label="Select Taxonomy from" help="">
+    <option value="ref">Cached Reference</option>
+    <option value="hist">History</option>
+   </param>
+   <when value="ref">
+    <param name="taxonomy" type="select" format="taxonomy" label="taxonomy - Taxonomy reference">
+     <options from_file="mothur_taxonomy.loc">
+      <column name="name" index="0" />
+      <column name="value" index="1" />
+     </options>
+    </param>
+   </when>
+   <when value="hist">
+    <param name="taxonomy" type="data" format="taxonomy" label="taxonomy - Taxonomy reference"/>
+   </when>
+  </conditional>
+  <conditional name="classify">
+   <param name="method" type="select" label="method - Select a classification method" help="">
+    <option value="bayesian">Bayesian (default)</option>
+    <option value="knn">K-Nearest Neighbor (knn)</option>
+   </param>
+   <when value="bayesian">
+    <param name="ksize" type="integer" value="8" label="ksize - kmer length between 5 and 12"/>
+    <param name="iters" type="integer" value="100" label="iters - iterations to do when calculating the bootstrap confidence score"/>
+    <param name="cutoff" type="integer" value="60" label="cutoff - Confindence percentage cutoff between 1 and 100"/>
+    <param name="probs" type="boolean" falsevalue="--probs=false" truevalue="" checked="true" label="probs - Show probabilities"/>
+   </when>
+   <when value="knn">
+    <param name="numwanted" type="integer" value="10" label="numwanted - "/>
+    <conditional name="search">
+     <param name="algorithm" type="select" label="algorithm - " help="">
+      <option value="kmer">Kmer (default)</option>
+      <option value="blast">BLAST</option>
+     </param>
+     <when value="kmer">
+      <param name="ksize" type="integer" value="8" label="ksize - kmer length between 5 and 12"/>
+     </when>
+     <when value="blast">
+      <param name="match" type="integer" value="1" label="match - Pairwise alignment reward for a match"/>
+      <param name="mismatch" type="integer" value="-1" label="mismatch - Pairwise alignment penalty for a mismatch"/>
+      <param name="gapopen" type="integer" value="-2" label="gapopen - Pairwise alignment penalty for opening a gap"/>
+      <param name="gapextend" type="integer" value="-1" label="gapextend - Pairwise alignment penalty for extending a gap"/>
+     </when>
+     <when value="suffix"/>
+     <when value="distance"/>
+    </conditional>
+   </when>
+  </conditional>
+ </inputs>
+ <outputs>
+  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
+  <data format="taxonomy" name="taxonomy_out" label="${tool.name} on ${on_string}: taxonomy" />
+  <data format="tax.summary" name="tax_summary" label="${tool.name} on ${on_string}: tax.summary" />
+ </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 classify.seqs_ command assigns sequences to chosen taxonomy outline.
+
+.. _classify.seqs: http://www.mothur.org/wiki/Classify.seqs
+
+
+ </help>
+</tool>