diff mothur/tools/mothur/chimera.slayer.xml @ 1:fcc0778f6987

Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository

--- a/mothur/tools/mothur/chimera.slayer.xml	Tue Jun 07 17:32:23 2011 -0400
+++ b/mothur/tools/mothur/chimera.slayer.xml	Tue Jun 07 17:35:35 2011 -0400
@@ -1,4 +1,4 @@
-<tool id="mothur_chimera_slayer" name="Chimera.slayer" version="1.15.0">
+<tool id="mothur_chimera_slayer" name="Chimera.slayer" version="1.16.0">
  <description>Find putative chimeras using slayer</description>
  <command interpreter="python">
   mothur_wrapper.py 
@@ -7,7 +7,14 @@
   --outputdir='$logfile.extra_files_path'
   --tmpdir='${logfile.extra_files_path}/input'
   --fasta=$fasta
-  --template=$alignment.template
+  #if $alignment.source == 'self':
+   --template='self'
+   #if $alignment.name.__str__ != "None" and len($alignment.name.__str__) > 0:
+    --name=$alignment.name
+   #end if
+  #else:
+   --template=$alignment.template
+  #end if
   #if $options.setby == 'user':
    --search=$options.search
    --window=$options.window
@@ -22,7 +29,9 @@
    --minbs=$options.minbs
    --minsnp=$options.minsnp
    --divergence=$options.divergence
+   $options.trim
   #end if
+  --processors=2
  </command>
  <inputs>
   <param name="fasta" type="data" format="fasta" label="fasta - Candiate Sequences"/>
@@ -30,6 +39,7 @@
    <param name="source" type="select" label="Select 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="">
@@ -42,6 +52,9 @@
    <when value="hist">
     <param name="template" type="data" format="fasta" label="template - Template to align with" help=""/>
    </when>
+   <when value="self">
+    <param name="name" type="data" format="names" optional="true" label="names - Sequences Names"/>
+   </when>
   </conditional>
   <conditional name="options">
    <param name="setby" type="select" label="Slayer Options" help="">
@@ -67,6 +80,7 @@
     <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" />
    </when>
   </conditional>
  </inputs>