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

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

--- a/mothur/tools/mothur/chimera.check.xml	Tue Jun 07 17:35:35 2011 -0400
+++ b/mothur/tools/mothur/chimera.check.xml	Tue Jun 07 17:39:06 2011 -0400
@@ -1,4 +1,4 @@
-<tool id="mothur_chimera_check" name="Chimera.check" version="1.16.0" force_history_refresh="True">
+<tool id="mothur_chimera_check" name="Chimera.check" version="1.19.0" force_history_refresh="True">
  <description>Find putative chimeras using chimeraCheck</description>
  <command interpreter="python">
   mothur_wrapper.py 
@@ -6,7 +6,7 @@
   --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.chimeracheck\.chimeras$:'$out_file
   --outputdir='$logfile.extra_files_path'
   --fasta=$fasta
-  --template=$alignment.template
+  --reference=$alignment.template
   #if int($ksize.__str__) > 0:
    --ksize=$ksize
   #end if
@@ -15,23 +15,25 @@
   #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'
+   #if $svg.name.__str__ != "None" and len($svg.name.__str__) > 0:
+    --name='$svg.name'
+   #end if
+   #if $svg.as_datasets.__str__ == "yes":
+    --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
+    --new_datasets='^(\S+)\.chimeracheck\.svg$:svg'
    #end if
   #end if
   --processors=2
  </command>
  <inputs>
-  <param name="fasta" type="data" format="fasta" label="fasta - Candiate Sequences"/>
+  <param name="fasta" type="data" format="align" label="fasta - Candiate Aligned 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>
    </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" />
@@ -39,7 +41,7 @@
     </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>
   </conditional>
   <param name="ksize" type="integer" value="7" label="ksize - kmer length to determine differences between sequence fragments (uses default if &lt; 1)"/>
@@ -53,6 +55,7 @@
    <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"/>
+    <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Create a new history dataset for each image"/>
    </when>
   </conditional>
  </inputs>
@@ -76,7 +79,9 @@
 
 **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.
+The chimera.check_ command identifies putative chimeras using the chimeraCheck approach. It looks at distance of left side of query to it's closest match + distance of right side of query to it's closest match - distance of whole query and its closest match over several windows.  
+
+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