diff kmersvm/nullseq.xml @ 7:fd740d515502 draft default tip

Uploaded revised kmer-SVM to include modules from kmer-visual.

--- a/kmersvm/nullseq.xml	Mon Aug 20 21:42:29 2012 -0400
+++ b/kmersvm/nullseq.xml	Sun Jun 16 18:06:14 2013 -0400
@@ -7,9 +7,9 @@
   	-x $fold -r $rseed -g $gc_err -t $rpt_err $input $dbkey ${indices_path.fields.path}
   </command>
   <inputs>
-    <param name="fold" type="integer" value="1" label="# of Fold-Increase" />
-    <param name="gc_err" type="float" value="0.02" label="Allowable GC Error" />
-    <param name="rpt_err" type="float" value="0.02" label="Allowable Repeat Error" />
+    <param name="fold" type="integer" value="10" label="# of Fold-Increase" min="1" max="50" />
+    <param name="gc_err" type="float" value="0.02" label="Allowable GC Error" min="0.01" max="0.1"/>
+    <param name="rpt_err" type="float" value="0.02" label="Allowable Repeat Error" min="0.01" max="0.1"/>
     <param name="rseed" type="integer" value="1" label="Random Number Seed" />    
     <param format="interval" name="input" type="data" label="BED File of Positive Regions" />
       <validator type="unspecified_build" />
@@ -44,6 +44,16 @@
 **What it does**
   
 Takes an input BED file and generates a set of sequences for use as negative data (null sequences) in Train SVM similar in length, GC content and repeat fraction.  Uses random sampling for efficiency.
+
+----
+
+**Recommended Settings**
+
+Fold-Increase: Default is recommended, up to 50x positive set.
+
+GC Error, Repeat Error: Default is recommended.
+
+----
   
 **Parameters**