# HG changeset patch
# User galaxyp
# Date 1373647853 14400
# Node ID 777264a5d0ed71812c1c47d7dd07ae97d097e25f
# Parent  7401093cca6ca64d6bf592472b5c898b86168f52
Uploaded

diff -r 7401093cca6c -r 777264a5d0ed decoy_fasta.xml
--- a/decoy_fasta.xml	Thu Jun 20 16:32:33 2013 -0400
+++ b/decoy_fasta.xml	Fri Jul 12 12:50:53 2013 -0400
@@ -19,10 +19,10 @@
   </command>
 
   <inputs>
-    <param format="fasta" name="input" type="data" label="FASTA Input" />
-    <param name="include_original" type="boolean" truevalue="" falsevalue="-no_orig" label="Include original entries in output database" checked="True" />
+    <param format="fasta" name="input" type="data" label="FASTA Input" help="select input file from history in FASTA format" />
+    <param name="include_original" type="boolean" truevalue="" falsevalue="-no_orig" label="Include original entries in output database" checked="True" help="(default) keep checked in all standard searches" />
     <conditional name="freq_type">
-      <param name="advanced" type="select" label="Specify advanced decoy frequency options?">
+      <param name="advanced" type="select" label="Specify advanced decoy frequency options?" help=""Decoy Prefix" will name the prefix of each decoy sequence, "Frequency" will specify how many decoy sequences are created">
         <option value="no">No, just create database with one reversed sequence for every input sequence</option>
         <option value="yes">Yes, I want to specify multiple prefixes and specific frequencies</option>
       </param>
@@ -48,8 +48,7 @@
 **What it does**
 
 Given an input database, this tool will produce another database with
-reversed sequences to use as decoys for FDR estimation in protein
-search identification. This tool employs the decoyFASTA program from
+reversed sequences to use as decoys for False Discovery Rate (FDR) estimation in protein search identification. This tool employs the decoyFASTA program from
 the Transproteomic Pipeline.
 
 ------