--- a/peptide_prophet.xml	Tue Jul 01 11:16:41 2014 -0400
+++ b/peptide_prophet.xml	Thu Mar 26 19:55:19 2015 -0400
@@ -1,7 +1,8 @@
-<tool id="proteomics_search_peptide_prophet_1" name="Peptide Prophet" version="1.0.1">
+<tool id="proteomics_search_peptide_prophet_1" name="Peptide Prophet" version="1.1.0">
     <requirements>
-        <requirement type="package" version="1.3">protk</requirement>
-        <requirement type="package" version="4.6.3">trans_proteomic_pipeline</requirement>
+        <container type="docker">iracooke/protk-1.4.1</container>
+        <requirement type="package" version="1.4">protk</requirement>
+        <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement>
    </requirements>
    
 	<description>Calculate Peptide Prophet statistics on search results</description>
@@ -23,6 +24,16 @@
         $force_fit 
         $allow_alt_instruments 
         $maldi
+        $usedecoys
+        --decoy-prefix $decoy_prefix_string
+
+#if $experiment_label
+        --experiment-label $experiment_label
+#end if
+
+        --p-thresh $p_thresh
+
+        --threads $threads
 
 	</command>
 
@@ -44,18 +55,23 @@
 	<param name="force_fit" type="boolean" label="Force fitting" help="Bypasses automatic mixture model checks and forces fitting of a mixture model" truevalue="--force-fit" falsevalue=""/>
 	<param name="allow_alt_instruments" type="boolean" label="Allow multiple instrument types" help="Warning instead of exit with error if instrument types between runs is different" truevalue="--allow-alt-instruments" falsevalue=""/>
 	<param name="maldi" type="boolean" label="Maldi data" truevalue="-l" falsevalue=""/>
-	
+    <param name="usedecoys" type="boolean" label="Use decoys to pin down the negative distribution" truevalue="" falsevalue="--no-decoy"/>
+    <param name="decoy_prefix_string" help="Prefix string for decoy ids" type="text" value="decoy_" label="Decoy Prefix String" size="20"/>	
+    <param name="experiment_label" help="Used to commonly label all spectra from one experiment" type="text" value="" label="Experiment Label" size="20"/>
+    <param name="p_thresh" help="Peptides scoring less than this value are discarded" type="float" value="0.05" min="0" max="1" label="Probability Threshold"/>
+    <param name="threads" type="integer" value="1" min="0" label="Threads" help="Number of threads to use"/>
 	
   </inputs>
   <outputs>
     <data format="peptideprophet_pepxml" name="output" metadata_source="input_file" label="peptide_prophet.${input_file.display_name}.pep.xml" from_work_dir="peptide_prophet_output.pep.xml"/>
   </outputs>
 
+
 <help>
 
 **What it does**
 
-Given raw search engine scores as inputs this tool estimates the accuracy of peptide assignments.  From a practical perspective it estimates the probability that each peptide assignment is correct (providing probabilities as outputs), given raw scores (possibly on some arbitrary scale) as inputs. 
+Given raw search engine scores as inputs this tool estimates the accuracy of peptide assignments.
 
 ----