--- a/FalseDiscoveryRate.xml	Thu Apr 27 13:19:21 2017 -0400
+++ b/FalseDiscoveryRate.xml	Wed Aug 09 09:06:45 2017 -0400
@@ -1,7 +1,7 @@
 <?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
 <!--Proposed Tool Section: [ID Processing]-->
-<tool id="FalseDiscoveryRate" name="FalseDiscoveryRate" version="2.1.0">
+<tool id="FalseDiscoveryRate" name="FalseDiscoveryRate" version="2.2.0">
   <description>Estimates the false discovery rate on peptide and protein level using decoy searches.</description>
   <macros>
     <token name="@EXECUTABLE@">FalseDiscoveryRate</token>
@@ -15,20 +15,30 @@
 #if $param_in:
   -in $param_in
 #end if
-#if $param_in_target:
-  -in_target $param_in_target
-#end if
-#if $param_in_decoy:
-  -in_decoy $param_in_decoy
-#end if
 #if $param_out:
   -out $param_out
 #end if
-#if $param_proteins_only:
-  -proteins_only
+#if $param_PSM:
+  -PSM
+  #if " " in str($param_PSM):
+    "$param_PSM"
+  #else
+    $param_PSM
+  #end if
 #end if
-#if $param_peptides_only:
-  -peptides_only
+#if $param_protein:
+  -protein
+  #if " " in str($param_protein):
+    "$param_protein"
+  #else
+    $param_protein
+  #end if
+#end if
+#if $param_FDR_PSM:
+  -FDR:PSM $param_FDR_PSM
+#end if
+#if $param_FDR_protein:
+  -FDR:protein $param_FDR_protein
 #end if
 #if $param_algorithm_no_qvalues:
   -algorithm:no_qvalues
@@ -52,11 +62,17 @@
 #end if
 </command>
   <inputs>
-    <param name="param_in" type="data" format="idxml" optional="True" label="Identification input file containing a search against a concatenated sequence database" help="(-in) Either specify '-in' alone or 'in_target' together with 'in_decoy' as input"/>
-    <param name="param_in_target" type="data" format="idxml" optional="True" label="Identification input file containing a search against a target-only database" help="(-in_target) "/>
-    <param name="param_in_decoy" type="data" format="idxml" optional="True" label="Identification input file containing a search against a decoy-only database" help="(-in_decoy) "/>
-    <param name="param_proteins_only" display="radio" type="boolean" truevalue="-proteins_only" falsevalue="" checked="false" optional="True" label="If set only the FDR on protein level is calculated" help="(-proteins_only) "/>
-    <param name="param_peptides_only" display="radio" type="boolean" truevalue="-peptides_only" falsevalue="" checked="false" optional="True" label="If set only the FDR on peptide (PSM) level is calculated" help="(-peptides_only) "/>
+    <param name="param_in" type="data" format="idxml" optional="False" label="Identifications from searching a target-decoy database" help="(-in) "/>
+    <param name="param_PSM" display="radio" type="select" optional="False" value="true" label="Perform FDR calculation on PSM level" help="(-PSM) ">
+      <option value="true" selected="true">true</option>
+      <option value="false">false</option>
+    </param>
+    <param name="param_protein" display="radio" type="select" optional="False" value="true" label="Perform FDR calculation on protein level" help="(-protein) ">
+      <option value="true" selected="true">true</option>
+      <option value="false">false</option>
+    </param>
+    <param name="param_FDR_PSM" type="float" min="0.0" max="1.0" optional="True" value="1.0" label="Filter PSMs based on q-value (" help="(-PSM) e.g., 0.05 = 5% FDR, disabled for 1)"/>
+    <param name="param_FDR_protein" type="float" min="0.0" max="1.0" optional="True" value="1.0" label="Filter proteins based on q-value (" help="(-protein) e.g., 0.05 = 5% FDR, disabled for 1)"/>
     <param name="param_algorithm_no_qvalues" display="radio" type="boolean" truevalue="-algorithm:no_qvalues" falsevalue="" checked="false" optional="True" label="If 'true' strict FDRs will be calculated instead of q-values (the default)" help="(-no_qvalues) "/>
     <param name="param_algorithm_use_all_hits" display="radio" type="boolean" truevalue="-algorithm:use_all_hits" falsevalue="" checked="false" optional="True" label="If 'true' not only the first hit, but all are used (peptides only)" help="(-use_all_hits) "/>
     <param name="param_algorithm_split_charge_variants" display="radio" type="boolean" truevalue="-algorithm:split_charge_variants" falsevalue="" checked="false" optional="True" label="If 'true' charge variants are treated separately (for peptides of combined target/decoy searches only)" help="(-split_charge_variants) "/>