--- a/FalseDiscoveryRate.xml	Mon Oct 13 10:18:22 2014 -0400
+++ b/FalseDiscoveryRate.xml	Wed Jan 27 10:06:49 2016 -0500
@@ -1,51 +1,77 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<tool id="FalseDiscoveryRate" name="FalseDiscoveryRate" version="1.12.0">
-  <description>Estimates the false discovery rate on peptide and protein level using decoy searches.</description>
-  <macros>
-    <token name="@EXECUTABLE@">FalseDiscoveryRate</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="stdio"/>
-  <expand macro="requirements"/>
-  <command>FalseDiscoveryRate
+<?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="2.0.0">
+    <description>Estimates the false discovery rate on peptide and protein level using decoy searches.</description>
+    <macros>
+      <token name="@EXECUTABLE@">FalseDiscoveryRate</token>
+      <import>macros.xml</import>
+    </macros>
+    <expand macro="references"/>
+    <expand macro="stdio"/>
+    <expand macro="requirements"/>
+    <command>FalseDiscoveryRate
 
--in ${param_in}
--fwd_in ${param_fwd_in}
--rev_in ${param_rev_in}
--out ${param_out}
-${param_proteins_only}
-${param_peptides_only}
--threads \${GALAXY_SLOTS:-24} 
-${param_q_value}
-${param_use_all_hits}
-${param_split_charge_variants}
-${param_treat_runs_separately}
--algorithm:decoy_string ${param_decoy_string}
-${param_add_decoy_peptides}
+#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
+#end if
+#if $param_peptides_only:
+  -peptides_only
+#end if
+-threads \${GALAXY_SLOTS:-24}
+#if $param_algorithm_no_qvalues:
+  -algorithm:no_qvalues
+#end if
+#if $param_algorithm_use_all_hits:
+  -algorithm:use_all_hits
+#end if
+#if $param_algorithm_split_charge_variants:
+  -algorithm:split_charge_variants
+#end if
+#if $param_algorithm_treat_runs_separately:
+  -algorithm:treat_runs_separately
+#end if
+#if $param_algorithm_add_decoy_peptides:
+  -algorithm:add_decoy_peptides
+#end if
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_force:
+  -force
+#end if
+#end if
 </command>
-  <inputs>
-    <param name="param_in" type="data" format="idXML" optional="True" label="Identification input file which contains a search against a concatenated sequence database. Either specify '-in' alone or 'fwd_in' together with 'rev_in' as input." help="(-in)"/>
-    <param name="param_fwd_in" type="data" format="idXML" optional="True" label="Identification input to estimate FDR, forward run." help="(-fwd_in)"/>
-    <param name="param_rev_in" type="data" format="idXML" optional="True" label="Identification input to estimate FDR, decoy run." help="(-rev_in)"/>
-    <param name="param_proteins_only" type="boolean" truevalue="-proteins_only true" falsevalue="-proteins_only false" checked="false" optional="True" label="If set, the FDR of the proteins only is calculated" help="(-proteins_only)"/>
-    <param name="param_peptides_only" type="boolean" truevalue="-peptides_only true" falsevalue="-peptides_only false" checked="false" optional="True" label="If set, the FDR of the peptides only is calculated" help="(-peptides_only)"/>
-    <param name="param_q_value" type="boolean" truevalue="-algorithm:q_value true" falsevalue="-algorithm:q_value false" checked="true" optional="True" label="If 'true', the q-values will be calculated instead of the FDRs" help="(-q_value)"/>
-    <param name="param_use_all_hits" type="boolean" truevalue="-algorithm:use_all_hits true" falsevalue="-algorithm:use_all_hits false" 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_split_charge_variants" type="boolean" truevalue="-algorithm:split_charge_variants true" falsevalue="-algorithm:split_charge_variants false" checked="false" optional="True" label="If set to 'true' charge variants are treated separately (for peptides of combined target/decoy searches only)." help="(-split_charge_variants)"/>
-    <param name="param_treat_runs_separately" type="boolean" truevalue="-algorithm:treat_runs_separately true" falsevalue="-algorithm:treat_runs_separately false" checked="false" optional="True" label="If set to 'true' different search runs are treated separately (for peptides of combined target/decoy searches only)." help="(-treat_runs_separately)"/>
-    <param name="param_decoy_string" type="text" size="20" value="_rev" label="String which is appended at the accession of the protein to indicate that it is a decoy protein (for proteins only)." help="(-decoy_string)"/>
-    <param name="param_add_decoy_peptides" type="boolean" truevalue="-algorithm:add_decoy_peptides true" falsevalue="-algorithm:add_decoy_peptides false" checked="false" optional="True" label="If set to true, decoy peptides will be written to output file, too. The q-value is set to the closest target score." help="(-add_decoy_peptides)"/>
-  </inputs>
-  <outputs>
-    <data name="param_out" label="Identification output with annotated FDR" format="idXML"/>
-  </outputs>
-  <help>**What it does**
-
-Estimates the false discovery rate on peptide and protein level using decoy searches.
+    <inputs>
+      <param format="xml" help="(-in) Either specify '-in' alone or 'in_target' together with 'in_decoy' as input" label="Identification input file containing a search against a concatenated sequence database" name="param_in" optional="True" type="data"/>
+      <param format="xml" help="(-in_target) " label="Identification input file containing a search against a target-only database" name="param_in_target" optional="True" type="data"/>
+      <param format="xml" help="(-in_decoy) " label="Identification input file containing a search against a decoy-only database" name="param_in_decoy" optional="True" type="data"/>
+      <param checked="false" falsevalue="" help="(-proteins_only) " label="If set only the FDR on protein level is calculated" name="param_proteins_only" optional="True" truevalue="-proteins_only" type="boolean"/>
+      <param checked="false" falsevalue="" help="(-peptides_only) " label="If set only the FDR on peptide (PSM) level is calculated" name="param_peptides_only" optional="True" truevalue="-peptides_only" type="boolean"/>
+      <param checked="false" falsevalue="" help="(-no_qvalues) " label="If 'true' strict FDRs will be calculated instead of q-values (the default)" name="param_algorithm_no_qvalues" optional="True" truevalue="-algorithm:no_qvalues" type="boolean"/>
+      <param checked="false" falsevalue="" help="(-use_all_hits) " label="If 'true' not only the first hit, but all are used (peptides only)" name="param_algorithm_use_all_hits" optional="True" truevalue="-algorithm:use_all_hits" type="boolean"/>
+      <param checked="false" falsevalue="" help="(-split_charge_variants) " label="If 'true' charge variants are treated separately (for peptides of combined target/decoy searches only)" name="param_algorithm_split_charge_variants" optional="True" truevalue="-algorithm:split_charge_variants" type="boolean"/>
+      <param checked="false" falsevalue="" help="(-treat_runs_separately) " label="If 'true' different search runs are treated separately (for peptides of combined target/decoy searches only)" name="param_algorithm_treat_runs_separately" optional="True" truevalue="-algorithm:treat_runs_separately" type="boolean"/>
+      <param checked="false" falsevalue="" help="(-add_decoy_peptides) The q-value is set to the closest target score" label="If 'true' decoy peptides will be written to output file, too" name="param_algorithm_add_decoy_peptides" optional="True" truevalue="-algorithm:add_decoy_peptides" type="boolean"/>
+      <expand macro="advanced_options">
+        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
+      </expand>
+    </inputs>
+    <outputs>
+      <data format="xml" name="param_out"/>
+    </outputs>
+    <help>Estimates the false discovery rate on peptide and protein level using decoy searches.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FalseDiscoveryRate.html
-
-@REFERENCES@
-</help>
-</tool>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FalseDiscoveryRate.html</help>
+  </tool>