--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/FalseDiscoveryRate.xml	Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,51 @@
+<?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
+
+-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}
+</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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FalseDiscoveryRate.html
+
+@REFERENCES@
+</help>
+</tool>