--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/FalseDiscoveryRate.xml	Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,88 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<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="stdio"/>
+  <expand macro="requirements"/>
+  <command>FalseDiscoveryRate
+
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_fwd_in:
+  -fwd_in $param_fwd_in
+#end if
+#if $param_rev_in:
+  -rev_in $param_rev_in
+#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_q_value:
+  -algorithm:q_value
+#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 $param_algorithm_decoy_string:
+  -algorithm:decoy_string     "$param_algorithm_decoy_string"
+#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" help="(-in) Either specify '-in' alone or 'fwd_in' together with 'rev_in' as input"/>
+    <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" falsevalue="" 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" falsevalue="" checked="false" optional="True" label="If set, the FDR of the peptides only is calculated" help="(-peptides_only) "/>
+    <param name="param_algorithm_q_value" type="boolean" truevalue="-algorithm:q_value" falsevalue="" checked="true" optional="True" label="If 'true', the q-values will be calculated instead of the FDRs" help="(-q_value) "/>
+    <param name="param_algorithm_use_all_hits" 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" type="boolean" truevalue="-algorithm:split_charge_variants" falsevalue="" 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_algorithm_treat_runs_separately" type="boolean" truevalue="-algorithm:treat_runs_separately" falsevalue="" 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_algorithm_decoy_string" type="text" size="30" 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) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_algorithm_add_decoy_peptides" type="boolean" truevalue="-algorithm:add_decoy_peptides" falsevalue="" checked="false" optional="True" label="If set to true, decoy peptides will be written to output file, too" help="(-add_decoy_peptides) The q-value is set to the closest target score"/>
+    <expand macro="advanced_options">
+      <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
+    </expand>
+  </inputs>
+  <outputs>
+    <data name="param_out" 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</help>
+  <expand macro="references"/>
+</tool>