--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/OpenSwathDecoyGenerator.xml	Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,59 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="OpenSwathDecoyGenerator" name="OpenSwathDecoyGenerator" version="1.12.0">
+  <description>Generates decoys according to different models for a specific TraML</description>
+  <macros>
+    <token name="@EXECUTABLE@">OpenSwathDecoyGenerator</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>OpenSwathDecoyGenerator
+
+-in ${param_in}
+-out ${param_out}
+-method ${param_method}
+-decoy_tag ${param_decoy_tag}
+${param_theoretical}
+-mz_threshold ${param_mz_threshold}
+${param_exclude_similar}
+-similarity_threshold ${param_similarity_threshold}
+${param_append}
+${param_remove_CNterm_mods}
+${param_remove_unannotated}
+${param_enable_losses}
+-identity_threshold ${param_identity_threshold}
+-max_attempts ${param_max_attempts}
+-mz_shift ${param_mz_shift}
+-precursor_mass_shift ${param_precursor_mass_shift}
+-threads \${GALAXY_SLOTS:-24} 
+</command>
+  <inputs>
+    <param name="param_in" type="data" format="" optional="False" label="input file ('traML')" help="(-in)"/>
+    <param name="param_method" type="text" size="20" value="shuffle" label="decoy generation method ('shuffle','pseudo-reverse','reverse','shift')" help="(-method)"/>
+    <param name="param_decoy_tag" type="text" size="20" value="DECOY_" label="decoy tag" help="(-decoy_tag)"/>
+    <param name="param_theoretical" type="boolean" truevalue="-theoretical true" falsevalue="-theoretical false" checked="false" optional="True" label="set this flag if only annotated transitions should be used and be corrected to the theoretical mz." help="(-theoretical)"/>
+    <param name="param_mz_threshold" type="float" value="0.05" label="MZ threshold in Thomson for fragment ion annotation" help="(-mz_threshold)"/>
+    <param name="param_exclude_similar" type="boolean" truevalue="-exclude_similar true" falsevalue="-exclude_similar false" checked="false" optional="True" label="set this flag if decoy assays with similarity of the peptide sequence to the target assays higher than the identity_threshold should be excluded. If similarity_threshold is over 0, decoy assays with an absolute difference of the decoy and target product mz smaller than similarity_threshold are further excluded." help="(-exclude_similar)"/>
+    <param name="param_similarity_threshold" type="float" value="-1.0" label="Similarity threshold for absolute difference of the product mz of target and decoy assays for exclusion in Dalton. Suggested value: 0.05" help="(-similarity_threshold)"/>
+    <param name="param_append" type="boolean" truevalue="-append true" falsevalue="-append false" checked="false" optional="True" label="set this flag if non-decoy TraML should be appended to the output." help="(-append)"/>
+    <param name="param_remove_CNterm_mods" type="boolean" truevalue="-remove_CNterm_mods true" falsevalue="-remove_CNterm_mods false" checked="false" optional="True" label="set this flag to remove decoy peptides with C/N terminal modifications (may be necessary depending on the decoy generation method)." help="(-remove_CNterm_mods)"/>
+    <param name="param_remove_unannotated" type="boolean" truevalue="-remove_unannotated true" falsevalue="-remove_unannotated false" checked="false" optional="True" label="set this flag if target assays with unannotated ions should be ignored from decoy generation." help="(-remove_unannotated)"/>
+    <param name="param_enable_losses" type="boolean" truevalue="-enable_losses true" falsevalue="-enable_losses false" checked="false" optional="True" label="set this flag if fragment ions should also be annotated with neutral losses." help="(-enable_losses)"/>
+    <param name="param_identity_threshold" type="float" value="0.7" label="shuffle: identity threshold for the shuffle algorithm" help="(-identity_threshold)"/>
+    <param name="param_max_attempts" type="integer" value="10" label="shuffle: maximum attempts to lower the sequence identity between target and decoy for the shuffle algorithm" help="(-max_attempts)"/>
+    <param name="param_mz_shift" type="float" value="20.0" label="shift: MZ shift in Thomson for shift decoy method" help="(-mz_shift)"/>
+    <param name="param_precursor_mass_shift" type="float" value="0.0" label="Mass shift to apply to the precursor ion" help="(-precursor_mass_shift)"/>
+  </inputs>
+  <outputs>
+    <data name="param_out" label="output file" format="data"/>
+  </outputs>
+  <help>**What it does**
+
+Generates decoys according to different models for a specific TraML
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathDecoyGenerator.html
+
+@REFERENCES@
+</help>
+</tool>