--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/OpenSwathDecoyGenerator.xml	Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,111 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="OpenSwathDecoyGenerator" name="OpenSwathDecoyGenerator" version="2.0.0">
+  <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
+
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_method:
+  -method     "$param_method"
+#end if
+#if $param_decoy_tag:
+  -decoy_tag     "$param_decoy_tag"
+#end if
+#if $param_theoretical:
+  -theoretical
+#end if
+#if $param_mz_threshold:
+  -mz_threshold $param_mz_threshold
+#end if
+#if $param_exclude_similar:
+  -exclude_similar
+#end if
+#if $param_similarity_threshold:
+  -similarity_threshold $param_similarity_threshold
+#end if
+#if $param_append:
+  -append
+#end if
+#if $param_remove_CNterm_mods:
+  -remove_CNterm_mods
+#end if
+#if $param_remove_unannotated:
+  -remove_unannotated
+#end if
+#if $param_enable_losses:
+  -enable_losses
+#end if
+#if $param_identity_threshold:
+  -identity_threshold $param_identity_threshold
+#end if
+#if $param_max_attempts:
+  -max_attempts $param_max_attempts
+#end if
+#if $param_mz_shift:
+  -mz_shift $param_mz_shift
+#end if
+#if $param_precursor_mass_shift:
+  -precursor_mass_shift $param_precursor_mass_shift
+#end if
+-threads \${GALAXY_SLOTS:-24} 
+#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="traml" optional="False" label="input file ('traML')" help="(-in) "/>
+    <param name="param_method" type="text" size="30" value="shuffle" label="decoy generation method ('shuffle','pseudo-reverse','reverse','shift')" help="(-method) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_decoy_tag" type="text" size="30" value="DECOY_" label="decoy tag" help="(-decoy_tag) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_theoretical" type="boolean" truevalue="-theoretical" falsevalue="" 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" falsevalue="" 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" help="(-exclude_similar) 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"/>
+    <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" help="(-similarity_threshold) Suggested value: 0.05"/>
+    <param name="param_append" type="boolean" truevalue="-append" falsevalue="" 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" falsevalue="" 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" falsevalue="" 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" falsevalue="" 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) "/>
+    <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="traml"/>
+  </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</help>
+  <expand macro="references"/>
+</tool>