--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SpectraFilterParentPeakMower.xml	Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,51 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="SpectraFilterParentPeakMower" name="SpectraFilterParentPeakMower" version="1.12.0">
+  <description>Applies thresholdfilter to peak spectra.</description>
+  <macros>
+    <token name="@EXECUTABLE@">SpectraFilterParentPeakMower</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>SpectraFilterParentPeakMower
+
+-in ${param_in}
+-out ${param_out}
+-threads \${GALAXY_SLOTS:-24} 
+-algorithm:window_size ${param_window_size}
+-algorithm:default_charge ${param_default_charge}
+-algorithm:consider_NH3_loss ${param_consider_NH3_loss}
+-algorithm:consider_H2O_loss ${param_consider_H2O_loss}
+#if $adv_opts.adv_opts_selector=='advanced':
+    -algorithm:clean_all_charge_states ${adv_opts.param_clean_all_charge_states}
+    -algorithm:reduce_by_factor ${adv_opts.param_reduce_by_factor}
+    -algorithm:factor ${adv_opts.param_factor}
+    -algorithm:set_to_zero ${adv_opts.param_set_to_zero}
+#end if
+</command>
+  <inputs>
+    <param name="param_in" type="data" format="mzML" optional="False" label="input file " help="(-in)"/>
+    <param name="param_window_size" type="float" value="2.0" label="The size of the m/z window where the peaks are removed, +/- window_size." help="(-window_size)"/>
+    <param name="param_default_charge" type="integer" value="2" label="If the precursor has no charge set, the default charge is assumed." help="(-default_charge)"/>
+    <param name="param_consider_NH3_loss" type="integer" value="1" label="Whether NH3 loss peaks from the precursor should be removed." help="(-consider_NH3_loss)"/>
+    <param name="param_consider_H2O_loss" type="integer" value="1" label="Whether H2O loss peaks from the precursor should be removed." help="(-consider_H2O_loss)"/>
+    <expand macro="advanced_options">
+      <param name="param_clean_all_charge_states" type="integer" value="1" label="Set to 1 if precursor ions of all possible charge states should be removed." help="(-clean_all_charge_states)"/>
+      <param name="param_reduce_by_factor" type="integer" value="0" label="Reduce the intensities of the precursor and related ions by a given factor (set 'set_to_zero' to 0)." help="(-reduce_by_factor)"/>
+      <param name="param_factor" type="float" value="1000.0" label="Factor which is used to reduce the intensities if 'reduce_by_factor' is selected." help="(-factor)"/>
+      <param name="param_set_to_zero" type="integer" value="1" label="Reduce the intensities of the precursor and related ions to zero." help="(-set_to_zero)"/>
+    </expand>
+  </inputs>
+  <outputs>
+    <data name="param_out" label="output file " format="mzML"/>
+  </outputs>
+  <help>**What it does**
+
+Applies thresholdfilter to peak spectra.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraFilterParentPeakMower.html
+
+@REFERENCES@
+</help>
+</tool>