--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SpectraFilterParentPeakMower.xml	Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,73 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="SpectraFilterParentPeakMower" name="SpectraFilterParentPeakMower" version="2.0.0">
+  <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
+
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+-threads \${GALAXY_SLOTS:-24} 
+#if $param_algorithm_window_size:
+  -algorithm:window_size $param_algorithm_window_size
+#end if
+#if $param_algorithm_default_charge:
+  -algorithm:default_charge $param_algorithm_default_charge
+#end if
+#if $param_algorithm_consider_NH3_loss:
+  -algorithm:consider_NH3_loss $param_algorithm_consider_NH3_loss
+#end if
+#if $param_algorithm_consider_H2O_loss:
+  -algorithm:consider_H2O_loss $param_algorithm_consider_H2O_loss
+#end if
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_force:
+  -force
+#end if
+    #if $adv_opts.param_algorithm_clean_all_charge_states:
+  -algorithm:clean_all_charge_states $adv_opts.param_algorithm_clean_all_charge_states
+#end if
+    #if $adv_opts.param_algorithm_reduce_by_factor:
+  -algorithm:reduce_by_factor $adv_opts.param_algorithm_reduce_by_factor
+#end if
+    #if $adv_opts.param_algorithm_factor:
+  -algorithm:factor $adv_opts.param_algorithm_factor
+#end if
+    #if $adv_opts.param_algorithm_set_to_zero:
+  -algorithm:set_to_zero $adv_opts.param_algorithm_set_to_zero
+#end if
+#end if
+</command>
+  <inputs>
+    <param name="param_in" type="data" format="mzml" optional="False" label="input file" help="(-in) "/>
+    <param name="param_algorithm_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_algorithm_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_algorithm_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_algorithm_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_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
+      <param name="param_algorithm_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_algorithm_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_algorithm_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_algorithm_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" 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</help>
+  <expand macro="references"/>
+</tool>