--- a/SpectraFilterParentPeakMower.xml	Mon Oct 13 10:18:22 2014 -0400
+++ b/SpectraFilterParentPeakMower.xml	Wed Jan 27 10:06:49 2016 -0500
@@ -1,51 +1,73 @@
-<?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
+<?xml version="1.0" encoding="UTF-8"?>
+  <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
+  <!--Proposed Tool Section: [Identification]-->
+  <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="references"/>
+    <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 $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':
-    -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}
+    #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_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.
+    <inputs>
+      <param format="mzml" help="(-in) " label="input file" name="param_in" optional="False" type="data"/>
+      <param help="(-window_size) " label="The size of the m/z window where the peaks are removed, +/- window_size" name="param_algorithm_window_size" type="float" value="2.0"/>
+      <param help="(-default_charge) " label="If the precursor has no charge set, the default charge is assumed" name="param_algorithm_default_charge" type="integer" value="2"/>
+      <param help="(-consider_NH3_loss) " label="Whether NH3 loss peaks from the precursor should be removed" name="param_algorithm_consider_NH3_loss" type="integer" value="1"/>
+      <param help="(-consider_H2O_loss) " label="Whether H2O loss peaks from the precursor should be removed" name="param_algorithm_consider_H2O_loss" type="integer" value="1"/>
+      <expand macro="advanced_options">
+        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
+        <param help="(-clean_all_charge_states) " label="Set to 1 if precursor ions of all possible charge states should be removed" name="param_algorithm_clean_all_charge_states" type="integer" value="1"/>
+        <param help="(-reduce_by_factor) " label="Reduce the intensities of the precursor and related ions by a given factor (set 'set_to_zero' to 0)" name="param_algorithm_reduce_by_factor" type="integer" value="0"/>
+        <param help="(-factor) " label="Factor which is used to reduce the intensities if 'reduce_by_factor' is selected" name="param_algorithm_factor" type="float" value="1000.0"/>
+        <param help="(-set_to_zero) " label="Reduce the intensities of the precursor and related ions to zero" name="param_algorithm_set_to_zero" type="integer" value="1"/>
+      </expand>
+    </inputs>
+    <outputs>
+      <data format="mzml" name="param_out"/>
+    </outputs>
+    <help>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>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraFilterParentPeakMower.html</help>
+  </tool>