--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/RNPxlXICFilter.xml	Wed Mar 01 12:33:47 2017 -0500
@@ -0,0 +1,56 @@
+<?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: [Utilities]-->
+<tool id="RNPxlXICFilter" name="RNPxlXICFilter" version="2.1.0">
+  <description>Remove MS2 spectra from treatment based on the fold change between control and treatment.</description>
+  <macros>
+    <token name="@EXECUTABLE@">RNPxlXICFilter</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="references"/>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>RNPxlXICFilter
+
+#if $param_control:
+  -control $param_control
+#end if
+#if $param_treatment:
+  -treatment $param_treatment
+#end if
+#if $param_fold_change:
+  -fold_change $param_fold_change
+#end if
+#if $param_rt_tol:
+  -rt_tol $param_rt_tol
+#end if
+#if $param_mz_tol:
+  -mz_tol $param_mz_tol
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_force:
+  -force
+#end if
+#end if
+</command>
+  <inputs>
+    <param name="param_control" type="data" format="mzml" optional="False" label="input mzML file" help="(-control) "/>
+    <param name="param_treatment" type="data" format="mzml" optional="False" label="input mzML file" help="(-treatment) "/>
+    <param name="param_fold_change" type="float" value="2.0" label="fold change between XICs" help="(-fold_change) "/>
+    <param name="param_rt_tol" type="float" value="20.0" label="RT tolerance in [s] for finding max peak (whole RT range around RT middle)" help="(-rt_tol) "/>
+    <param name="param_mz_tol" type="float" value="10.0" label="m/z tolerance in [ppm] for finding a peak" help="(-mz_tol) "/>
+    <expand macro="advanced_options">
+      <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
+    </expand>
+  </inputs>
+  <outputs>
+    <data name="param_out" format="mzml"/>
+  </outputs>
+  <help>Remove MS2 spectra from treatment based on the fold change between control and treatment.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_RNPxlXICFilter.html</help>
+</tool>