<?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>