annotate SpectraFilterNormalizer.xml @ 5:7a973f4ac2d2 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b

<?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 CTDConverter.-->
<!--Proposed Tool Section: [Identification]-->
<tool id="SpectraFilterNormalizer" name="SpectraFilterNormalizer" version="2.3.0">
  <description>Normalizes intensity of peak spectra.</description>
  <macros>
    <token name="@EXECUTABLE@">SpectraFilterNormalizer</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>SpectraFilterNormalizer

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_algorithm_method:
  -algorithm:method
  #if " " in str($param_algorithm_method):
    "$param_algorithm_method"
  #else
    $param_algorithm_method
  #end if
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#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_method" display="radio" type="select" optional="False" value="to_one" label="Normalize via dividing by TIC ('to_TIC') per spectrum or normalize to max" help="(-method) intensity of one ('to_one') per spectrum">
      <option value="to_one" selected="true">to_one</option>
      <option value="to_TIC">to_TIC</option>
    </param>
    <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>Normalizes intensity of peak spectra.


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraFilterNormalizer.html</help>
</tool>