annotate SpectraFilterBernNorm.xml @ 5:e253f64ae49f 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="SpectraFilterBernNorm" name="SpectraFilterBernNorm" version="2.3.0">
  <description>Applies thresholdfilter to peak spectra.</description>
  <macros>
    <token name="@EXECUTABLE@">SpectraFilterBernNorm</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>SpectraFilterBernNorm

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_algorithm_threshold:
  -algorithm:threshold $param_algorithm_threshold
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
    #if $adv_opts.param_algorithm_C1:
  -algorithm:C1 $adv_opts.param_algorithm_C1
#end if
    #if $adv_opts.param_algorithm_C2:
  -algorithm:C2 $adv_opts.param_algorithm_C2
#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_threshold" type="float" value="0.1" label="Threshold of the Bern et al. normalization" help="(-threshold) "/>
    <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) "/>
      <param name="param_algorithm_C1" type="float" value="28.0" label="C1 value of the normalization" help="(-C1) "/>
      <param name="param_algorithm_C2" type="float" value="400.0" label="C2 value of the normalization" help="(-C2) "/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" format="mzml"/>
  </outputs>
  <help>Applies thresholdfilter to peak spectra.


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