annotate SpectraFilterParentPeakMower.xml @ 2:6325a03ec249 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 1e51bed3a1c10c67ef0404216608e9333db04c64

<?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="2.2.0">
  <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

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
#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':
    #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_algorithm_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_algorithm_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_algorithm_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_algorithm_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_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
      <param name="param_algorithm_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_algorithm_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_algorithm_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_algorithm_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" format="mzml"/>
  </outputs>
  <help>Applies thresholdfilter to peak spectra.


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