view SpectraFilterParentPeakMower.xml @ 4:6ead64a594bd draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty

<?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="2.0.0">
    <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
-threads \${GALAXY_SLOTS:-24}
#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 format="mzml" help="(-in) " label="input file" name="param_in" optional="False" type="data"/>
      <param help="(-window_size) " label="The size of the m/z window where the peaks are removed, +/- window_size" name="param_algorithm_window_size" type="float" value="2.0"/>
      <param help="(-default_charge) " label="If the precursor has no charge set, the default charge is assumed" name="param_algorithm_default_charge" type="integer" value="2"/>
      <param help="(-consider_NH3_loss) " label="Whether NH3 loss peaks from the precursor should be removed" name="param_algorithm_consider_NH3_loss" type="integer" value="1"/>
      <param help="(-consider_H2O_loss) " label="Whether H2O loss peaks from the precursor should be removed" name="param_algorithm_consider_H2O_loss" type="integer" value="1"/>
      <expand macro="advanced_options">
        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
        <param help="(-clean_all_charge_states) " label="Set to 1 if precursor ions of all possible charge states should be removed" name="param_algorithm_clean_all_charge_states" type="integer" value="1"/>
        <param help="(-reduce_by_factor) " label="Reduce the intensities of the precursor and related ions by a given factor (set 'set_to_zero' to 0)" name="param_algorithm_reduce_by_factor" type="integer" value="0"/>
        <param help="(-factor) " label="Factor which is used to reduce the intensities if 'reduce_by_factor' is selected" name="param_algorithm_factor" type="float" value="1000.0"/>
        <param help="(-set_to_zero) " label="Reduce the intensities of the precursor and related ions to zero" name="param_algorithm_set_to_zero" type="integer" value="1"/>
      </expand>
    </inputs>
    <outputs>
      <data format="mzml" name="param_out"/>
    </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>