view SpectraFilterParentPeakMower.xml @ 0:3d84209d3178 draft

Uploaded

<?xml version='1.0' encoding='UTF-8'?>
<tool id="SpectraFilterParentPeakMower" name="SpectraFilterParentPeakMower" version="1.12.0">
  <description>Applies thresholdfilter to peak spectra.</description>
  <macros>
    <token name="@EXECUTABLE@">SpectraFilterParentPeakMower</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>SpectraFilterParentPeakMower

-in ${param_in}
-out ${param_out}
-threads \${GALAXY_SLOTS:-24} 
-algorithm:window_size ${param_window_size}
-algorithm:default_charge ${param_default_charge}
-algorithm:consider_NH3_loss ${param_consider_NH3_loss}
-algorithm:consider_H2O_loss ${param_consider_H2O_loss}
#if $adv_opts.adv_opts_selector=='advanced':
    -algorithm:clean_all_charge_states ${adv_opts.param_clean_all_charge_states}
    -algorithm:reduce_by_factor ${adv_opts.param_reduce_by_factor}
    -algorithm:factor ${adv_opts.param_factor}
    -algorithm:set_to_zero ${adv_opts.param_set_to_zero}
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="mzML" optional="False" label="input file " help="(-in)"/>
    <param name="param_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_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_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_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_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_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_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_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" label="output file " format="mzML"/>
  </outputs>
  <help>**What it does**

Applies thresholdfilter to peak spectra.


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

@REFERENCES@
</help>
</tool>