<?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="SpectraFilterParentPeakMower" name="SpectraFilterParentPeakMower" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
  <description>Applies thresholdfilter to peak spectra.</description>
  <macros>
    <token name="@EXECUTABLE@">SpectraFilterParentPeakMower</token>
    <import>macros.xml</import>
    <import>macros_autotest.xml</import>
    <import>macros_test.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
@EXT_FOO@
#import re

## Preprocessing
mkdir in &&
ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
mkdir out &&

## Main program call

set -o pipefail &&
@EXECUTABLE@ -write_ctd ./ &&
python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
@EXECUTABLE@ -ini @EXECUTABLE@.ctd
-in
'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
-out
'out/output.${gxy2omsext("mzml")}'

## Postprocessing
&& mv 'out/output.${gxy2omsext("mzml")}' '$out'
#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
  && mv '@EXECUTABLE@.ctd' '$ctd_out'
#end if]]></command>
  <configfiles>
    <inputs name="args_json" data_style="paths"/>
    <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
  </configfiles>
  <inputs>
    <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/>
    <section name="algorithm" title="Algorithm parameter subsection" help="" expanded="false">
      <param name="window_size" argument="-algorithm:window_size" type="float" optional="true" value="2.0" label="The size of the m/z window where the peaks are removed, +/- window_size" help=""/>
      <param name="default_charge" argument="-algorithm:default_charge" type="integer" optional="true" value="2" label="If the precursor has no charge set, the default charge is assumed" help=""/>
      <param name="clean_all_charge_states" argument="-algorithm:clean_all_charge_states" type="integer" optional="true" value="1" label="Set to 1 if precursor ions of all possible charge states should be removed" help=""/>
      <param name="consider_NH3_loss" argument="-algorithm:consider_NH3_loss" type="integer" optional="true" value="1" label="Whether NH3 loss peaks from the precursor should be removed" help=""/>
      <param name="consider_H2O_loss" argument="-algorithm:consider_H2O_loss" type="integer" optional="true" value="1" label="Whether H2O loss peaks from the precursor should be removed" help=""/>
      <param name="reduce_by_factor" argument="-algorithm:reduce_by_factor" type="integer" optional="true" value="0" label="Reduce the intensities of the precursor and related ions by a given factor (set 'set_to_zero' to 0)" help=""/>
      <param name="factor" argument="-algorithm:factor" type="float" optional="true" value="1000.0" label="Factor which is used to reduce the intensities if 'reduce_by_factor' is selected" help=""/>
      <param name="set_to_zero" argument="-algorithm:set_to_zero" type="integer" optional="true" value="1" label="Reduce the intensities of the precursor and related ions to zero" help=""/>
    </section>
    <expand macro="adv_opts_macro">
      <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
      <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
        <expand macro="list_string_san"/>
      </param>
    </expand>
    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
    </param>
  </inputs>
  <outputs>
    <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
  </outputs>
  <tests>
    <expand macro="autotest_SpectraFilterParentPeakMower"/>
    <expand macro="manutest_SpectraFilterParentPeakMower"/>
  </tests>
  <help><![CDATA[Applies thresholdfilter to peak spectra.


For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_SpectraFilterParentPeakMower.html]]></help>
  <expand macro="references"/>
</tool>