comparison PrecursorIonSelector.xml @ 13:1cae2aac2260 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3

12:598f53ccd9b8

<?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: [Targeted Experiments]-->
<tool id="PrecursorIonSelector" name="PrecursorIonSelector" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
  <description>PrecursorIonSelector</description>
  <macros>
    <token name="@EXECUTABLE@">PrecursorIonSelector</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@

  <configfiles>
    <inputs name="args_json" data_style="paths"/>
    <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true, "algorithm": {"Preprocessing": {"tmp_dir": "\$TMP_DIR"}}}]]></configfile>
  </configfiles>
  <inputs>
    <param name="in" argument="-in" type="data" format="featurexml" optional="false" label="Input feature map file (featureXML)" help=" select featurexml data sets(s)"/>
    <param name="ids" argument="-ids" type="data" format="idxml" optional="false" label="file containing results of identification" help=" select idxml data sets(s)"/>
    <param name="num_precursors" argument="-num_precursors" type="integer" optional="true" value="1" label="number of precursors to be selected" help=""/>
    <param name="raw_data" argument="-raw_data" type="data" format="mzml" optional="true" label="Input profile data" help=" select mzml data sets(s)"/>
    <param name="load_preprocessing" argument="-load_preprocessing" type="boolean" truevalue="true" falsevalue="false" checked="false" label="The preprocessed db is loaded from file, not calculated" help=""/>
    <param name="store_preprocessing" argument="-store_preprocessing" type="boolean" truevalue="true" falsevalue="false" checked="false" label="The preprocessed db is stored" help=""/>
    <param name="simulation" argument="-simulation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Simulate the whole LC-MS/MS run" help=""/>
    <param name="db_path" argument="-db_path" type="data" format="fasta" optional="true" label="db file" help=" select fasta data sets(s)"/>
    <param name="rt_model" argument="-rt_model" type="data" format="txt" optional="true" label="SVM Model for RTPredict" help=" select txt data sets(s)"/>
    <param name="dt_model" argument="-dt_model" type="data" format="txt" optional="true" label="SVM Model for PTPredict" help=" select txt data sets(s)"/>
    <param name="fixed_modifications" argument="-fixed_modifications" type="text" optional="true" value="" label="the modifications i.e. Carboxymethyl (C)" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
      <expand macro="list_string_val"/>
      <expand macro="list_string_san"/>
    </param>
    <section name="algorithm" title="Settings for the compound list creation and rescoring" help="" expanded="false">
      <param name="type" argument="-algorithm:type" type="select" optional="false" label="Strategy for precursor ion selection" help="">
        <option value="ILP_IPS">ILP_IPS</option>
        <option value="IPS" selected="true">IPS</option>
        <option value="SPS">SPS</option>
        <option value="Upshift">Upshift</option>
        <option value="Downshift">Downshift</option>
        <option value="DEX">DEX</option>
        <expand macro="list_string_san"/>
      </param>
      <param name="max_iteration" argument="-algorithm:max_iteration" type="integer" optional="true" min="1" value="100" label="Maximal number of iterations" help=""/>
      <param name="rt_bin_capacity" argument="-algorithm:rt_bin_capacity" type="integer" optional="true" min="1" value="10" label="Maximal number of precursors per rt bin" help=""/>
      <param name="step_size" argument="-algorithm:step_size" type="integer" optional="true" min="1" value="1" label="Maximal number of precursors per iteration" help=""/>
      <param name="peptide_min_prob" argument="-algorithm:peptide_min_prob" type="float" optional="true" value="0.2" label="Minimal peptide probability" help=""/>

          <param name="max_number_precursors_per_feature" argument="-algorithm:MIPFormulation:feature_based:max_number_precursors_per_feature" type="integer" optional="true" min="1" value="1" label="The maximal number of precursors per feature" help=""/>
        </section>
      </section>
      <section name="Preprocessing" title="" help="" expanded="false">
        <param name="precursor_mass_tolerance" argument="-algorithm:Preprocessing:precursor_mass_tolerance" type="float" optional="true" min="0.0" value="10.0" label="Precursor mass tolerance which is used to query the peptide database for peptides" help=""/>
        <param name="precursor_mass_tolerance_unit" argument="-algorithm:Preprocessing:precursor_mass_tolerance_unit" display="radio" type="select" optional="false" label="Precursor mass tolerance unit" help="">
          <option value="ppm" selected="true">ppm</option>
          <option value="Da">Da</option>
          <expand macro="list_string_san"/>
        </param>
        <param name="preprocessed_db_path" argument="-algorithm:Preprocessing:preprocessed_db_path" type="text" optional="true" value="" label="Path where the preprocessed database should be stored" help="">
          <expand macro="list_string_san"/>
        </param>
        <param name="preprocessed_db_pred_rt_path" argument="-algorithm:Preprocessing:preprocessed_db_pred_rt_path" type="text" optional="true" value="" label="Path where the predicted rts of the preprocessed database should be stored" help="">
          <expand macro="list_string_san"/>
        </param>
        <param name="preprocessed_db_pred_dt_path" argument="-algorithm:Preprocessing:preprocessed_db_pred_dt_path" type="text" optional="true" value="" label="Path where the predicted rts of the preprocessed database should be stored" help="">
          <expand macro="list_string_san"/>
        </param>
        <param name="max_peptides_per_run" argument="-algorithm:Preprocessing:max_peptides_per_run" type="integer" optional="true" min="1" value="100000" label="Number of peptides for that the pt and rt are parallely predicted" help=""/>
        <param name="missed_cleavages" argument="-algorithm:Preprocessing:missed_cleavages" type="integer" optional="true" min="0" value="1" label="Number of allowed missed cleavages" help=""/>
        <param name="taxonomy" argument="-algorithm:Preprocessing:taxonomy" type="text" optional="true" value="" label="Taxonomy" help="">
          <expand macro="list_string_san"/>
        </param>
        <param name="store_peptide_sequences" argument="-algorithm:Preprocessing:store_peptide_sequences" type="text" optional="true" value="false" label="Flag if peptide sequences should be stored" help="">
          <expand macro="list_string_san"/>
        </param>
        <section name="rt_settings" title="" help="" expanded="false">
          <param name="min_rt" argument="-algorithm:Preprocessing:rt_settings:min_rt" type="float" optional="true" min="1.0" value="960.0" label="Minimal RT in the experiment (in seconds)" help=""/>
          <param name="max_rt" argument="-algorithm:Preprocessing:rt_settings:max_rt" type="float" optional="true" value="3840.0" label="Maximal RT in the experiment (in seconds)" help=""/>
          <param name="rt_step_size" argument="-algorithm:Preprocessing:rt_settings:rt_step_size" type="float" optional="true" value="30.0" label="Time between two consecutive spectra (in seconds)" help=""/>
          <param name="gauss_mean" argument="-algorithm:Preprocessing:rt_settings:gauss_mean" type="float" optional="true" value="-1.0" label="mean of the gauss curve" help=""/>
          <param name="gauss_sigma" argument="-algorithm:Preprocessing:rt_settings:gauss_sigma" type="float" optional="true" value="3.0" label="std of the gauss curve" help=""/>
        </section>
      </section>
    </section>
    <expand macro="adv_opts_macro">
      <param name="solver" argument="-solver" display="radio" type="select" optional="false" label="LP solver type" help="">
        <option value="GLPK" selected="true">GLPK</option>
        <option value="COINOR">COINOR</option>
        <expand macro="list_string_san"/>
      </param>
      <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="out_FLAG">out (modified feature map)</option>
      <option value="next_feat_FLAG">next_feat (feature map (featureXML) file with the selected precursors)</option>

    </data>
    <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_PrecursorIonSelector"/>
    <expand macro="manutest_PrecursorIonSelector"/>
  </tests>
  <help><![CDATA[PrecursorIonSelector


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

13:1cae2aac2260

<?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: [Targeted Experiments]-->
<tool id="PrecursorIonSelector" name="PrecursorIonSelector" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
  <description>PrecursorIonSelector</description>
  <macros>
    <token name="@EXECUTABLE@">PrecursorIonSelector</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
@EXT_FOO@

  <configfiles>
    <inputs name="args_json" data_style="paths"/>
    <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true, "algorithm": {"Preprocessing": {"tmp_dir": "\$TMP_DIR"}}}]]></configfile>
  </configfiles>
  <inputs>
    <param argument="-in" type="data" format="featurexml" optional="false" label="Input feature map file (featureXML)" help=" select featurexml data sets(s)"/>
    <param argument="-ids" type="data" format="idxml" optional="false" label="file containing results of identification" help=" select idxml data sets(s)"/>
    <param argument="-num_precursors" type="integer" optional="true" value="1" label="number of precursors to be selected" help=""/>
    <param argument="-raw_data" type="data" format="mzml" optional="true" label="Input profile data" help=" select mzml data sets(s)"/>
    <param argument="-load_preprocessing" type="boolean" truevalue="true" falsevalue="false" checked="false" label="The preprocessed db is loaded from file, not calculated" help=""/>
    <param argument="-store_preprocessing" type="boolean" truevalue="true" falsevalue="false" checked="false" label="The preprocessed db is stored" help=""/>
    <param argument="-simulation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Simulate the whole LC-MS/MS run" help=""/>
    <param argument="-db_path" type="data" format="fasta" optional="true" label="db file" help=" select fasta data sets(s)"/>
    <param argument="-rt_model" type="data" format="txt" optional="true" label="SVM Model for RTPredict" help=" select txt data sets(s)"/>
    <param argument="-dt_model" type="data" format="txt" optional="true" label="SVM Model for PTPredict" help=" select txt data sets(s)"/>
    <param argument="-fixed_modifications" type="text" optional="true" value="" label="the modifications i.e. Carboxymethyl (C)" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
      <expand macro="list_string_val" name="fixed_modifications"/>
      <expand macro="list_string_san" name="fixed_modifications"/>
    </param>
    <section name="algorithm" title="Settings for the compound list creation and rescoring" help="" expanded="false">
      <param name="type" argument="-algorithm:type" type="select" optional="true" label="Strategy for precursor ion selection" help="">
        <option value="ILP_IPS">ILP_IPS</option>
        <option value="IPS" selected="true">IPS</option>
        <option value="SPS">SPS</option>
        <option value="Upshift">Upshift</option>
        <option value="Downshift">Downshift</option>
        <option value="DEX">DEX</option>
        <expand macro="list_string_san" name="type"/>
      </param>
      <param name="max_iteration" argument="-algorithm:max_iteration" type="integer" optional="true" min="1" value="100" label="Maximal number of iterations" help=""/>
      <param name="rt_bin_capacity" argument="-algorithm:rt_bin_capacity" type="integer" optional="true" min="1" value="10" label="Maximal number of precursors per rt bin" help=""/>
      <param name="step_size" argument="-algorithm:step_size" type="integer" optional="true" min="1" value="1" label="Maximal number of precursors per iteration" help=""/>
      <param name="peptide_min_prob" argument="-algorithm:peptide_min_prob" type="float" optional="true" value="0.2" label="Minimal peptide probability" help=""/>

          <param name="max_number_precursors_per_feature" argument="-algorithm:MIPFormulation:feature_based:max_number_precursors_per_feature" type="integer" optional="true" min="1" value="1" label="The maximal number of precursors per feature" help=""/>
        </section>
      </section>
      <section name="Preprocessing" title="" help="" expanded="false">
        <param name="precursor_mass_tolerance" argument="-algorithm:Preprocessing:precursor_mass_tolerance" type="float" optional="true" min="0.0" value="10.0" label="Precursor mass tolerance which is used to query the peptide database for peptides" help=""/>
        <param name="precursor_mass_tolerance_unit" argument="-algorithm:Preprocessing:precursor_mass_tolerance_unit" type="select" optional="true" label="Precursor mass tolerance unit" help="">
          <option value="ppm" selected="true">ppm</option>
          <option value="Da">Da</option>
          <expand macro="list_string_san" name="precursor_mass_tolerance_unit"/>
        </param>
        <param name="preprocessed_db_path" argument="-algorithm:Preprocessing:preprocessed_db_path" type="text" optional="true" value="" label="Path where the preprocessed database should be stored" help="">
          <expand macro="list_string_san" name="preprocessed_db_path"/>
        </param>
        <param name="preprocessed_db_pred_rt_path" argument="-algorithm:Preprocessing:preprocessed_db_pred_rt_path" type="text" optional="true" value="" label="Path where the predicted rts of the preprocessed database should be stored" help="">
          <expand macro="list_string_san" name="preprocessed_db_pred_rt_path"/>
        </param>
        <param name="preprocessed_db_pred_dt_path" argument="-algorithm:Preprocessing:preprocessed_db_pred_dt_path" type="text" optional="true" value="" label="Path where the predicted rts of the preprocessed database should be stored" help="">
          <expand macro="list_string_san" name="preprocessed_db_pred_dt_path"/>
        </param>
        <param name="max_peptides_per_run" argument="-algorithm:Preprocessing:max_peptides_per_run" type="integer" optional="true" min="1" value="100000" label="Number of peptides for that the pt and rt are parallelly predicted" help=""/>
        <param name="missed_cleavages" argument="-algorithm:Preprocessing:missed_cleavages" type="integer" optional="true" min="0" value="1" label="Number of allowed missed cleavages" help=""/>
        <param name="taxonomy" argument="-algorithm:Preprocessing:taxonomy" type="text" optional="true" value="" label="Taxonomy" help="">
          <expand macro="list_string_san" name="taxonomy"/>
        </param>
        <param name="store_peptide_sequences" argument="-algorithm:Preprocessing:store_peptide_sequences" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Flag if peptide sequences should be stored" help=""/>
        <section name="rt_settings" title="" help="" expanded="false">
          <param name="min_rt" argument="-algorithm:Preprocessing:rt_settings:min_rt" type="float" optional="true" min="1.0" value="960.0" label="Minimal RT in the experiment (in seconds)" help=""/>
          <param name="max_rt" argument="-algorithm:Preprocessing:rt_settings:max_rt" type="float" optional="true" value="3840.0" label="Maximal RT in the experiment (in seconds)" help=""/>
          <param name="rt_step_size" argument="-algorithm:Preprocessing:rt_settings:rt_step_size" type="float" optional="true" value="30.0" label="Time between two consecutive spectra (in seconds)" help=""/>
          <param name="gauss_mean" argument="-algorithm:Preprocessing:rt_settings:gauss_mean" type="float" optional="true" value="-1.0" label="mean of the gauss curve" help=""/>
          <param name="gauss_sigma" argument="-algorithm:Preprocessing:rt_settings:gauss_sigma" type="float" optional="true" value="3.0" label="std of the gauss curve" help=""/>
        </section>
      </section>
    </section>
    <expand macro="adv_opts_macro">
      <param argument="-solver" type="select" optional="true" label="LP solver type" help="">
        <option value="GLPK" selected="true">GLPK</option>
        <option value="COINOR">COINOR</option>
        <expand macro="list_string_san" name="solver"/>
      </param>
      <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
        <expand macro="list_string_san" name="test"/>
      </param>
    </expand>
    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
      <option value="out_FLAG">out (modified feature map)</option>
      <option value="next_feat_FLAG">next_feat (feature map (featureXML) file with the selected precursors)</option>

    </data>
    <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><!-- TOPP_PrecursorIonSelector_1 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="solver" value="GLPK"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="PrecursorIonSelector_features.featureXML"/>
      <param name="ids" value="PrecursorIonSelector_ids.idXML"/>
      <param name="num_precursors" value="1"/>
      <param name="load_preprocessing" value="false"/>
      <param name="store_preprocessing" value="false"/>
      <param name="simulation" value="true"/>
      <output name="sim_results" file="PrecursorIonSelector_1_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
      <param name="db_path" value="PrecursorIonSelector_db.fasta"/>
      <param name="fixed_modifications" value=""/>
      <section name="algorithm">
        <param name="type" value="IPS"/>
        <param name="max_iteration" value="10"/>
        <param name="rt_bin_capacity" value="10"/>
        <param name="step_size" value="1"/>
        <param name="peptide_min_prob" value="0.2"/>
        <param name="sequential_spectrum_order" value="false"/>
        <section name="MIPFormulation">
          <section name="thresholds">
            <param name="min_protein_probability" value="0.2"/>
            <param name="min_protein_id_probability" value="0.95"/>
            <param name="min_pt_weight" value="0.5"/>
            <param name="min_mz" value="500.0"/>
            <param name="max_mz" value="5000.0"/>
            <param name="min_pred_pep_prob" value="0.5"/>
            <param name="min_rt_weight" value="0.5"/>
            <param name="use_peptide_rule" value="true"/>
            <param name="min_peptide_ids" value="2"/>
            <param name="min_peptide_probability" value="0.95"/>
          </section>
          <section name="combined_ilp">
            <param name="k1" value="0.2"/>
            <param name="k2" value="0.2"/>
            <param name="k3" value="0.4"/>
            <param name="scale_matching_probs" value="true"/>
          </section>
          <section name="feature_based">
            <param name="no_intensity_normalization" value="false"/>
            <param name="max_number_precursors_per_feature" value="1"/>
          </section>
        </section>
        <section name="Preprocessing">
          <param name="precursor_mass_tolerance" value="0.9"/>
          <param name="precursor_mass_tolerance_unit" value="Da"/>
          <param name="preprocessed_db_path" value=""/>
          <param name="preprocessed_db_pred_rt_path" value=""/>
          <param name="preprocessed_db_pred_dt_path" value=""/>
          <param name="max_peptides_per_run" value="100000"/>
          <param name="missed_cleavages" value="1"/>
          <param name="taxonomy" value=""/>
          <param name="store_peptide_sequences" value="false"/>
          <section name="rt_settings">
            <param name="min_rt" value="960.0"/>
            <param name="max_rt" value="3840.0"/>
            <param name="rt_step_size" value="30.0"/>
            <param name="gauss_mean" value="-1.0"/>
            <param name="gauss_sigma" value="3.0"/>
          </section>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,sim_results_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <!-- TOPP_PrecursorIonSelector_2 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="solver" value="GLPK"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="PrecursorIonSelector_features.featureXML"/>
      <output name="out" file="PrecursorIonSelector_2_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
      <param name="ids" value="PrecursorIonSelector_ids.idXML"/>
      <param name="num_precursors" value="1"/>
      <param name="load_preprocessing" value="false"/>
      <param name="store_preprocessing" value="false"/>
      <param name="simulation" value="false"/>
      <param name="db_path" value="PrecursorIonSelector_db.fasta"/>
      <param name="fixed_modifications" value=""/>
      <section name="algorithm">
        <param name="type" value="IPS"/>
        <param name="max_iteration" value="10"/>
        <param name="rt_bin_capacity" value="10"/>
        <param name="step_size" value="1"/>
        <param name="peptide_min_prob" value="0.2"/>
        <param name="sequential_spectrum_order" value="false"/>
        <section name="MIPFormulation">
          <section name="thresholds">
            <param name="min_protein_probability" value="0.2"/>
            <param name="min_protein_id_probability" value="0.95"/>
            <param name="min_pt_weight" value="0.5"/>
            <param name="min_mz" value="500.0"/>
            <param name="max_mz" value="5000.0"/>
            <param name="min_pred_pep_prob" value="0.5"/>
            <param name="min_rt_weight" value="0.5"/>
            <param name="use_peptide_rule" value="true"/>
            <param name="min_peptide_ids" value="2"/>
            <param name="min_peptide_probability" value="0.95"/>
          </section>
          <section name="combined_ilp">
            <param name="k1" value="0.2"/>
            <param name="k2" value="0.2"/>
            <param name="k3" value="0.4"/>
            <param name="scale_matching_probs" value="true"/>
          </section>
          <section name="feature_based">
            <param name="no_intensity_normalization" value="false"/>
            <param name="max_number_precursors_per_feature" value="1"/>
          </section>
        </section>
        <section name="Preprocessing">
          <param name="precursor_mass_tolerance" value="0.9"/>
          <param name="precursor_mass_tolerance_unit" value="Da"/>
          <param name="preprocessed_db_path" value=""/>
          <param name="preprocessed_db_pred_rt_path" value=""/>
          <param name="preprocessed_db_pred_dt_path" value=""/>
          <param name="max_peptides_per_run" value="100000"/>
          <param name="missed_cleavages" value="1"/>
          <param name="taxonomy" value=""/>
          <param name="store_peptide_sequences" value="false"/>
          <section name="rt_settings">
            <param name="min_rt" value="960.0"/>
            <param name="max_rt" value="3840.0"/>
            <param name="rt_step_size" value="30.0"/>
            <param name="gauss_mean" value="-1.0"/>
            <param name="gauss_sigma" value="3.0"/>
          </section>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
  </tests>
  <help><![CDATA[PrecursorIonSelector


For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_PrecursorIonSelector.html]]></help>
  <expand macro="references"/>
</tool>