annotate FeatureFinderSuperHirn.xml @ 1:6ef5f164d057 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb

<?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: [Quantitation]-->
<tool id="FeatureFinderSuperHirn" name="FeatureFinderSuperHirn" version="2.1.0">
  <description>Finds mass spectrometric features in mass spectra.</description>
  <macros>
    <token name="@EXECUTABLE@">FeatureFinderSuperHirn</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>FeatureFinderSuperHirn

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_algorithm_centroiding_active:
  -algorithm:centroiding:active
#end if
#if $param_algorithm_centroiding_window_width:
  -algorithm:centroiding:window_width $param_algorithm_centroiding_window_width
#end if
#if $param_algorithm_centroiding_absolute_isotope_mass_precision:
  -algorithm:centroiding:absolute_isotope_mass_precision $param_algorithm_centroiding_absolute_isotope_mass_precision
#end if
#if $param_algorithm_centroiding_relative_isotope_mass_precision:
  -algorithm:centroiding:relative_isotope_mass_precision $param_algorithm_centroiding_relative_isotope_mass_precision
#end if
#if $param_algorithm_centroiding_minimal_peak_height:
  -algorithm:centroiding:minimal_peak_height $param_algorithm_centroiding_minimal_peak_height
#end if
#if $param_algorithm_centroiding_min_ms_signal_intensity:
  -algorithm:centroiding:min_ms_signal_intensity $param_algorithm_centroiding_min_ms_signal_intensity
#end if

#if $rep_param_algorithm_ms1_precursor_detection_scan_levels:
-algorithm:ms1:precursor_detection_scan_levels
  #for token in $rep_param_algorithm_ms1_precursor_detection_scan_levels:
    #if " " in str(token):
      "$token.param_algorithm_ms1_precursor_detection_scan_levels"
    #else
      $token.param_algorithm_ms1_precursor_detection_scan_levels
    #end if
  #end for
#end if
#if $param_algorithm_ms1_max_inter_scan_distance:
  -algorithm:ms1:max_inter_scan_distance $param_algorithm_ms1_max_inter_scan_distance
#end if
#if $param_algorithm_ms1_tr_resolution:
  -algorithm:ms1:tr_resolution $param_algorithm_ms1_tr_resolution
#end if
#if $param_algorithm_ms1_intensity_threshold:
  -algorithm:ms1:intensity_threshold $param_algorithm_ms1_intensity_threshold
#end if
#if $param_algorithm_ms1_max_inter_scan_rt_distance:
  -algorithm:ms1:max_inter_scan_rt_distance $param_algorithm_ms1_max_inter_scan_rt_distance
#end if
#if $param_algorithm_ms1_min_nb_cluster_members:
  -algorithm:ms1:min_nb_cluster_members $param_algorithm_ms1_min_nb_cluster_members
#end if
#if $param_algorithm_ms1_detectable_isotope_factor:
  -algorithm:ms1:detectable_isotope_factor $param_algorithm_ms1_detectable_isotope_factor
#end if
#if $param_algorithm_ms1_intensity_cv:
  -algorithm:ms1:intensity_cv $param_algorithm_ms1_intensity_cv
#end if
#if $param_algorithm_ms1_retention_time_tolerance:
  -algorithm:ms1:retention_time_tolerance $param_algorithm_ms1_retention_time_tolerance
#end if
#if $param_algorithm_ms1_mz_tolerance:
  -algorithm:ms1:mz_tolerance $param_algorithm_ms1_mz_tolerance
#end if
#if $param_algorithm_ms1_feature_merger_active:
  -algorithm:ms1_feature_merger:active
  #if " " in str($param_algorithm_ms1_feature_merger_active):
    "$param_algorithm_ms1_feature_merger_active"
  #else
    $param_algorithm_ms1_feature_merger_active
  #end if
#end if
#if $param_algorithm_ms1_feature_merger_tr_resolution:
  -algorithm:ms1_feature_merger:tr_resolution $param_algorithm_ms1_feature_merger_tr_resolution
#end if
#if $param_algorithm_ms1_feature_merger_initial_apex_tr_tolerance:
  -algorithm:ms1_feature_merger:initial_apex_tr_tolerance $param_algorithm_ms1_feature_merger_initial_apex_tr_tolerance
#end if
#if $param_algorithm_ms1_feature_merger_feature_merging_tr_tolerance:
  -algorithm:ms1_feature_merger:feature_merging_tr_tolerance $param_algorithm_ms1_feature_merger_feature_merging_tr_tolerance
#end if
#if $param_algorithm_ms1_feature_merger_intensity_variation_percentage:
  -algorithm:ms1_feature_merger:intensity_variation_percentage $param_algorithm_ms1_feature_merger_intensity_variation_percentage
#end if
#if $param_algorithm_ms1_feature_merger_ppm_tolerance_for_mz_clustering:
  -algorithm:ms1_feature_merger:ppm_tolerance_for_mz_clustering $param_algorithm_ms1_feature_merger_ppm_tolerance_for_mz_clustering
#end if
#if $param_algorithm_ms1_feature_selection_options_start_elution_window:
  -algorithm:ms1_feature_selection_options:start_elution_window $param_algorithm_ms1_feature_selection_options_start_elution_window
#end if
#if $param_algorithm_ms1_feature_selection_options_end_elution_window:
  -algorithm:ms1_feature_selection_options:end_elution_window $param_algorithm_ms1_feature_selection_options_end_elution_window
#end if
#if $param_algorithm_ms1_feature_selection_options_mz_range_min:
  -algorithm:ms1_feature_selection_options:mz_range_min $param_algorithm_ms1_feature_selection_options_mz_range_min
#end if
#if $param_algorithm_ms1_feature_selection_options_mz_range_max:
  -algorithm:ms1_feature_selection_options:mz_range_max $param_algorithm_ms1_feature_selection_options_mz_range_max
#end if
#if $param_algorithm_ms1_feature_selection_options_chrg_range_min:
  -algorithm:ms1_feature_selection_options:chrg_range_min $param_algorithm_ms1_feature_selection_options_chrg_range_min
#end if
#if $param_algorithm_ms1_feature_selection_options_chrg_range_max:
  -algorithm:ms1_feature_selection_options:chrg_range_max $param_algorithm_ms1_feature_selection_options_chrg_range_max
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="mzml" optional="False" label="input profile data file" help="(-in) "/>
    <param name="param_algorithm_centroiding_active" display="radio" type="boolean" truevalue="-algorithm:centroiding:active" falsevalue="" checked="false" optional="True" label="MS1 data centroid data" help="(-active) "/>
    <param name="param_algorithm_centroiding_window_width" type="integer" min="1" optional="True" value="5" label="Centroid window width" help="(-window_width) "/>
    <param name="param_algorithm_centroiding_absolute_isotope_mass_precision" type="float" min="0.0" optional="True" value="0.01" label="Absolute isotope mass precision (Da)" help="(-absolute_isotope_mass_precision) "/>
    <param name="param_algorithm_centroiding_relative_isotope_mass_precision" type="float" min="0.0" optional="True" value="10.0" label="Relative isotope mass precision" help="(-relative_isotope_mass_precision) "/>
    <param name="param_algorithm_centroiding_minimal_peak_height" type="float" min="0.0" optional="True" value="0.0" label="Minimal peak height" help="(-minimal_peak_height) "/>
    <param name="param_algorithm_centroiding_min_ms_signal_intensity" type="float" min="0.0" optional="True" value="50.0" label="Minimal Centroid MS Signal Intensity" help="(-min_ms_signal_intensity) "/>
    <repeat name="rep_param_algorithm_ms1_precursor_detection_scan_levels" min="0" max="1" title="param_algorithm_ms1_precursor_detection_scan_levels">
      <param name="param_algorithm_ms1_precursor_detection_scan_levels" type="text" size="30" value="1" label="Precursor detection scan levels" help="(-precursor_detection_scan_levels) ">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
    </repeat>
    <param name="param_algorithm_ms1_max_inter_scan_distance" type="integer" min="0" optional="True" value="0" label="MS1 max inter scan distance" help="(-max_inter_scan_distance) "/>
    <param name="param_algorithm_ms1_tr_resolution" type="float" min="0.0" optional="True" value="0.01" label="MS1 LC retention time resolution" help="(-tr_resolution) "/>
    <param name="param_algorithm_ms1_intensity_threshold" type="float" min="0.0" optional="True" value="1000.0" label="FT peak detect MS1 intensity min threshold" help="(-intensity_threshold) "/>
    <param name="param_algorithm_ms1_max_inter_scan_rt_distance" type="float" min="0.0" optional="True" value="0.1" label="MS1 max inter scan distance" help="(-max_inter_scan_rt_distance) "/>
    <param name="param_algorithm_ms1_min_nb_cluster_members" type="integer" min="0" optional="True" value="4" label="FT peak detect MS1 min nb peak members" help="(-min_nb_cluster_members) "/>
    <param name="param_algorithm_ms1_detectable_isotope_factor" type="float" min="0.0" optional="True" value="0.05" label="Detectable isotope facto" help="(-detectable_isotope_factor) "/>
    <param name="param_algorithm_ms1_intensity_cv" type="float" min="0.0" optional="True" value="0.9" label="IntensityCV" help="(-intensity_cv) "/>
    <param name="param_algorithm_ms1_retention_time_tolerance" type="float" min="0.0" optional="True" value="0.5" label="MS1 retention time tolerance (minutes)" help="(-retention_time_tolerance) "/>
    <param name="param_algorithm_ms1_mz_tolerance" type="float" min="0.0" optional="True" value="0.0" label="MS1 m/z tolerance (ppm)" help="(-mz_tolerance) "/>
    <param name="param_algorithm_ms1_feature_merger_active" display="radio" type="select" optional="False" value="true" label="Activation of MS1 feature merging post processing" help="(-active) ">
      <option value="true" selected="true">true</option>
      <option value="false">false</option>
    </param>
    <param name="param_algorithm_ms1_feature_merger_tr_resolution" type="float" min="0.0" optional="True" value="0.01" label="MS1 LC retention time resolution" help="(-tr_resolution) "/>
    <param name="param_algorithm_ms1_feature_merger_initial_apex_tr_tolerance" type="float" min="0.0" optional="True" value="5.0" label="Initial Apex Tr tolerance" help="(-initial_apex_tr_tolerance) "/>
    <param name="param_algorithm_ms1_feature_merger_feature_merging_tr_tolerance" type="float" min="0.0" optional="True" value="1.0" label="MS1 feature Tr merging tolerance" help="(-feature_merging_tr_tolerance) "/>
    <param name="param_algorithm_ms1_feature_merger_intensity_variation_percentage" type="float" min="0.0" max="100.0" optional="True" value="25.0" label="Percentage of intensity variation between LC border peaks" help="(-intensity_variation_percentage) "/>
    <param name="param_algorithm_ms1_feature_merger_ppm_tolerance_for_mz_clustering" type="float" min="0.0" optional="True" value="10.0" label="PPM value for the m/z clustering of merging candidates" help="(-ppm_tolerance_for_mz_clustering) "/>
    <param name="param_algorithm_ms1_feature_selection_options_start_elution_window" type="float" min="0.0" optional="True" value="0.0" label="start elution window (minutes)" help="(-start_elution_window) "/>
    <param name="param_algorithm_ms1_feature_selection_options_end_elution_window" type="float" min="0.0" optional="True" value="180.0" label="end elution window (minutes)" help="(-end_elution_window) "/>
    <param name="param_algorithm_ms1_feature_selection_options_mz_range_min" type="float" min="0.0" optional="True" value="0.0" label="MS1 feature mz range min" help="(-mz_range_min) "/>
    <param name="param_algorithm_ms1_feature_selection_options_mz_range_max" type="float" min="0.0" optional="True" value="2000.0" label="MS1 feature mz range max" help="(-mz_range_max) "/>
    <param name="param_algorithm_ms1_feature_selection_options_chrg_range_min" type="integer" min="0" optional="True" value="1" label="MS1 feature CHRG range min" help="(-chrg_range_min) "/>
    <param name="param_algorithm_ms1_feature_selection_options_chrg_range_max" type="integer" min="0" optional="True" value="5" label="MS1 feature CHRG range max" help="(-chrg_range_max) "/>
    <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) "/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" format="featurexml"/>
  </outputs>
  <help>Finds mass spectrometric features in mass spectra.


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