annotate FeatureFinderCentroided.xml @ 4:c6c2a3359393 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 1e51bed3a1c10c67ef0404216608e9333db04c64

<?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="FeatureFinderCentroided" name="FeatureFinderCentroided" version="2.2.0">
  <description>Detects two-dimensional features in LC-MS data.</description>
  <macros>
    <token name="@EXECUTABLE@">FeatureFinderCentroided</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>FeatureFinderCentroided

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_seeds:
  -seeds $param_seeds
#end if
#if $param_out_mzq:
  -out_mzq $param_out_mzq
#end if
#if $param_algorithm_intensity_bins:
  -algorithm:intensity:bins $param_algorithm_intensity_bins
#end if
#if $param_algorithm_mass_trace_mz_tolerance:
  -algorithm:mass_trace:mz_tolerance $param_algorithm_mass_trace_mz_tolerance
#end if
#if $param_algorithm_mass_trace_min_spectra:
  -algorithm:mass_trace:min_spectra $param_algorithm_mass_trace_min_spectra
#end if
#if $param_algorithm_mass_trace_max_missing:
  -algorithm:mass_trace:max_missing $param_algorithm_mass_trace_max_missing
#end if
#if $param_algorithm_mass_trace_slope_bound:
  -algorithm:mass_trace:slope_bound $param_algorithm_mass_trace_slope_bound
#end if
#if $param_algorithm_isotopic_pattern_charge_low:
  -algorithm:isotopic_pattern:charge_low $param_algorithm_isotopic_pattern_charge_low
#end if
#if $param_algorithm_isotopic_pattern_charge_high:
  -algorithm:isotopic_pattern:charge_high $param_algorithm_isotopic_pattern_charge_high
#end if
#if $param_algorithm_isotopic_pattern_mz_tolerance:
  -algorithm:isotopic_pattern:mz_tolerance $param_algorithm_isotopic_pattern_mz_tolerance
#end if
#if $param_algorithm_seed_min_score:
  -algorithm:seed:min_score $param_algorithm_seed_min_score
#end if
#if $param_algorithm_feature_min_score:
  -algorithm:feature:min_score $param_algorithm_feature_min_score
#end if
#if $param_algorithm_feature_reported_mz:
  -algorithm:feature:reported_mz
  #if " " in str($param_algorithm_feature_reported_mz):
    "$param_algorithm_feature_reported_mz"
  #else
    $param_algorithm_feature_reported_mz
  #end if
#end if
#if $param_algorithm_user_seed_rt_tolerance:
  -algorithm:user-seed:rt_tolerance $param_algorithm_user_seed_rt_tolerance
#end if
#if $param_algorithm_user_seed_mz_tolerance:
  -algorithm:user-seed:mz_tolerance $param_algorithm_user_seed_mz_tolerance
#end if
#if $param_algorithm_user_seed_min_score:
  -algorithm:user-seed:min_score $param_algorithm_user_seed_min_score
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
    #if $adv_opts.param_algorithm_debug_pseudo_rt_shift:
  -algorithm:debug:pseudo_rt_shift $adv_opts.param_algorithm_debug_pseudo_rt_shift
#end if
    #if $adv_opts.param_algorithm_isotopic_pattern_intensity_percentage:
  -algorithm:isotopic_pattern:intensity_percentage $adv_opts.param_algorithm_isotopic_pattern_intensity_percentage
#end if
    #if $adv_opts.param_algorithm_isotopic_pattern_intensity_percentage_optional:
  -algorithm:isotopic_pattern:intensity_percentage_optional $adv_opts.param_algorithm_isotopic_pattern_intensity_percentage_optional
#end if
    #if $adv_opts.param_algorithm_isotopic_pattern_optional_fit_improvement:
  -algorithm:isotopic_pattern:optional_fit_improvement $adv_opts.param_algorithm_isotopic_pattern_optional_fit_improvement
#end if
    #if $adv_opts.param_algorithm_isotopic_pattern_mass_window_width:
  -algorithm:isotopic_pattern:mass_window_width $adv_opts.param_algorithm_isotopic_pattern_mass_window_width
#end if
    #if $adv_opts.param_algorithm_isotopic_pattern_abundance_12C:
  -algorithm:isotopic_pattern:abundance_12C $adv_opts.param_algorithm_isotopic_pattern_abundance_12C
#end if
    #if $adv_opts.param_algorithm_isotopic_pattern_abundance_14N:
  -algorithm:isotopic_pattern:abundance_14N $adv_opts.param_algorithm_isotopic_pattern_abundance_14N
#end if
    #if $adv_opts.param_algorithm_fit_max_iterations:
  -algorithm:fit:max_iterations $adv_opts.param_algorithm_fit_max_iterations
#end if
    #if $adv_opts.param_algorithm_feature_min_isotope_fit:
  -algorithm:feature:min_isotope_fit $adv_opts.param_algorithm_feature_min_isotope_fit
#end if
    #if $adv_opts.param_algorithm_feature_min_trace_score:
  -algorithm:feature:min_trace_score $adv_opts.param_algorithm_feature_min_trace_score
#end if
    #if $adv_opts.param_algorithm_feature_min_rt_span:
  -algorithm:feature:min_rt_span $adv_opts.param_algorithm_feature_min_rt_span
#end if
    #if $adv_opts.param_algorithm_feature_max_rt_span:
  -algorithm:feature:max_rt_span $adv_opts.param_algorithm_feature_max_rt_span
#end if
    #if $adv_opts.param_algorithm_feature_rt_shape:
  -algorithm:feature:rt_shape
  #if " " in str($adv_opts.param_algorithm_feature_rt_shape):
    "$adv_opts.param_algorithm_feature_rt_shape"
  #else
    $adv_opts.param_algorithm_feature_rt_shape
  #end if
#end if
    #if $adv_opts.param_algorithm_feature_max_intersection:
  -algorithm:feature:max_intersection $adv_opts.param_algorithm_feature_max_intersection
#end if
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="mzml" optional="False" label="input file" help="(-in) "/>
    <param name="param_seeds" type="data" format="featurexml" optional="True" label="User specified seed list" help="(-seeds) "/>
    <param name="param_algorithm_intensity_bins" type="integer" min="1" optional="True" value="10" label="Number of bins per dimension (RT and m/z)" help="(-bins) The higher this value, the more local the intensity significance score is. &lt;br&gt;This parameter should be decreased, if the algorithm is used on small regions of a map"/>
    <param name="param_algorithm_mass_trace_mz_tolerance" type="float" min="0.0" optional="True" value="0.03" label="Tolerated m/z deviation of peaks belonging to the same mass trace" help="(-mz_tolerance) &lt;br&gt;It should be larger than the m/z resolution of the instrument. &lt;br&gt;This value must be smaller than that 1/charge_high!"/>
    <param name="param_algorithm_mass_trace_min_spectra" type="integer" min="1" optional="True" value="10" label="Number of spectra that have to show a similar peak mass in a mass trace" help="(-min_spectra) "/>
    <param name="param_algorithm_mass_trace_max_missing" type="integer" min="0" optional="True" value="1" label="Number of consecutive spectra where a high mass deviation or missing peak is acceptable" help="(-max_missing) &lt;br&gt;This parameter should be well below 'min_spectra'!"/>
    <param name="param_algorithm_mass_trace_slope_bound" type="float" min="0.0" optional="True" value="0.1" label="The maximum slope of mass trace intensities when extending from the highest peak" help="(-slope_bound) &lt;br&gt;This parameter is important to seperate overlapping elution peaks. &lt;br&gt;It should be increased if feature elution profiles fluctuate a lot"/>
    <param name="param_algorithm_isotopic_pattern_charge_low" type="integer" min="1" optional="True" value="1" label="Lowest charge to search fo" help="(-charge_low) "/>
    <param name="param_algorithm_isotopic_pattern_charge_high" type="integer" min="1" optional="True" value="4" label="Highest charge to search fo" help="(-charge_high) "/>
    <param name="param_algorithm_isotopic_pattern_mz_tolerance" type="float" min="0.0" optional="True" value="0.03" label="Tolerated m/z deviation from the theoretical isotopic pattern" help="(-mz_tolerance) &lt;br&gt;It should be larger than the m/z resolution of the instrument. &lt;br&gt;This value must be smaller than that 1/charge_high!"/>
    <param name="param_algorithm_seed_min_score" type="float" min="0.0" max="1.0" optional="True" value="0.8" label="Minimum seed score a peak has to reach to be used as seed" help="(-min_score) &lt;br&gt;The seed score is the geometric mean of intensity score, mass trace score and isotope pattern score. &lt;br&gt;If your features show a large deviation from the averagene isotope distribution or from an gaussian elution profile, lower this score"/>
    <param name="param_algorithm_feature_min_score" type="float" min="0.0" max="1.0" optional="True" value="0.7" label="Feature score threshold for a feature to be reported" help="(-min_score) &lt;br&gt;The feature score is the geometric mean of the average relative deviation and the correlation between the model and the observed peaks"/>
    <param name="param_algorithm_feature_reported_mz" display="radio" type="select" optional="False" value="monoisotopic" label="The mass type that is reported for features" help="(-reported_mz) &lt;br&gt;'maximum' returns the m/z value of the highest mass trace. &lt;br&gt;'average' returns the intensity-weighted average m/z value of all contained peaks. &lt;br&gt;'monoisotopic' returns the monoisotopic m/z value derived from the fitted isotope model">
      <option value="maximum">maximum</option>
      <option value="average">average</option>
      <option value="monoisotopic" selected="true">monoisotopic</option>
    </param>
    <param name="param_algorithm_user_seed_rt_tolerance" type="float" min="0.0" optional="True" value="5.0" label="Allowed RT deviation of seeds from the user-specified seed position" help="(-rt_tolerance) "/>
    <param name="param_algorithm_user_seed_mz_tolerance" type="float" min="0.0" optional="True" value="1.1" label="Allowed m/z deviation of seeds from the user-specified seed position" help="(-mz_tolerance) "/>
    <param name="param_algorithm_user_seed_min_score" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Overwrites 'seed:min_score' for user-specified seeds" help="(-min_score) The cutoff is typically a bit lower in this case"/>
    <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) "/>
      <param name="param_algorithm_debug_pseudo_rt_shift" type="float" min="1.0" optional="True" value="500.0" label="Pseudo RT shift used when" help="(-pseudo_rt_shift) "/>
      <param name="param_algorithm_isotopic_pattern_intensity_percentage" type="float" min="0.0" max="100.0" optional="True" value="10.0" label="Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity must be present" help="(-intensity_percentage) "/>
      <param name="param_algorithm_isotopic_pattern_intensity_percentage_optional" type="float" min="0.0" max="100.0" optional="True" value="0.1" label="Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity can be missing" help="(-intensity_percentage_optional) "/>
      <param name="param_algorithm_isotopic_pattern_optional_fit_improvement" type="float" min="0.0" max="100.0" optional="True" value="2.0" label="Minimal percental improvement of isotope fit to allow leaving out an optional peak" help="(-optional_fit_improvement) "/>
      <param name="param_algorithm_isotopic_pattern_mass_window_width" type="float" min="1.0" max="200.0" optional="True" value="25.0" label="Window width in Dalton for precalculation of estimated isotope distributions" help="(-mass_window_width) "/>
      <param name="param_algorithm_isotopic_pattern_abundance_12C" type="float" min="0.0" max="100.0" optional="True" value="98.93" label="Rel" help="(-abundance_12C) abundance of the light carbon. Modify if labeled"/>
      <param name="param_algorithm_isotopic_pattern_abundance_14N" type="float" min="0.0" max="100.0" optional="True" value="99.632" label="Rel" help="(-abundance_14N) abundance of the light nitrogen. Modify if labeled"/>
      <param name="param_algorithm_fit_max_iterations" type="integer" min="1" optional="True" value="500" label="Maximum number of iterations of the fit" help="(-max_iterations) "/>
      <param name="param_algorithm_feature_min_isotope_fit" type="float" min="0.0" max="1.0" optional="True" value="0.8" label="Minimum isotope fit of the feature before model fitting" help="(-min_isotope_fit) "/>
      <param name="param_algorithm_feature_min_trace_score" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Trace score threshold" help="(-min_trace_score) &lt;br&gt;Traces below this threshold are removed after the model fitting. &lt;br&gt;This parameter is important for features that overlap in m/z dimension"/>
      <param name="param_algorithm_feature_min_rt_span" type="float" min="0.0" max="1.0" optional="True" value="0.333" label="Minimum RT span in relation to extended area that has to remain after model fitting" help="(-min_rt_span) "/>
      <param name="param_algorithm_feature_max_rt_span" type="float" min="0.5" optional="True" value="2.5" label="Maximum RT span in relation to extended area that the model is allowed to have" help="(-max_rt_span) "/>
      <param name="param_algorithm_feature_rt_shape" display="radio" type="select" optional="False" value="symmetric" label="Choose model used for RT profile fitting" help="(-rt_shape) If set to symmetric a gauss shape is used, in case of asymmetric an EGH shape is used">
        <option value="symmetric" selected="true">symmetric</option>
        <option value="asymmetric">asymmetric</option>
      </param>
      <param name="param_algorithm_feature_max_intersection" type="float" min="0.0" max="1.0" optional="True" value="0.35" label="Maximum allowed intersection of features" help="(-max_intersection) "/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" format="featurexml"/>
    <data name="param_out_mzq" format="mzq"/>
  </outputs>
  <help>Detects two-dimensional features in LC-MS data.


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