view FeatureFinderIdentification.xml @ 1:6a3bbd5b8cb6 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="FeatureFinderIdentification" name="FeatureFinderIdentification" version="2.1.0">
  <description>Detects features in MS1 data based on peptide identifications.</description>
  <macros>
    <token name="@EXECUTABLE@">FeatureFinderIdentification</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>FeatureFinderIdentification

#if $param_in:
  -in $param_in
#end if
#if $param_id:
  -id $param_id
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_lib_out:
  -lib_out $param_lib_out
#end if
#if $param_chrom_out:
  -chrom_out $param_chrom_out
#end if
#if $param_trafo_out:
  -trafo_out $param_trafo_out
#end if
#if $param_extract_reference_rt:
  -extract:reference_rt
  #if " " in str($param_extract_reference_rt):
    "$param_extract_reference_rt"
  #else
    $param_extract_reference_rt
  #end if
#end if
#if $param_extract_rt_window:
  -extract:rt_window $param_extract_rt_window
#end if
#if $param_extract_mz_window:
  -extract:mz_window $param_extract_mz_window
#end if
#if $param_extract_isotope_pmin:
  -extract:isotope_pmin $param_extract_isotope_pmin
#end if
#if $param_detect_peak_width:
  -detect:peak_width $param_detect_peak_width
#end if
#if $param_model_type:
  -model:type
  #if " " in str($param_model_type):
    "$param_model_type"
  #else
    $param_model_type
  #end if
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
    #if $adv_opts.param_detect_all_features:
  -detect:all_features
#end if
    #if $adv_opts.param_model_add_zeros:
  -model:add_zeros $adv_opts.param_model_add_zeros
#end if
    #if $adv_opts.param_model_unweighted_fit:
  -model:unweighted_fit
#end if
    #if $adv_opts.param_model_no_imputation:
  -model:no_imputation
#end if
    #if $adv_opts.param_model_check_boundaries:
  -model:check:boundaries $adv_opts.param_model_check_boundaries
#end if
    #if $adv_opts.param_model_check_width:
  -model:check:width $adv_opts.param_model_check_width
#end if
    #if $adv_opts.param_model_check_asymmetry:
  -model:check:asymmetry $adv_opts.param_model_check_asymmetry
#end if
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="mzml" optional="False" label="Input file (LC-MS raw data)" help="(-in) "/>
    <param name="param_id" type="data" format="idxml" optional="False" label="Input file (peptide identifications)" help="(-id) "/>
    <param name="param_extract_reference_rt" type="select" optional="False" value="adapt" label="Method for selecting the reference RT, if there are multiple IDs for a peptide and charge" help="(-reference_rt) 'adapt': adapt (extend) RT windows based on IDs; 'score': RT of the best-scoring ID; 'intensity': RT of the ID with the most intense precursor; 'median': median RT of all IDs; 'all': no single reference, use RTs of all IDs (requires further processing of results)">
      <option value="adapt" selected="true">adapt</option>
      <option value="score">score</option>
      <option value="intensity">intensity</option>
      <option value="median">median</option>
      <option value="all">all</option>
    </param>
    <param name="param_extract_rt_window" type="float" min="0.0" optional="True" value="60.0" label="RT window size (in sec.) for chromatogram extraction" help="(-rt_window) "/>
    <param name="param_extract_mz_window" type="float" min="0.0" optional="True" value="10.0" label="m/z window size for chromatogram extraction (unit: ppm if 1 or greater, else Da/Th)" help="(-mz_window) "/>
    <param name="param_extract_isotope_pmin" type="float" min="0.0" max="1.0" optional="True" value="0.03" label="Minimum probability for an isotope to be included in the assay for a peptide" help="(-isotope_pmin) "/>
    <param name="param_detect_peak_width" type="float" min="0.0" optional="True" value="30.0" label="Elution peak width in seconds for smoothing (Gauss filter)" help="(-peak_width) "/>
    <param name="param_model_type" display="radio" type="select" optional="False" value="symmetric" label="Type of elution model to fit to features" help="(-type) ">
      <option value="symmetric" selected="true">symmetric</option>
      <option value="asymmetric">asymmetric</option>
      <option value="none">none</option>
    </param>
    <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_detect_all_features" display="radio" type="boolean" truevalue="-detect:all_features" falsevalue="" checked="false" optional="True" label="Return all features detected by OpenSWATH for an assay, instead of only the best one" help="(-all_features) (This requires further processing of the results.)"/>
      <param name="param_model_add_zeros" type="float" min="0.0" optional="True" value="0.2" label="Add zero-intensity points outside the feature range to constrain the model fit" help="(-add_zeros) This parameter sets the weight given to these points during model fitting; '0' to disable"/>
      <param name="param_model_unweighted_fit" display="radio" type="boolean" truevalue="-model:unweighted_fit" falsevalue="" checked="false" optional="True" label="Suppress weighting of mass traces according to theoretical intensities when fitting elution models" help="(-unweighted_fit) "/>
      <param name="param_model_no_imputation" display="radio" type="boolean" truevalue="-model:no_imputation" falsevalue="" checked="false" optional="True" label="If fitting the elution model fails for a feature, set its intensity to zero instead of imputing a value from the initial intensity estimate" help="(-no_imputation) "/>
      <param name="param_model_check_boundaries" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Time points corresponding to this fraction of the elution model height have to be within the data region used for model fitting" help="(-boundaries) "/>
      <param name="param_model_check_width" type="float" min="0.0" optional="True" value="10.0" label="Upper limit for acceptable widths of elution models (Gaussian or EGH), expressed in terms of modified (median-based) z-scores; '0' to disable" help="(-width) "/>
      <param name="param_model_check_asymmetry" type="float" min="0.0" optional="True" value="10.0" label="Upper limit for acceptable asymmetry of elution models (EGH only), expressed in terms of modified (median-based) z-scores; '0' to disable" help="(-asymmetry) "/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" format="featurexml"/>
    <data name="param_lib_out" format="traml"/>
    <data name="param_chrom_out" format="mzml"/>
    <data name="param_trafo_out" format="trafoxml"/>
  </outputs>
  <help>Detects features in MS1 data based on peptide identifications.


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