comparison FeatureFinderMetabo.xml @ 9:b6e4da302f66 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5

8:a1c76c5160ee

    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>FeatureFinderMetabo

#if $param_in:
  -in $param_in
#end if
#if $param_out:

  #else
    $param_algorithm_ffm_isotope_filtering_model
  #end if
#end if
#if $param_algorithm_ffm_mz_scoring_13C:
  -algorithm:ffm:mz_scoring_13C
#end if
#if $param_algorithm_ffm_report_convex_hulls:
  -algorithm:ffm:report_convex_hulls
#end if
#if $adv_opts.adv_opts_selector=='advanced':

  #else
    $adv_opts.param_algorithm_ffm_use_smoothed_intensities
  #end if
#end if
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="mzml" optional="False" label="Centroided mzML file" help="(-in) "/>
    <param name="param_algorithm_common_noise_threshold_int" type="float" value="10.0" label="Intensity threshold below which peaks are regarded as noise" help="(-noise_threshold_int) "/>
    <param name="param_algorithm_common_chrom_peak_snr" type="float" value="3.0" label="Minimum signal-to-noise a mass trace should have" help="(-chrom_peak_snr) "/>
    <param name="param_algorithm_common_chrom_fwhm" type="float" value="5.0" label="Expected chromatographic peak width (in seconds)" help="(-chrom_fwhm) "/>

    <param name="param_algorithm_ffm_isotope_filtering_model" display="radio" type="select" optional="False" value="metabolites (5% RMS)" label="Remove/score candidate assemblies based on isotope intensities" help="(-isotope_filtering_model) SVM isotope models for metabolites were trained with either 2% or 5% RMS error. For peptides, an averagine cosine scoring is used. Select the appropriate noise model according to the quality of measurement or MS device">
      <option value="metabolites (2% RMS)">metabolites (2% RMS)</option>
      <option value="metabolites (5% RMS)" selected="true">metabolites (5% RMS)</option>
      <option value="peptides">peptides</option>
      <option value="none">none</option>
    </param>
    <param name="param_algorithm_ffm_mz_scoring_13C" display="radio" type="boolean" truevalue="-algorithm:ffm:mz_scoring_13C" falsevalue="" checked="false" optional="True" label="Use the 13C isotope peak position (~1.003355 Da) as the expected shift in m/z for isotope mass traces (highly recommended for lipidomics!)" help="(-mz_scoring_13C) Disable for general metabolites (as described in Kenar et al. 2014, MCP.)"/>
    <param name="param_algorithm_ffm_report_convex_hulls" display="radio" type="boolean" truevalue="-algorithm:ffm:report_convex_hulls" falsevalue="" checked="false" optional="True" label="Augment each reported feature with the convex hull of the underlying mass traces (increases featureXML file size considerably)" help="(-report_convex_hulls) "/>
    <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) "/>

    <data name="param_out_chrom" format="mzml"/>
  </outputs>
  <help>Assembles metabolite features from centroided (LC-)MS data using the mass trace approach.


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

9:b6e4da302f66

    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command detect_errors="aggressive"><![CDATA[FeatureFinderMetabo

#if $param_in:
  -in $param_in
#end if
#if $param_out:

  #else
    $param_algorithm_ffm_isotope_filtering_model
  #end if
#end if
#if $param_algorithm_ffm_mz_scoring_13C:
  -algorithm:ffm:mz_scoring_13C true
#end if
#if $param_algorithm_ffm_report_convex_hulls:
  -algorithm:ffm:report_convex_hulls
#end if
#if $adv_opts.adv_opts_selector=='advanced':

  #else
    $adv_opts.param_algorithm_ffm_use_smoothed_intensities
  #end if
#end if
#end if
]]></command>
  <inputs>
    <param name="param_in" type="data" format="mzml" optional="False" label="Centroided mzML file" help="(-in) "/>
    <param name="param_algorithm_common_noise_threshold_int" type="float" value="10.0" label="Intensity threshold below which peaks are regarded as noise" help="(-noise_threshold_int) "/>
    <param name="param_algorithm_common_chrom_peak_snr" type="float" value="3.0" label="Minimum signal-to-noise a mass trace should have" help="(-chrom_peak_snr) "/>
    <param name="param_algorithm_common_chrom_fwhm" type="float" value="5.0" label="Expected chromatographic peak width (in seconds)" help="(-chrom_fwhm) "/>

    <param name="param_algorithm_ffm_isotope_filtering_model" display="radio" type="select" optional="False" value="metabolites (5% RMS)" label="Remove/score candidate assemblies based on isotope intensities" help="(-isotope_filtering_model) SVM isotope models for metabolites were trained with either 2% or 5% RMS error. For peptides, an averagine cosine scoring is used. Select the appropriate noise model according to the quality of measurement or MS device">
      <option value="metabolites (2% RMS)">metabolites (2% RMS)</option>
      <option value="metabolites (5% RMS)" selected="true">metabolites (5% RMS)</option>
      <option value="peptides">peptides</option>
      <option value="none">none</option>
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_algorithm_ffm_mz_scoring_13C" display="radio" type="boolean" truevalue="-algorithm:ffm:mz_scoring_13C" falsevalue="" checked="false" optional="True" label="Use the 13C isotope peak position (~1.003355 Da) as the expected shift in m/z for isotope mass traces (highly recommended for lipidomics!)" help="(-mz_scoring_13C) Disable for general metabolites (as described in Kenar et al. 2014, MCP.)"/>
    <param name="param_algorithm_ffm_report_convex_hulls" display="radio" type="boolean" truevalue="-algorithm:ffm:report_convex_hulls" falsevalue="" checked="false" optional="True" label="Augment each reported feature with the convex hull of the underlying mass traces (increases featureXML file size considerably)" help="(-report_convex_hulls) "/>
    <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) "/>

    <data name="param_out_chrom" format="mzml"/>
  </outputs>
  <help>Assembles metabolite features from centroided (LC-)MS data using the mass trace approach.


For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_FeatureFinderMetabo.html</help>
</tool>