view FeatureFinderMetabo.xml @ 13:00080bb4299e draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"

<?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: [Quantitation]-->
<tool id="FeatureFinderMetabo" name="FeatureFinderMetabo" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
  <description>Assembles metabolite features from centroided (LC-)MS data using the mass trace approach.</description>
  <macros>
    <token name="@EXECUTABLE@">FeatureFinderMetabo</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@
#import re

## Preprocessing
mkdir in &&
ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
mkdir out &&
#if "out_chrom_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  mkdir out_chrom &&
#end if

## Main program call

set -o pipefail &&
@EXECUTABLE@ -write_ctd ./ &&
python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
@EXECUTABLE@ -ini @EXECUTABLE@.ctd
-in
'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
-out
'out/output.${gxy2omsext("featurexml")}'
#if "out_chrom_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  -out_chrom
  'out_chrom/output.${gxy2omsext("mzml")}'
#end if
#if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
  | tee '$stdout'
#end if

## Postprocessing
&& mv 'out/output.${gxy2omsext("featurexml")}' '$out'
#if "out_chrom_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  && mv 'out_chrom/output.${gxy2omsext("mzml")}' '$out_chrom'
#end if
#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
  && mv '@EXECUTABLE@.ctd' '$ctd_out'
#end if]]></command>
  <configfiles>
    <inputs name="args_json" data_style="paths"/>
    <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
  </configfiles>
  <inputs>
    <param name="in" argument="-in" type="data" format="mzml" optional="false" label="Centroided mzML file" help=" select mzml data sets(s)"/>
    <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
      <section name="common" title="Common parameters for all other subsections" help="" expanded="false">
        <param name="noise_threshold_int" argument="-algorithm:common:noise_threshold_int" type="float" optional="true" value="10.0" label="Intensity threshold below which peaks are regarded as noise" help=""/>
        <param name="chrom_peak_snr" argument="-algorithm:common:chrom_peak_snr" type="float" optional="true" value="3.0" label="Minimum signal-to-noise a mass trace should have" help=""/>
        <param name="chrom_fwhm" argument="-algorithm:common:chrom_fwhm" type="float" optional="true" value="5.0" label="Expected chromatographic peak width (in seconds)" help=""/>
      </section>
      <section name="mtd" title="Mass Trace Detection parameters" help="" expanded="false">
        <param name="mass_error_ppm" argument="-algorithm:mtd:mass_error_ppm" type="float" optional="true" value="20.0" label="Allowed mass deviation (in ppm)" help=""/>
        <param name="reestimate_mt_sd" argument="-algorithm:mtd:reestimate_mt_sd" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Enables dynamic re-estimation of m/z variance during mass trace collection stage" help=""/>
        <param name="quant_method" argument="-algorithm:mtd:quant_method" display="radio" type="select" optional="false" label="Method of quantification for mass traces" help="For LC data 'area' is recommended, 'median' for direct injection data. 'max_height' simply uses the most intense peak in the trace">
          <option value="area" selected="true">area</option>
          <option value="median">median</option>
          <option value="max_height">max_height</option>
          <expand macro="list_string_san"/>
        </param>
        <param name="trace_termination_criterion" argument="-algorithm:mtd:trace_termination_criterion" display="radio" type="select" optional="false" label="Termination criterion for the extension of mass traces" help="In 'outlier' mode, trace extension cancels if a predefined number of consecutive outliers are found (see trace_termination_outliers parameter). In 'sample_rate' mode, trace extension in both directions stops if ratio of found peaks versus visited spectra falls below the 'min_sample_rate' threshold">
          <option value="outlier" selected="true">outlier</option>
          <option value="sample_rate">sample_rate</option>
          <expand macro="list_string_san"/>
        </param>
        <param name="trace_termination_outliers" argument="-algorithm:mtd:trace_termination_outliers" type="integer" optional="true" value="5" label="Mass trace extension in one direction cancels if this number of consecutive spectra with no detectable peaks is reached" help=""/>
        <param name="min_sample_rate" argument="-algorithm:mtd:min_sample_rate" type="float" optional="true" value="0.5" label="Minimum fraction of scans along the mass trace that must contain a peak" help=""/>
        <param name="min_trace_length" argument="-algorithm:mtd:min_trace_length" type="float" optional="true" value="5.0" label="Minimum expected length of a mass trace (in seconds)" help=""/>
        <param name="max_trace_length" argument="-algorithm:mtd:max_trace_length" type="float" optional="true" value="-1.0" label="Maximum expected length of a mass trace (in seconds)" help="Set to a negative value to disable maximal length check during mass trace detection"/>
      </section>
      <section name="epd" title="Elution Profile Detection (to separate isobaric Mass Traces by elution time)" help="" expanded="false">
        <param name="enabled" argument="-algorithm:epd:enabled" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Enable splitting of isobaric mass traces by chromatographic peak detection" help="Disable for direct injection"/>
        <param name="width_filtering" argument="-algorithm:epd:width_filtering" display="radio" type="select" optional="false" label="Enable filtering of unlikely peak widths" help="The fixed setting filters out mass traces outside the [min_fwhm, max_fwhm] interval (set parameters accordingly!). The auto setting filters with the 5 and 95% quantiles of the peak width distribution">
          <option value="off">off</option>
          <option value="fixed" selected="true">fixed</option>
          <option value="auto">auto</option>
          <expand macro="list_string_san"/>
        </param>
        <param name="min_fwhm" argument="-algorithm:epd:min_fwhm" type="float" optional="true" value="1.0" label="Minimum full-width-at-half-maximum of chromatographic peaks (in seconds)" help="Ignored if parameter width_filtering is off or auto"/>
        <param name="max_fwhm" argument="-algorithm:epd:max_fwhm" type="float" optional="true" value="60.0" label="Maximum full-width-at-half-maximum of chromatographic peaks (in seconds)" help="Ignored if parameter width_filtering is off or auto"/>
        <param name="masstrace_snr_filtering" argument="-algorithm:epd:masstrace_snr_filtering" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Apply post-filtering by signal-to-noise ratio after smoothing" help=""/>
      </section>
      <section name="ffm" title="FeatureFinder parameters (assembling mass traces to charged features)" help="" expanded="false">
        <param name="local_rt_range" argument="-algorithm:ffm:local_rt_range" type="float" optional="true" value="10.0" label="RT range where to look for coeluting mass traces" help=""/>
        <param name="local_mz_range" argument="-algorithm:ffm:local_mz_range" type="float" optional="true" value="6.5" label="MZ range where to look for isotopic mass traces" help=""/>
        <param name="charge_lower_bound" argument="-algorithm:ffm:charge_lower_bound" type="integer" optional="true" value="1" label="Lowest charge state to conside" help=""/>
        <param name="charge_upper_bound" argument="-algorithm:ffm:charge_upper_bound" type="integer" optional="true" value="3" label="Highest charge state to conside" help=""/>
        <param name="report_summed_ints" argument="-algorithm:ffm:report_summed_ints" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set to true for a feature intensity summed up over all traces rather than using monoisotopic trace intensity alone" help=""/>
        <param name="enable_RT_filtering" argument="-algorithm:ffm:enable_RT_filtering" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Require sufficient overlap in RT while assembling mass traces" help="Disable for direct injection data"/>
        <param name="isotope_filtering_model" argument="-algorithm:ffm:isotope_filtering_model" display="radio" type="select" optional="false" label="Remove/score candidate assemblies based on isotope intensities" help="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>
          <expand macro="list_string_san"/>
        </param>
        <param name="mz_scoring_13C" argument="-algorithm:ffm:mz_scoring_13C" type="boolean" truevalue="true" falsevalue="false" checked="false" 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="Disable for general metabolites (as described in Kenar et al. 2014, MCP.)"/>
        <param name="use_smoothed_intensities" argument="-algorithm:ffm:use_smoothed_intensities" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use LOWESS intensities instead of raw intensities" help=""/>
        <param name="report_convex_hulls" argument="-algorithm:ffm:report_convex_hulls" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Augment each reported feature with the convex hull of the underlying mass traces (increases featureXML file size considerably)" help=""/>
        <param name="remove_single_traces" argument="-algorithm:ffm:remove_single_traces" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove unassembled traces (single traces)" help=""/>
        <param name="mz_scoring_by_elements" argument="-algorithm:ffm:mz_scoring_by_elements" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the m/z range of the assumed elements to detect isotope peaks" help="A expected m/z range is computed from the isotopes of the assumed elements. If enabled, this ignores 'mz_scoring_13C'"/>
        <param name="elements" argument="-algorithm:ffm:elements" type="text" optional="true" value="CHNOPS" label="Elements assumes to be present in the sample (this influences isotope detection)" help="">
          <expand macro="list_string_san"/>
        </param>
      </section>
    </section>
    <expand macro="adv_opts_macro">
      <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_chrom_FLAG">out_chrom (Optional mzML file with chromatograms)</option>
      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
    </param>
  </inputs>
  <outputs>
    <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/>
    <data name="out_chrom" label="${tool.name} on ${on_string}: out_chrom" format="mzml">
      <filter>OPTIONAL_OUTPUTS is not None and "out_chrom_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
    <data name="ctd_out" format="xml" label="${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_FeatureFinderMetabo"/>
    <expand macro="manutest_FeatureFinderMetabo"/>
  </tests>
  <help><![CDATA[Assembles metabolite features from centroided (LC-)MS data using the mass trace approach.


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