view MassTraceExtractor.xml @ 4:6ead64a594bd draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty

<?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: [Signal processing and preprocessing]-->
  <tool id="MassTraceExtractor" name="MassTraceExtractor" version="2.0.0">
    <description>Detects mass traces in centroided LC-MS data.</description>
    <macros>
      <token name="@EXECUTABLE@">MassTraceExtractor</token>
      <import>macros.xml</import>
    </macros>
    <expand macro="references"/>
    <expand macro="stdio"/>
    <expand macro="requirements"/>
    <command>MassTraceExtractor

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_out_type:
  -out_type
  #if &quot; &quot; in str($param_out_type):
    &quot;$param_out_type&quot;
  #else
    $param_out_type
  #end if
#end if
-threads \${GALAXY_SLOTS:-24}
#if $param_algorithm_common_noise_threshold_int:
  -algorithm:common:noise_threshold_int $param_algorithm_common_noise_threshold_int
#end if
#if $param_algorithm_common_chrom_peak_snr:
  -algorithm:common:chrom_peak_snr $param_algorithm_common_chrom_peak_snr
#end if
#if $param_algorithm_common_chrom_fwhm:
  -algorithm:common:chrom_fwhm $param_algorithm_common_chrom_fwhm
#end if
#if $param_algorithm_mtd_mass_error_ppm:
  -algorithm:mtd:mass_error_ppm $param_algorithm_mtd_mass_error_ppm
#end if
#if $param_algorithm_mtd_reestimate_mt_sd:
  -algorithm:mtd:reestimate_mt_sd
#end if
#if $param_algorithm_epd_width_filtering:
  -algorithm:epd:width_filtering
  #if &quot; &quot; in str($param_algorithm_epd_width_filtering):
    &quot;$param_algorithm_epd_width_filtering&quot;
  #else
    $param_algorithm_epd_width_filtering
  #end if
#end if
#if $param_algorithm_epd_enabled:
  -algorithm:epd:enabled
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
    #if $adv_opts.param_algorithm_mtd_trace_termination_criterion:
  -algorithm:mtd:trace_termination_criterion
  #if &quot; &quot; in str($adv_opts.param_algorithm_mtd_trace_termination_criterion):
    &quot;$adv_opts.param_algorithm_mtd_trace_termination_criterion&quot;
  #else
    $adv_opts.param_algorithm_mtd_trace_termination_criterion
  #end if
#end if
    #if $adv_opts.param_algorithm_mtd_trace_termination_outliers:
  -algorithm:mtd:trace_termination_outliers $adv_opts.param_algorithm_mtd_trace_termination_outliers
#end if
    #if $adv_opts.param_algorithm_mtd_min_sample_rate:
  -algorithm:mtd:min_sample_rate $adv_opts.param_algorithm_mtd_min_sample_rate
#end if
    #if $adv_opts.param_algorithm_mtd_min_trace_length:
  -algorithm:mtd:min_trace_length $adv_opts.param_algorithm_mtd_min_trace_length
#end if
    #if $adv_opts.param_algorithm_mtd_max_trace_length:
  -algorithm:mtd:max_trace_length $adv_opts.param_algorithm_mtd_max_trace_length
#end if
    #if $adv_opts.param_algorithm_epd_min_fwhm:
  -algorithm:epd:min_fwhm $adv_opts.param_algorithm_epd_min_fwhm
#end if
    #if $adv_opts.param_algorithm_epd_max_fwhm:
  -algorithm:epd:max_fwhm $adv_opts.param_algorithm_epd_max_fwhm
#end if
    #if $adv_opts.param_algorithm_epd_masstrace_snr_filtering:
  -algorithm:epd:masstrace_snr_filtering
#end if
#end if
</command>
    <inputs>
      <param format="mzml" help="(-in) " label="input centroided mzML file" name="param_in" optional="False" type="data"/>
      <param help="(-out_type) " label="output file type -- default: determined from file extension or content" name="param_out_type" optional="True" type="select">
        <option value="featureXML">featureXML</option>
        <option value="consensusXML">consensusXML</option>
      </param>
      <param help="(-noise_threshold_int) " label="Intensity threshold below which peaks are regarded as noise" name="param_algorithm_common_noise_threshold_int" type="float" value="10.0"/>
      <param help="(-chrom_peak_snr) " label="Minimum signal-to-noise a mass trace should have" name="param_algorithm_common_chrom_peak_snr" type="float" value="3.0"/>
      <param help="(-chrom_fwhm) " label="Expected chromatographic peak width (in seconds)" name="param_algorithm_common_chrom_fwhm" type="float" value="5.0"/>
      <param help="(-mass_error_ppm) " label="Allowed mass deviation (in ppm)" name="param_algorithm_mtd_mass_error_ppm" type="float" value="20.0"/>
      <param checked="true" falsevalue="" help="(-reestimate_mt_sd) " label="Enables dynamic re-estimation of m/z variance during mass trace collection stage" name="param_algorithm_mtd_reestimate_mt_sd" optional="True" truevalue="-algorithm:mtd:reestimate_mt_sd" type="boolean"/>
      <param help="(-width_filtering) 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" label="Enable filtering of unlikely peak widths" name="param_algorithm_epd_width_filtering" optional="True" type="select" value="fixed">
        <option value="off">off</option>
        <option value="fixed">fixed</option>
        <option value="auto">auto</option>
      </param>
      <param checked="true" falsevalue="" help="(-enabled) " label="Enables/disables the chromatographic peak detection of mass traces" name="param_algorithm_epd_enabled" optional="True" truevalue="-algorithm:epd:enabled" type="boolean"/>
      <expand macro="advanced_options">
        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
        <param help="(-trace_termination_criterion) 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" label="Termination criterion for the extension of mass traces" name="param_algorithm_mtd_trace_termination_criterion" optional="True" type="select" value="outlier">
          <option value="outlier">outlier</option>
          <option value="sample_rate">sample_rate</option>
        </param>
        <param help="(-trace_termination_outliers) " label="Mass trace extension in one direction cancels if this number of consecutive spectra with no detectable peaks is reached" name="param_algorithm_mtd_trace_termination_outliers" type="integer" value="5"/>
        <param help="(-min_sample_rate) " label="Minimum fraction of scans along the mass trace that must contain a peak" name="param_algorithm_mtd_min_sample_rate" type="float" value="0.5"/>
        <param help="(-min_trace_length) " label="Minimum expected length of a mass trace (in seconds)" name="param_algorithm_mtd_min_trace_length" type="float" value="5.0"/>
        <param help="(-max_trace_length) " label="Maximum expected length of a mass trace (in seconds)" name="param_algorithm_mtd_max_trace_length" type="float" value="300.0"/>
        <param help="(-min_fwhm) Ignored if parameter width_filtering is off or auto" label="Minimum full-width-at-half-maximum of chromatographic peaks (in seconds)" name="param_algorithm_epd_min_fwhm" type="float" value="3.0"/>
        <param help="(-max_fwhm) Ignored if parameter width_filtering is off or auto" label="Maximum full-width-at-half-maximum of chromatographic peaks (in seconds)" name="param_algorithm_epd_max_fwhm" type="float" value="60.0"/>
        <param checked="false" falsevalue="" help="(-masstrace_snr_filtering) " label="Apply post-filtering by signal-to-noise ratio after smoothing" name="param_algorithm_epd_masstrace_snr_filtering" optional="True" truevalue="-algorithm:epd:masstrace_snr_filtering" type="boolean"/>
      </expand>
    </inputs>
    <outputs>
      <data format="xml" name="param_out"/>
    </outputs>
    <help>Detects mass traces in centroided LC-MS data.


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